diff --git a/.travis.yml b/.travis.yml index 127edacd18f78a497ee4043a8a596b93812079ad..13ca5c06124cde891f9985517b0315b7d63358b2 100644 --- a/.travis.yml +++ b/.travis.yml @@ -2,21 +2,27 @@ 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: - tcl8.5 install: + # pydot (dep for python-graph-dot) 1.2.0 and more recent doesn't work with Python 2.6 + - if [ "x$TRAVIS_PYTHON_VERSION" == 'x2.6' ]; then pip install pydot==1.1.0; else pip install pydot; fi # required for test_dep_graph - pip install python-graph-core python-graph-dot # install easybuild-framework/easybuild-easyblocks (and dependencies) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 2b32873f47d07c495a09f592041bdacdbe96f10c..3ed16807e4006b18697ed57048bffc9ea2391d5b 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,196 @@ 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 6,193 easyconfig files, for 944 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 1,136 different software packages, +25 different (compiler) toolchains, 13 software bundles and 1 meta-package. + +v3.0.2 (December 22nd 2016) +--------------------------- + +bugfix release +- added example easyconfig files for 13 new software packages: + - CryptoMiniSat (#3952), MATSim (#3902), Molcas (#2084), ne (#3376), psmc (#3910), PyCogent (#3897), + PyNAST (#3897), RASPA2 (#3903, #3946), SimPEG (#3876), SolexaQA++ (#3892), taco (#3882), + UCLUST (#3896), USPEX (#3767) +- added additional easyconfigs for various supported software packages, including: + - Mono 4.6.2.7, PGI 16.10, ROOT 6.08.02 +- various enhancements, including: + - trivial style fixes (#3878, #3893, #3895) +- various bug fixes, including: + - add X11 develop libs to ncview easyconfig (#3881) + - fix source_urls in pkg-config easyconfigs (#3907) + - install numpy/scipy as .egg to ensure shadowing of numpy/scipy in parent Python installation (#3921) + - fix broken source URL + homepage for Infernal (#3928) + - fix test that verifies dumped easyconfig, take into account that dumped dependencies may include hardcoded dependency (#3932) + - include libGLU as dependency in freeglut easyconfigs with recent Mesa (#3936) + - add patch for FreeSurfer to fix issue with MATLAB 2013 (#3954) + + +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) +----------------------- + +bugfix release +- added example easyconfig files for 54 new software packages: + Amber (#3200), Bullet (#3175), CONTRAlign (#690), Cluster-Buster (#3191), damageproto (#3222, #3308), + DCA++ (#3219), EIGENSOFT (#3147, #3163), Extrae (#507), fdstools (#3237), ffnet (#3273), GP2C (#3257), + Gurobi (#3239), gc (#3202, #3261), gputools (#546), IMa2p (#3300), IOzone (#3253), i-cisTarget (#3191, #3194), + icmake (#3243), io_lib (#3255), Kent_tools (#3191), libcmaes (#3256), libpsortb (#3259), libxsmm (#3099), + MEGACC (#3263), MM-align (#1428), MOSAIK (#880), MView (#1345), MySQL-python (#3172, #3189), magma (#3219), + mrFAST (#862), mrsFAST (#862), mysqlclient (#3172, #3232), NTL (#3183), PARI-GP (#3257), Paraver (#508), + psutil (#3171, #3231), PSI4 (#3293), Qwt (#3157), RMBlast (#3142), STAMP (#3191), Seqmagick (#3264), + splitRef (#946), TAU (#509), TRF (#3141), TVB (#3053, #3247, #3251), TVB-deps (#3053, #3247, #3251), + tvb-data (#3053, #3247, #3251), tvb-framework (#3053, #3247, #3251), tvb-library (#3053, #3247, #3251), + VampirTrace (#509), Voro++ (#3174), wheel (#3235), wxPropertyGrid (#508), xonsh (#3159) +- added easyconfigs for update of common toolchains: foss/2016b (#3271), intel/2016b (#3270) +- added new easyconfigs for existing toolchains: CrayGNU 2016.03 & 2016.04 (#3291), foss/2016.06 (#3184), intel/2016.03-GCC-5.4 (#3185) +- added additional easyconfigs for various supported software packages, including: + Boost 1.61.0, GCC 5.4.0, GROMACS 3.3.3, HDF5 1.8.17, netCDF 4.4.1, numpy 1.11.0, Perl 5.24.0, PETSc 3.7.2, + Python 2.7.12, Python 3.5.2, Qt 3.3.8, R 3.3.1 +- various enhancements, including: + - use check_conflicts function in easyconfigs tests (#2981) + - also include vsc-install in list of sources for recent EasyBuild easyconfigs, to support offline installation (#3203) + - enable building of libmysqld.* in MariaDB easyconfigs (#3230) + - add ALDEx2, phyloseq to bundles for Bioconductor 3.2 (#3211, #3241) + - add biom, geepack, lubridate, pim to list of R 3.2.3 extensions (#3186, #3211, #3275) +- various bug fixes, including: + - add patch for Boost 1.60.0 to fix bug resulting in TypeError (#3162) + - add fftw dependency to CP2K 2.6.0 easyconfigs using CrayGNU (#3176) + - fix location of libelf.h, only (also) installed as include/libelf.h is there's no /usr/include/libelf.h (#3201) + - fix software name for Guile & GnuTLS (was 'guile' & 'gnutls') (#3207) + - added missing space in Geant4 configopts to specify -DGEANT4_INSTALL_DATA (#3209) + - fix Cython download URL in Python 2.7.11 easyconfigs (#3212) + - add missing build deps for X stack in easyconfigs using foss/2016a or intel/2016a (#3222, #3308) + - fix overruling of exts_list in Perl 5.22.2 easyconfig (#3224) + - add missing dependency on GMP in R 3.2.3 easyconfigs (#3226) + - don't hard specify toolchain for binutils build dep in likwid easyconfig, since it matches parent toolchain (#3240) + - fix homepage & source_urls in HMMER easyconfigs (#3246) + - stick to pydot 1.1.0 for Python 2.6 in Travis config (#3282) + - add python-dev(el) to osdeps in GC3Pie easyconfigs (#3310) v2.8.1 (May 30th 2016) @@ -954,7 +1142,7 @@ 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 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a/easybuild/easyconfigs/b/Bison/Bison-2.7-iccifort-2011.13.367.eb b/easybuild/easyconfigs/__archive__/b/Bison/Bison-2.7-iccifort-2011.13.367.eb similarity index 100% rename from easybuild/easyconfigs/b/Bison/Bison-2.7-iccifort-2011.13.367.eb rename to easybuild/easyconfigs/__archive__/b/Bison/Bison-2.7-iccifort-2011.13.367.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/b/Bison/Bison-2.7-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/b/Bison/Bison-2.7-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/b/Bison/Bison-2.7-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/b/Bison/Bison-2.7-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/b/Bison/Bison-2.7-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-para-2014.12.eb b/easybuild/easyconfigs/__archive__/b/Bison/Bison-3.0.2-intel-para-2014.12.eb similarity index 100% rename from easybuild/easyconfigs/b/Bison/Bison-3.0.2-intel-para-2014.12.eb rename to easybuild/easyconfigs/__archive__/b/Bison/Bison-3.0.2-intel-para-2014.12.eb diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/Bonnie++/Bonnie++-1.03e-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/b/Bonnie++/Bonnie++-1.03e-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/b/Bonnie++/Bonnie++-1.03e-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/b/Bonnie++/Bonnie++-1.03e-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/b/Bonnie++/Bonnie++-1.03e-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.49.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.49.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/b/Boost/Boost-1.49.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/b/Boost/Boost-1.49.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.49.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.49.0-ictce-4.0.6-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/b/Boost/Boost-1.49.0-ictce-4.0.6-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/b/Boost/Boost-1.49.0-ictce-4.0.6-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.51.0-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/b/Boost/Boost-1.51.0-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/b/Boost/Boost-1.51.0-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.51.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/b/Boost/Boost-1.51.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/b/Boost/Boost-1.51.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.51.0-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/b/Boost/Boost-1.51.0-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/b/Boost/Boost-1.51.0-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.51.0-ictce-4.0.6-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-4.0.6-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/b/Boost/Boost-1.51.0-ictce-4.0.6-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.51.0-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/b/Boost/Boost-1.51.0-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.51.0-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/b/Boost/Boost-1.51.0-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/b/Boost/Boost-1.51.0-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-goalf-1.5.12-no-OFED-Python-2.7.5.eb b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.53.0-goalf-1.5.12-no-OFED-Python-2.7.5.eb similarity index 100% rename from easybuild/easyconfigs/b/Boost/Boost-1.53.0-goalf-1.5.12-no-OFED-Python-2.7.5.eb rename to easybuild/easyconfigs/__archive__/b/Boost/Boost-1.53.0-goalf-1.5.12-no-OFED-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000000000000000000000000000000000..621e1934a4f440176973f1b6bfdb849be4109c2c --- /dev/null +++ b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.53.0-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,22 @@ +name = 'Boost' +version = '1.53.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [('bzip2', '1.0.6')] + +configopts = '--without-libraries=python' + +# also build boost_mpi +boost_mpi = True + +osdependencies = [('zlib-devel', 'zlib1g-dev')] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.53.0-ictce-4.1.13-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-4.1.13-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/b/Boost/Boost-1.53.0-ictce-4.1.13-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/b/Boost/Boost-1.53.0-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/b/Boost/Boost-1.53.0-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/b/Boost/Boost-1.53.0-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.0.0-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/b/Bowtie/Bowtie-1.0.0-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/b/Bowtie/Bowtie-1.0.0-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/b/Bowtie/Bowtie-1.0.0-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.0.2-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.0.2-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.0.2-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.0.2-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/b/Bowtie2/Bowtie2-2.0.2-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/bbFTP/bbFTP-3.2.0-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/b/bbFTP/bbFTP-3.2.0-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/b/bbFTP/bbFTP-3.2.0-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/bbftpPRO/bbftpPRO-9.3.1-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/b/bbftpPRO/bbftpPRO-9.3.1-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/b/bbftpPRO/bbftpPRO-9.3.1-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/b/beagle-lib/beagle-lib-20120124-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/b/beagle-lib/beagle-lib-20120124-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/b/byacc/byacc-20120526-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/b/byacc/byacc-20120526-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/b/byacc/byacc-20120526-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/b/byacc/byacc-20120526-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/b/byacc/byacc-20120526-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/b/byacc/byacc-20120526-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/b/byacc/byacc-20120526-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.6-cgmpolf-1.1.6.eb similarity index 100% rename from easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-cgmpolf-1.1.6.eb rename to easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.6-cgmpolf-1.1.6.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.6-cgmvolf-1.1.12rc1.eb similarity index 100% rename from easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-cgmvolf-1.1.12rc1.eb rename to easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.6-cgmvolf-1.1.12rc1.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.6-cgmvolf-1.2.7.eb similarity index 100% rename from easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-cgmvolf-1.2.7.eb rename to easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.6-cgmvolf-1.2.7.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-cgoolf-1.1.7.eb b/easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.6-cgoolf-1.1.7.eb similarity index 100% rename from easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-cgoolf-1.1.7.eb rename to easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.6-cgoolf-1.1.7.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.6-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.6-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gmvolf-1.7.12.eb b/easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.6-gmvolf-1.7.12.eb similarity index 100% rename from easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-gmvolf-1.7.12.eb rename to easybuild/easyconfigs/__archive__/b/bzip2/bzip2-1.0.6-gmvolf-1.7.12.eb diff --git 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a/easybuild/easyconfigs/e/ESMF/ESMF-6.1.1-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/e/ESMF/ESMF-6.1.1-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/e/ESMF/ESMF-6.1.1-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/e/ESMF/ESMF-6.1.1-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-parallel.eb b/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-parallel.eb similarity index 100% rename from easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-parallel.eb rename to easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-parallel.eb diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-serial.eb b/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-serial.eb similarity index 100% rename from easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-serial.eb rename to easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-goalf-1.1.0-no-OFED-serial.eb diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-parallel.eb b/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-parallel.eb similarity index 100% rename from easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-parallel.eb rename to easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-parallel.eb diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-serial.eb b/easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-serial.eb similarity index 100% rename from easybuild/easyconfigs/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-serial.eb rename to easybuild/easyconfigs/__archive__/e/ESPResSo/ESPResSo-3.1.1-ictce-4.0.6-serial.eb diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.1.1-goalf-1.1.0-no-OFED.eb similarity index 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from easybuild/easyconfigs/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/e/Eigen/Eigen-3.1.4-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/__archive__/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000000000000000000000000000000000..b3d4b5ae5a81c57a982ddc2392369fdaf16d2bd3 --- /dev/null +++ b/easybuild/easyconfigs/__archive__/e/Extrae/Extrae-2.4.1-gompi-1.4.12-no-OFED.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 = 'Extrae' +version = '2.4.1' + +homepage = 'http://www.bsc.es/computer-sciences/performance-tools' +description = """Extrae is the core instrumentation package developed by the Performance Tools + group at BSC. Extrae is capable of instrumenting applications based on MPI, OpenMP, pthreads, + CUDA1, OpenCL1, and StarSs1 using different instrumentation approaches. The information gathered + by Extrae typically includes timestamped events of runtime calls, performance counters and source + code references. Besides, Extrae provides its own API to allow the user to manually instrument his + or her application.""" + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} +toolchainopts = {'usempi': True} + +# http://www.bsc.es/computer-sciences/performance-tools/downloads +# Requires input of email address for download +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['Extrae-%(version)s_configure-no-shared-binutils.patch'] + +# compiler toolchain depencies +dependencies = [ + ('zlib', '1.2.7'), + ('binutils', '2.22'), + ('Boost', '1.53.0'), + ('libunwind', '1.1'), + ('libxml2', '2.9.1'), + ('PAPI', '5.2.0'), +] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/__archive__/e/expat/expat-2.1.0-cgmpolf-1.1.6.eb similarity index 100% rename from easybuild/easyconfigs/e/expat/expat-2.1.0-cgmpolf-1.1.6.eb rename to easybuild/easyconfigs/__archive__/e/expat/expat-2.1.0-cgmpolf-1.1.6.eb diff --git 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b/easybuild/easyconfigs/__archive__/g/GMP/GMP-5.0.5-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/g/GMP/GMP-5.0.5-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/g/GMP/GMP-5.0.5-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/g/GPAW/GPAW-0.9.0.8965-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/g/GPAW/GPAW-0.9.0.8965-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/g/GPAW/GPAW-0.9.0.8965-ictce-4.0.6-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/g/GPAW/GPAW-0.9.0.8965-ictce-4.0.6-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/g/GPAW/GPAW-0.9.0.8965-ictce-4.0.6-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb similarity index 100% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb rename to easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb similarity index 100% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb rename to easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.1-goolfc-1.3.12-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb similarity index 100% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb rename to easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb similarity index 100% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb rename to easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmpolf-1.4.8-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-hybrid.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-hybrid.eb similarity index 100% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-hybrid.eb rename to easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-mt.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-mt.eb similarity index 100% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-mt.eb rename to easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-gmvolf-1.7.12-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-hybrid.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-hybrid.eb similarity index 100% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-hybrid.eb rename to easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-mt.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-mt.eb similarity index 100% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-mt.eb rename to easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goalf-1.1.0-no-OFED-mt.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb similarity index 100% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb rename to easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-hybrid.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb b/easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb similarity index 100% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb rename to easybuild/easyconfigs/__archive__/g/GROMACS/GROMACS-4.6.5-goolfc-2.6.10-mt.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/g/GSL/GSL-1.15-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/g/GSL/GSL-1.15-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.15-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/g/GSL/GSL-1.15-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb b/easybuild/easyconfigs/__archive__/g/GSL/GSL-1.16-goolfc-1.3.12.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-1.3.12.eb rename to easybuild/easyconfigs/__archive__/g/GSL/GSL-1.16-goolfc-1.3.12.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb b/easybuild/easyconfigs/__archive__/g/GSL/GSL-1.16-goolfc-2.6.10.eb similarity index 100% rename from easybuild/easyconfigs/g/GSL/GSL-1.16-goolfc-2.6.10.eb rename to easybuild/easyconfigs/__archive__/g/GSL/GSL-1.16-goolfc-2.6.10.eb diff --git a/easybuild/easyconfigs/g/GTI/GTI-1.2.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/GTI/GTI-1.2.0-gompi-1.4.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/g/GTI/GTI-1.2.0-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/g/GTI/GTI-1.2.0-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb similarity index 94% rename from easybuild/easyconfigs/g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb index 1e0d6874fa7a2bd69689995362c6d36c259d640b..2a6c5adf45e21bdaba55bf85f597c2a853a18afb 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/g/Geant4/Geant4-9.4.p02-ictce-4.0.6.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '2.8.4')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/Geant4/Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb similarity index 94% rename from easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/g/Geant4/Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb index b7af10a8488f92a7ac75b6754a3f72c55855d90e..2059df7ff07d5bd20fa71a581dd95e6001bdbd1d 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/g/Geant4/Geant4-9.5.p01-goalf-1.1.0-no-OFED.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '2.8.4')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb similarity index 94% rename from easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb index 3f34b45154796ac9bf226ecb5c370a1950786fe2..b5d179591ae2874eaa2318b55a6abf2298a75c8f 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/g/Geant4/Geant4-9.5.p01-ictce-4.0.6.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '2.8.4')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.10-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/g/Ghostscript/Ghostscript-9.10-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.10-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/g/Ghostscript/Ghostscript-9.10-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/GnuTLS/GnuTLS-3.1.8-goalf-1.1.0-no-OFED.eb similarity index 91% rename from easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/g/GnuTLS/GnuTLS-3.1.8-goalf-1.1.0-no-OFED.eb index 6090cb398e1f6908f6f0f7fb38e55229b8658126..3d16aad0af7ca4b2de7dc2e2f4cbcf71f20aaccd 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/g/GnuTLS/GnuTLS-3.1.8-goalf-1.1.0-no-OFED.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'gnutls' +name = 'GnuTLS' version = '3.1.8' homepage = 'http://www.gnutls.org/' @@ -9,12 +9,12 @@ description = "gnutls-3.0.22: GNU Transport Layer Security library" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = ['ftp://ftp.gnutls.org/pub/gnutls/'] -sources = [SOURCE_TAR_XZ] +sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('GMP', '5.0.5'), ('nettle', '2.6'), - ('guile', '1.8.8'), + ('Guile', '1.8.8'), ] configopts = "--with-guile-site-dir=$EBROOTGUILE" diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/g/Greenlet/Greenlet-0.4.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/g/Greenlet/Greenlet-0.4.0-ictce-4.1.13-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/Guile/Guile-1.8.8-goalf-1.1.0-no-OFED.eb similarity index 98% rename from easybuild/easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/g/Guile/Guile-1.8.8-goalf-1.1.0-no-OFED.eb index 35f61dcc34e7f05becb8db06d3180ae926594a51..2665630abaed419c1890f4ff7e0952e01f42d43d 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/g/Guile/Guile-1.8.8-goalf-1.1.0-no-OFED.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'guile' +name = 'Guile' version = '1.8.8' homepage = 'http://www.gnu.org/software/guile' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/g/Guile/Guile-1.8.8-ictce-4.0.6.eb similarity index 98% rename from easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/g/Guile/Guile-1.8.8-ictce-4.0.6.eb index 88054289c0763f8a4426be409b2f3b34ab51a1e3..d9d73c6e916874e3b53ccc55334de088216a72ed 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/g/Guile/Guile-1.8.8-ictce-4.0.6.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'guile' +name = 'Guile' version = '1.8.8' homepage = 'http://www.gnu.org/software/guile' diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/g2clib/g2clib-1.2.3-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/g/g2clib/g2clib-1.2.3-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/__archive__/g/g2clib/g2clib-1.2.3-ictce-3.2.2.u3.eb similarity index 100% rename from easybuild/easyconfigs/g/g2clib/g2clib-1.2.3-ictce-3.2.2.u3.eb rename to easybuild/easyconfigs/__archive__/g/g2clib/g2clib-1.2.3-ictce-3.2.2.u3.eb diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/g/g2clib/g2clib-1.4.0-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/g/g2clib/g2clib-1.4.0-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/g/g2clib/g2clib-1.4.0-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/g2lib/g2lib-1.2.4-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/g/g2lib/g2lib-1.2.4-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/__archive__/g/g2lib/g2lib-1.2.4-ictce-3.2.2.u3.eb similarity index 100% rename from easybuild/easyconfigs/g/g2lib/g2lib-1.2.4-ictce-3.2.2.u3.eb rename to easybuild/easyconfigs/__archive__/g/g2lib/g2lib-1.2.4-ictce-3.2.2.u3.eb diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/g/g2lib/g2lib-1.4.0-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/g/g2lib/g2lib-1.4.0-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/g/g2lib/g2lib-1.4.0-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/g/g2lib/g2lib-1.4.0-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/g/g2lib/g2lib-1.4.0-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2.6.10.eb b/easybuild/easyconfigs/__archive__/g/gcccuda/gcccuda-2.6.10.eb similarity index 100% rename from easybuild/easyconfigs/g/gcccuda/gcccuda-2.6.10.eb rename to easybuild/easyconfigs/__archive__/g/gcccuda/gcccuda-2.6.10.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/__archive__/g/gettext/gettext-0.18.2-cgmpolf-1.1.6.eb similarity index 100% rename from easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmpolf-1.1.6.eb rename to easybuild/easyconfigs/__archive__/g/gettext/gettext-0.18.2-cgmpolf-1.1.6.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/__archive__/g/gettext/gettext-0.18.2-cgmvolf-1.1.12rc1.eb similarity index 100% rename from easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmvolf-1.1.12rc1.eb rename to easybuild/easyconfigs/__archive__/g/gettext/gettext-0.18.2-cgmvolf-1.1.12rc1.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/__archive__/g/gettext/gettext-0.18.2-cgmvolf-1.2.7.eb similarity index 100% rename from easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgmvolf-1.2.7.eb rename to easybuild/easyconfigs/__archive__/g/gettext/gettext-0.18.2-cgmvolf-1.2.7.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.18.2-cgoolf-1.1.7.eb b/easybuild/easyconfigs/__archive__/g/gettext/gettext-0.18.2-cgoolf-1.1.7.eb similarity index 100% rename from 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b/easybuild/easyconfigs/__archive__/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/g/grib_api/grib_api-1.9.18-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.5-cgoolf-1.1.7.eb b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-cgoolf-1.1.7.eb similarity index 100% rename from easybuild/easyconfigs/g/gzip/gzip-1.5-cgoolf-1.1.7.eb rename to easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-cgoolf-1.1.7.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.5-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/g/gzip/gzip-1.5-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/g/gzip/gzip-1.5-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.5-goalf-1.1.0-no-OFED.eb 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similarity index 100% rename from easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.4.10-no-OFED.eb rename to easybuild/easyconfigs/__archive__/g/gzip/gzip-1.6-goolf-1.4.10-no-OFED.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.5.14-no-OFED.eb b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.6-goolf-1.5.14-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/g/gzip/gzip-1.6-goolf-1.5.14-no-OFED.eb rename to easybuild/easyconfigs/__archive__/g/gzip/gzip-1.6-goolf-1.5.14-no-OFED.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-goolfc-1.4.10.eb b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.6-goolfc-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/g/gzip/gzip-1.6-goolfc-1.4.10.eb rename to easybuild/easyconfigs/__archive__/g/gzip/gzip-1.6-goolfc-1.4.10.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.6-iomkl-6.6.2.eb b/easybuild/easyconfigs/__archive__/g/gzip/gzip-1.6-iomkl-6.6.2.eb similarity index 100% rename from easybuild/easyconfigs/g/gzip/gzip-1.6-iomkl-6.6.2.eb rename to easybuild/easyconfigs/__archive__/g/gzip/gzip-1.6-iomkl-6.6.2.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/__archive__/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb similarity index 100% rename from easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb rename to easybuild/easyconfigs/__archive__/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/h/HDF/HDF-4.2.8-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/h/HDF/HDF-4.2.8-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs-mt.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs-mt.eb similarity index 100% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs-mt.eb rename to easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs-mt.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs.eb similarity index 100% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs.eb rename to easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.10-ictce-4.1.13-gpfs.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-no-mpi.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.10-ictce-4.1.13-no-mpi.eb similarity index 100% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13-no-mpi.eb rename to easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.10-ictce-4.1.13-no-mpi.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.10-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.10-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.10-patch1-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-patch1-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.10-patch1-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-4.1.13-zlib-1.2.7.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.12-ictce-4.1.13-zlib-1.2.7.eb similarity index 100% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-ictce-4.1.13-zlib-1.2.7.eb rename to easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.12-ictce-4.1.13-zlib-1.2.7.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.7-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.7-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.7-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.7-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.7-ictce-3.2.2.u3.eb similarity index 100% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-ictce-3.2.2.u3.eb rename to easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.7-ictce-3.2.2.u3.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.7-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.7-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.7-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.9-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.9-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.9-ictce-3.2.2.u3.eb similarity index 100% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-3.2.2.u3.eb rename to easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.9-ictce-3.2.2.u3.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.9-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.9-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/h/HDF5/HDF5-1.8.9-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/h/HH-suite/HH-suite-2.0.16-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/h/HH-suite/HH-suite-2.0.16-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/h/HH-suite/HH-suite-2.0.16-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/h/HH-suite/HH-suite-2.0.16-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.0-goalf-1.1.0-no-OFED.eb similarity index 79% rename from easybuild/easyconfigs/h/HMMER/HMMER-3.0-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.0-goalf-1.1.0-no-OFED.eb index 9f844f7f8c0b817a5d2427ba6b17da1cc22f5949..c14d1e9c4c6ed6212428eef69bd0ef5f25018677 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.0-goalf-1.1.0-no-OFED.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'HMMER' version = '3.0' -homepage = 'http://hmmer.janelia.org/' +homepage = 'http://hmmer.org/' description = """HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other @@ -27,10 +27,8 @@ description = """HMMER is used for searching sequence databases for homologs of toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -# eg. http://selab.janelia.org/software/hmmer3/3.0/hmmer-3.0-linux-intel-x86_64.tar.gz -versiondir = "hmmer%s" % ".".join(version.split('.')[:-1]) -sources = ['hmmer-%s-linux-intel-x86_64.tar.gz' % version] -source_urls = ['http://selab.janelia.org/software/%s/%s/' % (versiondir, version)] +source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] +sources = ['hmmer-%(version)s-linux-intel-x86_64.tar.gz'] sanity_check_paths = { 'files': ["bin/hmmemit", "bin/hmmsearch", "bin/hmmscan"], diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.0-ictce-4.0.6.eb similarity index 79% rename from easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.0-ictce-4.0.6.eb index 4f2f846bc8dee0d57a914f07dc53dc6c1a636f7f..882be30c22a76f5291b1462e5a2a464112ac6859 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/h/HMMER/HMMER-3.0-ictce-4.0.6.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'HMMER' version = '3.0' -homepage = 'http://hmmer.janelia.org/' +homepage = 'http://hmmer.org/' description = """HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other @@ -27,10 +27,8 @@ description = """HMMER is used for searching sequence databases for homologs of toolchain = {'version': '4.0.6', 'name': 'ictce'} -# eg. http://selab.janelia.org/software/hmmer3/3.0/hmmer-3.0-linux-intel-x86_64.tar.gz -versiondir = "hmmer%s" % ".".join(version.split('.')[:-1]) -sources = ['hmmer-%s-linux-intel-x86_64.tar.gz' % version] -source_urls = ['http://selab.janelia.org/software/%s/%s/' % (versiondir, version)] +source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] +sources = ['hmmer-%(version)s-linux-intel-x86_64.tar.gz'] sanity_check_paths = { 'files': ["bin/hmmemit", "bin/hmmsearch", "bin/hmmscan"], diff --git a/easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/h/HPCBIOS_Math/HPCBIOS_Math-20130829-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.0-cgmpolf-1.1.6.eb similarity index 100% rename from easybuild/easyconfigs/h/HPL/HPL-2.0-cgmpolf-1.1.6.eb rename to easybuild/easyconfigs/__archive__/h/HPL/HPL-2.0-cgmpolf-1.1.6.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.0-cgmvolf-1.1.12rc1.eb similarity index 100% rename from easybuild/easyconfigs/h/HPL/HPL-2.0-cgmvolf-1.1.12rc1.eb rename to easybuild/easyconfigs/__archive__/h/HPL/HPL-2.0-cgmvolf-1.1.12rc1.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/__archive__/h/HPL/HPL-2.0-cgmvolf-1.2.7.eb similarity index 100% rename from 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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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easybuild/easyconfigs/i/iompi/iompi-4.6.13.eb rename to easybuild/easyconfigs/__archive__/i/iompi/iompi-4.6.13.eb diff --git a/easybuild/easyconfigs/i/iompi/iompi-6.6.2.eb b/easybuild/easyconfigs/__archive__/i/iompi/iompi-6.6.2.eb similarity index 100% rename from easybuild/easyconfigs/i/iompi/iompi-6.6.2.eb rename to easybuild/easyconfigs/__archive__/i/iompi/iompi-6.6.2.eb diff --git a/easybuild/easyconfigs/i/iompi/iompi-6.6.4-no-OFED.eb b/easybuild/easyconfigs/__archive__/i/iompi/iompi-6.6.4-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/i/iompi/iompi-6.6.4-no-OFED.eb rename to easybuild/easyconfigs/__archive__/i/iompi/iompi-6.6.4-no-OFED.eb diff --git a/easybuild/easyconfigs/i/iompi/iompi-6.6.4.eb b/easybuild/easyconfigs/__archive__/i/iompi/iompi-6.6.4.eb similarity index 100% rename from easybuild/easyconfigs/i/iompi/iompi-6.6.4.eb rename to easybuild/easyconfigs/__archive__/i/iompi/iompi-6.6.4.eb diff --git a/easybuild/easyconfigs/i/ipsmpi/ipsmpi-2014.12.eb 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easybuild/easyconfigs/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb rename to easybuild/easyconfigs/__archive__/j/Jansson/Jansson-2.5-gcccuda-2.6.10.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/j/JasPer/JasPer-1.900.1-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/j/JasPer/JasPer-1.900.1-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/__archive__/j/JasPer/JasPer-1.900.1-ictce-3.2.2.u3.eb similarity index 100% rename from easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-ictce-3.2.2.u3.eb rename to easybuild/easyconfigs/__archive__/j/JasPer/JasPer-1.900.1-ictce-3.2.2.u3.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/j/JasPer/JasPer-1.900.1-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/j/JasPer/JasPer-1.900.1-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/j/JasPer/JasPer-1.900.1-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/j/JasPer/JasPer-1.900.1-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/k/kbproto/kbproto-1.0.6-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-testing.eb b/easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-testing.eb similarity index 100% rename from easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-testing.eb rename to easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4-testing.eb diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4.eb b/easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4.eb similarity index 100% rename from easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4.eb rename to easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED-ATLAS-3.8.4.eb diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.4.0-gompi-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gmpich-1.4.8.eb b/easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.4.2-gmpich-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gmpich-1.4.8.eb rename to easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.4.2-gmpich-1.4.8.eb diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.3.12.eb b/easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.4.2-gompi-1.3.12.eb similarity index 100% rename from easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.3.12.eb rename to easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.4.2-gompi-1.3.12.eb diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.5.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.4.2-gompi-1.5.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.5.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.4.2-gompi-1.5.12-no-OFED.eb diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.5.12.eb b/easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.4.2-gompi-1.5.12.eb similarity index 100% rename from easybuild/easyconfigs/l/LAPACK/LAPACK-3.4.2-gompi-1.5.12.eb rename to easybuild/easyconfigs/__archive__/l/LAPACK/LAPACK-3.4.2-gompi-1.5.12.eb diff --git a/easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.17-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/LIBSVM/LIBSVM-3.17-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/LIBSVM/LIBSVM-3.17-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/LIBSVM/LIBSVM-3.17-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/LWM2/LWM2-1.1-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.06-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.06-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/LZO/LZO-2.06-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/LZO/LZO-2.06-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.06-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/LZO/LZO-2.06-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-5.1.1.eb b/easybuild/easyconfigs/__archive__/l/LZO/LZO-2.06-ictce-5.1.1.eb similarity index 100% rename from easybuild/easyconfigs/l/LZO/LZO-2.06-ictce-5.1.1.eb rename to easybuild/easyconfigs/__archive__/l/LZO/LZO-2.06-ictce-5.1.1.eb diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/LibTIFF/LibTIFF-4.0.3-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/LibTIFF/LibTIFF-4.0.3-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-gmacml-1.7.0.eb b/easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.4-gmacml-1.7.0.eb similarity index 100% rename from easybuild/easyconfigs/l/Libint/Libint-1.1.4-gmacml-1.7.0.eb rename to easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.4-gmacml-1.7.0.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.4-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/Libint/Libint-1.1.4-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.4-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.4-ictce-3.2.2.u3.eb similarity index 100% rename from easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-3.2.2.u3.eb rename to easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.4-ictce-3.2.2.u3.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.4-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/Libint/Libint-1.1.4-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.4-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-para-2014.12.eb b/easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.4-intel-para-2014.12.eb similarity index 100% rename from easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-para-2014.12.eb rename to easybuild/easyconfigs/__archive__/l/Libint/Libint-1.1.4-intel-para-2014.12.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.0.3-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/Libint/Libint-2.0.3-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/Libint/Libint-2.0.3-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/Libint/Libint-2.0.3-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/lftp/lftp-4.4.1-goalf-1.1.0-no-OFED.eb similarity index 96% rename from easybuild/easyconfigs/l/lftp/lftp-4.4.1-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/lftp/lftp-4.4.1-goalf-1.1.0-no-OFED.eb index 143cec914499e94920e6bc42271f4fdd68367912..cca49e12bf84748b0d7f6a65a4a6d1f87af2a177 100644 --- a/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/l/lftp/lftp-4.4.1-goalf-1.1.0-no-OFED.eb @@ -30,7 +30,7 @@ source_urls = [ 'http://ftp.yar.ru/pub/source/lftp/old/', ] -dependencies = [('gnutls', '3.1.8')] +dependencies = [('GnuTLS', '3.1.8')] sanity_check_paths = { 'files': ['bin/lftp'], diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libICE/libICE-1.0.8-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libICE/libICE-1.0.8-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libICE/libICE-1.0.8-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libSM/libSM-1.2.1-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libSM/libSM-1.2.1-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libSM/libSM-1.2.1-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libX11/libX11-1.6.1-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libX11/libX11-1.6.1-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libX11/libX11-1.6.1-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libXau/libXau-1.0.8-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libXau/libXau-1.0.8-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libXau/libXau-1.0.8-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libXaw/libXaw-1.0.12-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libXaw/libXaw-1.0.12-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libXaw/libXaw-1.0.12-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libXext/libXext-1.3.2-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libXext/libXext-1.3.2-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libXext/libXext-1.3.2-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libXfixes/libXfixes-5.0.1-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libXfixes/libXfixes-5.0.1-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libXi/libXi-1.7.2-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libXi/libXi-1.7.2-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libXi/libXi-1.7.2-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libXmu/libXmu-1.1.2-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libXmu/libXmu-1.1.2-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libXmu/libXmu-1.1.2-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libXp/libXp-1.0.2-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libXp/libXp-1.0.2-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libXp/libXp-1.0.2-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libXpm/libXpm-3.5.11-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libXpm/libXpm-3.5.11-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libXpm/libXpm-3.5.11-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libXt/libXt-1.1.4-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libXt/libXt-1.1.4-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libXt/libXt-1.1.4-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libXtst/libXtst-1.2.2-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libXtst/libXtst-1.2.2-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libXtst/libXtst-1.2.2-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libXtst/libXtst-1.2.2-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libctl/libctl-3.2.1-goalf-1.1.0-no-OFED.eb similarity index 94% rename from easybuild/easyconfigs/l/libctl/libctl-3.2.1-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libctl/libctl-3.2.1-goalf-1.1.0-no-OFED.eb index c9f79a726b7928e6d3c0a30a3f8cc7f4f0db21fc..b65c18c3e27b8b1caed6effffb6270fc3ae5a5e1 100644 --- a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/l/libctl/libctl-3.2.1-goalf-1.1.0-no-OFED.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True} source_urls = ['http://ab-initio.mit.edu/libctl/'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('guile', '1.8.8')] +dependencies = [('Guile', '1.8.8')] # fix for guile-config being broken because shebang line contains full path to bin/guile configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' diff --git a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libctl/libctl-3.2.1-ictce-4.0.6.eb similarity index 94% rename from easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/libctl/libctl-3.2.1-ictce-4.0.6.eb index cd7968e31d0574a922d3df1f00df9327aff3148e..9c89029e06d1ce9cb35d089b2ea5b632365b1ba0 100644 --- a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/l/libctl/libctl-3.2.1-ictce-4.0.6.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True} source_urls = ['http://ab-initio.mit.edu/libctl/'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('guile', '1.8.8')] +dependencies = [('Guile', '1.8.8')] # fix for guile-config being broken because shebang line contains full path to bin/guile configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libdrm/libdrm-2.4.27-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libdrm/libdrm-2.4.27-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libdrm/libdrm-2.4.27-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/libdrm/libdrm-2.4.27-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libdrm/libdrm-2.4.27-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libdrm/libdrm-2.4.27-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libdrm/libdrm-2.4.27-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.0.11-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/l/libffi/libffi-3.0.11-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/l/libffi/libffi-3.0.11-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/l/libffi/libffi-3.0.11-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.0.11-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libffi/libffi-3.0.11-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libffi/libffi-3.0.11-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libffi/libffi-3.0.11-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.0.11-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libffi/libffi-3.0.11-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/l/libffi/libffi-3.0.11-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/libffi/libffi-3.0.11-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.0.13-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/l/libffi/libffi-3.0.13-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/l/libffi/libffi-3.0.13-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/l/libffi/libffi-3.0.13-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.0.13-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libffi/libffi-3.0.13-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libffi/libffi-3.0.13-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libffi/libffi-3.0.13-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.0.13-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libffi/libffi-3.0.13-gompi-1.4.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libffi/libffi-3.0.13-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libffi/libffi-3.0.13-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.0.13-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libffi/libffi-3.0.13-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/l/libffi/libffi-3.0.13-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/libffi/libffi-3.0.13-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.0.13-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libffi/libffi-3.0.13-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libffi/libffi-3.0.13-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libffi/libffi-3.0.13-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libgtextutils/libgtextutils-0.6.1-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libgtextutils/libgtextutils-0.6.1-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libgtextutils/libgtextutils-0.6.1-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/libgtextutils/libgtextutils-0.6.1-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/l/libharu/libharu-2.2.0-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libharu/libharu-2.2.0-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libharu/libharu-2.2.0-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libharu/libharu-2.2.0-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.27-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libidn/libidn-1.27-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libidn/libidn-1.27-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libidn/libidn-1.27-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libjpeg-turbo/libjpeg-turbo-1.3.0-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.0-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libjpeg-turbo/libjpeg-turbo-1.3.0-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-ictce-6.3.5.eb b/easybuild/easyconfigs/__archive__/l/libjpeg-turbo/libjpeg-turbo-1.3.1-ictce-6.3.5.eb similarity index 100% rename from easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-ictce-6.3.5.eb rename to easybuild/easyconfigs/__archive__/l/libjpeg-turbo/libjpeg-turbo-1.3.1-ictce-6.3.5.eb diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb similarity index 97% rename from easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb index f753b8b744e405d9f1dfc615b7409ac450b2b0a3..ef19cb94f186948096a74f0fdbba330b2aa23fc0 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/l/libmatheval/libmatheval-1.1.8-goalf-1.1.0-no-OFED.eb @@ -17,7 +17,7 @@ dependencies = [ ('flex', '2.5.35'), ('Bison', '2.5'), ('byacc', '20120526'), - ('guile', '1.8.8'), + ('Guile', '1.8.8'), ] configopts = '--with-pic ' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb similarity index 97% rename from easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb index a8ede070974aaaff7fcf2d7b399dd3bca92d9d46..c50391d5e21c3fb972e168c26d976bbf9a6ae3ac 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/l/libmatheval/libmatheval-1.1.8-ictce-4.0.6.eb @@ -17,7 +17,7 @@ dependencies = [ ('flex', '2.5.35'), ('Bison', '2.5'), ('byacc', '20120526'), - ('guile', '1.8.8'), + ('Guile', '1.8.8'), ] configopts = '--with-pic ' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libpciaccess/libpciaccess-0.13.1-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/libpciaccess/libpciaccess-0.13.1-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libpciaccess/libpciaccess-0.13.1-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.5.10-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.10-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.5.10-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.10-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.5.10-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.10-ictce-3.2.2.u3.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.5.10-ictce-3.2.2.u3.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.10-ictce-3.2.2.u3.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.5.10-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.10-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.5.10-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.10-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.5.11-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.11-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.5.11-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.11-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.5.11-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.11-ictce-3.2.2.u3.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.5.11-ictce-3.2.2.u3.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.11-ictce-3.2.2.u3.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.5.11-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.11-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.5.11-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.11-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.5.13-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.13-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.5.13-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.13-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.5.13-ictce-4.0.10.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.13-ictce-4.0.10.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.5.13-ictce-4.0.10.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.13-ictce-4.0.10.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.5.13-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.13-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.5.13-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.13-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.5.13-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.13-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.5.13-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.13-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.5.14-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.14-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.5.14-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.14-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.5.14-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.14-ictce-3.2.2.u3.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.5.14-ictce-3.2.2.u3.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.14-ictce-3.2.2.u3.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.5.14-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.14-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.5.14-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.14-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.5.14-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.14-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.5.14-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.5.14-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.12-ictce-6.3.5.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.6.12-ictce-6.3.5.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.6.12-ictce-6.3.5.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.6.12-ictce-6.3.5.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.6.2-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.6.2-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.6.2-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.6.2-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.6.2-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.6.2-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.2-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.6.2-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.6.2-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.6.2-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.3-ictce-4.1.13-zlib-1.2.8.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.6.3-ictce-4.1.13-zlib-1.2.8.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.6.3-ictce-4.1.13-zlib-1.2.8.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.6.3-ictce-4.1.13-zlib-1.2.8.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.3-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.6.3-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.6.3-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.6.3-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libpng/libpng-1.6.6-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libpng/libpng-1.6.6-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libpng/libpng-1.6.6-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libpthread-stubs/libpthread-stubs-0.3-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libpthread-stubs/libpthread-stubs-0.3-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libpthread-stubs/libpthread-stubs-0.3-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-cgmpolf-1.1.6.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-cgmvolf-1.1.12rc1.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-cgmvolf-1.2.7.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-cgoolf-1.1.7.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-gmvolf-1.7.12.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-gmvolf-1.7.12rc1.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-goalf-1.5.12-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-ictce-4.0.10.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.10.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-ictce-4.0.10.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-iomkl-4.6.13.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-iqacml-3.7.3.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.2-iqacml-4.4.13.eb diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb b/easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.3-ictce-6.3.5.eb similarity index 100% rename from easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-6.3.5.eb rename to easybuild/easyconfigs/__archive__/l/libreadline/libreadline-6.3-ictce-6.3.5.eb diff --git a/easybuild/easyconfigs/l/libsmm/libsmm-20111205-gmacml-1.7.0.eb b/easybuild/easyconfigs/__archive__/l/libsmm/libsmm-20111205-gmacml-1.7.0.eb similarity index 100% rename from easybuild/easyconfigs/l/libsmm/libsmm-20111205-gmacml-1.7.0.eb rename to easybuild/easyconfigs/__archive__/l/libsmm/libsmm-20111205-gmacml-1.7.0.eb diff --git a/easybuild/easyconfigs/l/libsmm/libsmm-20111205-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libsmm/libsmm-20111205-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libsmm/libsmm-20111205-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libsmm/libsmm-20111205-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.2-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libtool/libtool-2.4.2-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.2-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.2-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.2-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.2-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libtool/libtool-2.4.2-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libtool/libtool-2.4.2-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libunistring/libunistring-0.9.3-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/libunistring/libunistring-0.9.3-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000000000000000000000000000000000..cdac53c708aadffc4870fd14cb0c232f6406663e --- /dev/null +++ b/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-gompi-1.4.12-no-OFED.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 = 'libunwind' +version = '1.1' + +homepage = 'http://www.nongnu.org/libunwind/' +description = """The primary goal of this project 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.""" + +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://download.savannah.gnu.org/releases/libunwind/'] + +sanity_check_paths = { + 'files': ['include/libunwind.h', ('lib/libunwind.a', 'lib64/libunwind.a')], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libxc/libxc-2.0.1-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libxc/libxc-2.0.1-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libxc/libxc-2.0.1-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libxc/libxc-2.0.1-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libxc/libxc-2.0.1-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libxc/libxc-2.0.1-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libxc/libxc-2.0.2-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libxc/libxc-2.0.2-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libxc/libxc-2.0.2-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libxc/libxc-2.0.2-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libxc/libxc-2.0.2-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libxc/libxc-2.0.2-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.0.3-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libxc/libxc-2.0.3-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libxc/libxc-2.0.3-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libxc/libxc-2.0.3-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-para-2014.12.eb b/easybuild/easyconfigs/__archive__/l/libxc/libxc-2.2.1-intel-para-2014.12.eb similarity index 100% rename from easybuild/easyconfigs/l/libxc/libxc-2.2.1-intel-para-2014.12.eb rename to easybuild/easyconfigs/__archive__/l/libxc/libxc-2.2.1-intel-para-2014.12.eb diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/l/libxcb/libxcb-1.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/l/libxcb/libxcb-1.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/l/libxcb/libxcb-1.8-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/l/libxcb/libxcb-1.8-ictce-4.0.6-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.0.6-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/l/libxcb/libxcb-1.8-ictce-4.0.6-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/l/libxcb/libxcb-1.8-ictce-4.1.13-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/l/libxcb/libxcb-1.8-ictce-4.1.13-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/l/libxcb/libxcb-1.8-ictce-4.1.13-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 54% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index e98bac6018d8b2d18206da236d52f016c17c24fa..61ac8b0f98ec8d7dfff34222c0ec3cc9622150ed 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.8.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,20 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.7'), - ('Python', pythonver), + ('Python', '2.7.3'), ] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb similarity index 60% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb index 4a4a4816ab2e8285a429accaf788d3b62c0090a9..b5be030eb8f85a648cb8982246c5bb2ea78c89af 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.8.0' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb similarity index 53% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb index b82e8e6c939dd27f6797f6fc9bc243ce463660db..541f5b23a744b4129da041ea4fc9f8b706631e04 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.8.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,20 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.7'), - ('Python', pythonver), + ('Python', '2.7.3'), ] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb similarity index 60% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb index 91e1ffbc9cf78ac331e8e58b273a81ba7b6292a6..e30ea6f81026b2e59d02759db99415f8cb436d48 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.8.0' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb similarity index 53% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb index 31e824b5ea47acbaa1108c2d55569539d9a1a051..a089a50337ee911ab26e0ee38cfb544c9a22bd20 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.8.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,20 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.7'), - ('Python', pythonver), + ('Python', '2.7.3'), ] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb similarity index 60% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb index 0567c075f0559a02c44f88d45f7cba387fc5f747..d27cd00a3d66f7377005907deaf21b4ea0eb72ea 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.0' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb similarity index 60% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb index 06cdc26c7679d6dfc012fc3f827214ac9702c50a..7012fe4e03955bfc329e71343462ac1f7aa0d96a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.0' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb similarity index 60% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb index 3042a3cf37e83d5e1ec178f26e4a0c42bd539b99..c071752aa8d7a4ce88505a4d13bc55b9dfaf7c12 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.0' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb similarity index 60% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb index 33b6562e0fa336106df8fbd81e6b9f53227a9865..dacb6f49dad6dbb971002ebf54c2dd5bc180447c 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb similarity index 60% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb index e44ddd0d64ca5a953af7c2db67ae22180df00cad..db9d8e9f002bd6684b47b6fcf7e13d01e157cb25 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb similarity index 60% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb index 90b9bc8ea55a69d96978c8aeea8fe38b0163cec1..fe5357a0ea306e059f7a9b702ef0e61de0d2bab4 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb similarity index 60% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb index 487bf333ac32b6b12eb55d846e3619b50562435b..3549a115036daf0051c74924a483e4959065fbc5 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb similarity index 60% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb index 3e1cc777901a9cc7426ec2e6fb60fba31a39bff0..49bef39036d17e3ebf0b2ebc7d0ed23a6933d512 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb similarity index 60% rename from easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb index 5da629883240603b8ec01e430b14bc98e9c84afd..bbaaf19893231b652288e514831694b4294b7bba 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/__archive__/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libxslt/libxslt-1.1.28-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libxslt/libxslt-1.1.28-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/l/libxslt/libxslt-1.1.28-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/l/libxslt/libxslt-1.1.28-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/libxslt/libxslt-1.1.28-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/libxslt/libxslt-1.1.28-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/libxslt/libxslt-1.1.28-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/libyaml/libyaml-0.1.4-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/libyaml/libyaml-0.1.4-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/libyaml/libyaml-0.1.4-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-goalf-1.1.0-no-OFED-pinomp.eb b/easybuild/easyconfigs/__archive__/l/likwid/likwid-3.0.0-goalf-1.1.0-no-OFED-pinomp.eb similarity index 100% rename from easybuild/easyconfigs/l/likwid/likwid-3.0.0-goalf-1.1.0-no-OFED-pinomp.eb rename to easybuild/easyconfigs/__archive__/l/likwid/likwid-3.0.0-goalf-1.1.0-no-OFED-pinomp.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/l/likwid/likwid-3.0.0-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/l/likwid/likwid-3.0.0-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/l/likwid/likwid-3.0.0-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-4.1.13-pinomp.eb b/easybuild/easyconfigs/__archive__/l/likwid/likwid-3.0.0-ictce-4.1.13-pinomp.eb similarity index 100% rename from easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-4.1.13-pinomp.eb rename to easybuild/easyconfigs/__archive__/l/likwid/likwid-3.0.0-ictce-4.1.13-pinomp.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/likwid/likwid-3.0.0-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/likwid/likwid-3.0.0-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/likwid/likwid-3.0.0-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.0.1-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/likwid/likwid-4.0.1-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/likwid/likwid-4.0.1-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/likwid/likwid-4.0.1-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/l/lynx/lynx-2.8.7-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/l/lynx/lynx-2.8.7-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/l/lynx/lynx-2.8.7-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/l/lynx/lynx-2.8.7-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-ClangGCC-1.1.3.eb similarity index 100% rename from easybuild/easyconfigs/m/M4/M4-1.4.16-ClangGCC-1.1.3.eb rename to easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-ClangGCC-1.1.3.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-ClangGCC-1.2.3.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-ClangGCC-1.2.3.eb similarity index 100% rename from easybuild/easyconfigs/m/M4/M4-1.4.16-ClangGCC-1.2.3.eb rename to easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-ClangGCC-1.2.3.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-gcccuda-2.6.10.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-gcccuda-2.6.10.eb similarity index 100% rename from easybuild/easyconfigs/m/M4/M4-1.4.16-gcccuda-2.6.10.eb rename to easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-gcccuda-2.6.10.eb diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-gmacml-1.7.0.eb b/easybuild/easyconfigs/__archive__/m/M4/M4-1.4.16-gmacml-1.7.0.eb similarity index 100% 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 easybuild/easyconfigs/__archive__/m/METIS/METIS-4.0.1-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-4.0.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/m/METIS/METIS-4.0.3-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/m/METIS/METIS-4.0.3-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/m/METIS/METIS-4.0.3-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-4.0.3-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/m/METIS/METIS-4.0.3-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/m/METIS/METIS-4.0.3-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/m/METIS/METIS-4.0.3-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.0.2-gmpolf-1.4.8.eb b/easybuild/easyconfigs/__archive__/m/METIS/METIS-5.0.2-gmpolf-1.4.8.eb similarity index 100% rename from easybuild/easyconfigs/m/METIS/METIS-5.0.2-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/m/METIS/METIS-5.0.2-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/METIS/METIS-5.0.2-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/m/METIS/METIS-5.0.2-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/m/METIS/METIS-5.0.2-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.0.2-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/METIS/METIS-5.0.2-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/m/METIS/METIS-5.0.2-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/m/METIS/METIS-5.0.2-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.0.2-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/m/METIS/METIS-5.0.2-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/m/METIS/METIS-5.0.2-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/m/METIS/METIS-5.0.2-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/m/METIS/METIS-5.1.0-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/m/METIS/METIS-5.1.0-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/m/METIS/METIS-5.1.0-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/MPFR/MPFR-3.1.0-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/m/MPFR/MPFR-3.1.0-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/m/MPFR/MPFR-3.1.0-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.0-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/MPFR/MPFR-3.1.0-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/m/MPFR/MPFR-3.1.0-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/m/MPFR/MPFR-3.1.0-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/__archive__/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb similarity index 100% rename from easybuild/easyconfigs/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb rename to easybuild/easyconfigs/__archive__/m/MPICH/MPICH-3.0.3-ClangGCC-1.1.3.eb diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-4.10.0-gmpolf-1.4.8-metis.eb b/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-4.10.0-gmpolf-1.4.8-metis.eb similarity index 100% rename from easybuild/easyconfigs/m/MUMPS/MUMPS-4.10.0-gmpolf-1.4.8-metis.eb rename to easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-4.10.0-gmpolf-1.4.8-metis.eb diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-4.10.0-ictce-4.1.13-metis.eb b/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-4.10.0-ictce-4.1.13-metis.eb similarity index 100% rename from easybuild/easyconfigs/m/MUMPS/MUMPS-4.10.0-ictce-4.1.13-metis.eb rename to easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-4.10.0-ictce-4.1.13-metis.eb diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-4.10.0-ictce-4.1.13-parmetis.eb b/easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-4.10.0-ictce-4.1.13-parmetis.eb similarity index 100% rename from easybuild/easyconfigs/m/MUMPS/MUMPS-4.10.0-ictce-4.1.13-parmetis.eb rename to easybuild/easyconfigs/__archive__/m/MUMPS/MUMPS-4.10.0-ictce-4.1.13-parmetis.eb diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-4.1.13-Perl-5.16.3.eb b/easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-ictce-4.1.13-Perl-5.16.3.eb similarity index 100% rename from easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-ictce-4.1.13-Perl-5.16.3.eb rename to easybuild/easyconfigs/__archive__/m/MUMmer/MUMmer-3.23-ictce-4.1.13-Perl-5.16.3.eb diff --git a/easybuild/easyconfigs/m/MUST/MUST-1.2.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/MUST/MUST-1.2.0-gompi-1.4.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/m/MUST/MUST-1.2.0-gompi-1.4.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/m/MUST/MUST-1.2.0-gompi-1.4.12-no-OFED.eb diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/__archive__/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb similarity index 100% rename from easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb rename to easybuild/easyconfigs/__archive__/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.1.3.eb diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb b/easybuild/easyconfigs/__archive__/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb similarity index 100% rename from easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb rename to easybuild/easyconfigs/__archive__/m/MVAPICH2/MVAPICH2-1.9-ClangGCC-1.2.3.eb diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb b/easybuild/easyconfigs/__archive__/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb similarity index 100% rename from easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb rename to easybuild/easyconfigs/__archive__/m/MVAPICH2/MVAPICH2-1.9-iccifort-2011.13.367.eb diff --git a/easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/__archive__/m/MVAPICH2/MVAPICH2-1.9rc1-ClangGCC-1.1.3.eb similarity index 100% rename from easybuild/easyconfigs/m/MVAPICH2/MVAPICH2-1.9rc1-ClangGCC-1.1.3.eb rename to easybuild/easyconfigs/__archive__/m/MVAPICH2/MVAPICH2-1.9rc1-ClangGCC-1.1.3.eb diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/m/MariaDB/MariaDB-5.5.29-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/Meep/Meep-1.2-goalf-1.1.0-no-OFED.eb similarity index 97% rename from easybuild/easyconfigs/m/Meep/Meep-1.2-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/m/Meep/Meep-1.2-goalf-1.1.0-no-OFED.eb index c4caf8f33fe1cf971350c51d85d648f408c4f533..ec2b6857ef234534c1d38c4fdc1ae7042e796e4d 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/__archive__/m/Meep/Meep-1.2-goalf-1.1.0-no-OFED.eb @@ -21,6 +21,7 @@ dependencies = [ ('HDF5', '1.8.7'), ('libctl', '3.2.1'), ('GSL', '1.15'), + ('Guile', '1.8.8'), ] configopts = '--with-pic --with-mpi --without-gcc-arch --with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared ' diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/Meep/Meep-1.2-ictce-4.0.6.eb similarity index 95% rename from easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/m/Meep/Meep-1.2-ictce-4.0.6.eb index 15da01ed14e117a304d5c65055e367cc896ce186..87b8d836d89d9db9e9e0df578d1d6911c0c86a6d 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/__archive__/m/Meep/Meep-1.2-ictce-4.0.6.eb @@ -23,7 +23,8 @@ dependencies = [ ('HDF5', '1.8.7'), ('libctl', '3.2.1'), ('GSL', '1.15'), - ('FFTW', '3.3.1') + ('FFTW', '3.3.1'), + ('Guile', '1.8.8'), ] configopts = "--with-pic --with-mpi --with-blas=mkl_em64t --with-lapack=mkl_em64t --without-gcc-arch " diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-2.3.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-2.3.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-2.3.2-ictce-4.0.6-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/Mercurial/Mercurial-2.3.2-ictce-4.0.6-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-2.3.2-ictce-4.0.6-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-cgmpolf-1.1.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-2.5.2-cgmpolf-1.1.6-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-cgmpolf-1.1.6-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-2.5.2-cgmpolf-1.1.6-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-cgmvolf-1.1.12rc1-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-2.5.2-cgmvolf-1.1.12rc1-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/Mercurial/Mercurial-2.5.2-cgmvolf-1.1.12rc1-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/Mercurial/Mercurial-2.5.2-cgmvolf-1.1.12rc1-Python-2.7.3.eb diff --git 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 b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-1.2.0-ictce-4.1.13-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.0-ictce-4.1.13-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-1.2.0-ictce-4.1.13-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-1.2.1-ictce-4.1.13-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-ictce-4.1.13-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-1.2.1-ictce-4.1.13-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.0-ictce-4.1.13-Python-2.7.5.eb b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-1.3.0-ictce-4.1.13-Python-2.7.5.eb similarity index 100% rename from easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.0-ictce-4.1.13-Python-2.7.5.eb rename to easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-1.3.0-ictce-4.1.13-Python-2.7.5.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb b/easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb similarity index 100% rename from easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb rename to easybuild/easyconfigs/__archive__/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb diff --git a/easybuild/easyconfigs/m/mc/mc-4.6.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/mc/mc-4.6.1-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/m/mc/mc-4.6.1-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/m/mc/mc-4.6.1-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/m/mc/mc-4.6.1-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/mc/mc-4.6.1-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/m/mc/mc-4.6.1-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/m/mc/mc-4.6.1-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/molmod/molmod-1.0-ictce-4.1.13-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/molmod/molmod-1.0-ictce-4.1.13-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/molmod/molmod-1.0-ictce-4.1.13-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/motif/motif-2.2.4-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/m/motif/motif-2.2.4-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/m/motif/motif-2.2.4-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/m/motif/motif-2.2.4-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.4-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/m/motif/motif-2.3.4-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/m/motif/motif-2.3.4-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/m/motif/motif-2.3.4-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/mpi4py/mpi4py-1.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/mpi4py/mpi4py-1.3-ictce-4.0.6-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/m/mpi4py/mpi4py-1.3-ictce-4.1.13-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/m/mpiBLAST/mpiBLAST-1.6.0-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/m/mpiBLAST/mpiBLAST-1.6.0-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/m/mpiBLAST/mpiBLAST-1.6.0-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/m/mpiBLAST/mpiBLAST-1.6.0-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/m/mpiBLAST/mpiBLAST-1.6.0-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-gmvapich2-1.7.12-ibverbs.eb b/easybuild/easyconfigs/__archive__/n/NAMD/NAMD-2.9-gmvapich2-1.7.12-ibverbs.eb similarity index 76% rename from easybuild/easyconfigs/n/NAMD/NAMD-2.9-gmvapich2-1.7.12-ibverbs.eb rename to easybuild/easyconfigs/__archive__/n/NAMD/NAMD-2.9-gmvapich2-1.7.12-ibverbs.eb index e2998dd325353f8675de7b7e3667edba33f95651..35ee2734405941aae8d1828f1d1b418d41cea730 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-gmvapich2-1.7.12-ibverbs.eb +++ b/easybuild/easyconfigs/__archive__/n/NAMD/NAMD-2.9-gmvapich2-1.7.12-ibverbs.eb @@ -3,7 +3,8 @@ version = '2.9' versionsuffix = '-ibverbs' homepage = 'http://www.ks.uiuc.edu/Research/namd/' -description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" toolchain = {'name': 'gmvapich2', 'version': '1.7.12'} toolchainopts = {'opt': True, 'pic': True} @@ -15,6 +16,9 @@ dependencies = [ ('FFTW', '3.3.4'), ] +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + charm_arch = "net-linux-x86_64 ibverbs" moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-gmvolf-1.7.12-ibverbs.eb b/easybuild/easyconfigs/__archive__/n/NAMD/NAMD-2.9-gmvolf-1.7.12-ibverbs.eb similarity index 74% rename from easybuild/easyconfigs/n/NAMD/NAMD-2.9-gmvolf-1.7.12-ibverbs.eb rename to easybuild/easyconfigs/__archive__/n/NAMD/NAMD-2.9-gmvolf-1.7.12-ibverbs.eb index 9434c5a6023b01ecb826a89bd3f817391b67ba43..c1bef554889f38c8ab94dd51bfbf61a01ab5b05e 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-gmvolf-1.7.12-ibverbs.eb +++ b/easybuild/easyconfigs/__archive__/n/NAMD/NAMD-2.9-gmvolf-1.7.12-ibverbs.eb @@ -3,7 +3,8 @@ version = '2.9' versionsuffix = '-ibverbs' homepage = 'http://www.ks.uiuc.edu/Research/namd/' -description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" toolchain = {'name': 'gmvolf', 'version': '1.7.12'} toolchainopts = {'opt': True, 'pic': True} @@ -14,6 +15,9 @@ dependencies = [ ('Tcl', '8.5.12'), ] +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + charm_arch = "net-linux-x86_64 ibverbs" moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.07-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.07-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/n/NASM/NASM-2.07-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/n/NASM/NASM-2.07-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.07-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.07-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/n/NASM/NASM-2.07-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/n/NASM/NASM-2.07-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.07-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.07-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/n/NASM/NASM-2.07-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/n/NASM/NASM-2.07-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-ictce-6.3.5.eb b/easybuild/easyconfigs/__archive__/n/NASM/NASM-2.11.05-ictce-6.3.5.eb similarity index 100% rename from easybuild/easyconfigs/n/NASM/NASM-2.11.05-ictce-6.3.5.eb rename to easybuild/easyconfigs/__archive__/n/NASM/NASM-2.11.05-ictce-6.3.5.eb diff --git a/easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/n/NCBI-Toolkit/NCBI-Toolkit-9.0.0-goalf-1.1.0-no-OFED.eb rename to 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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 100% rename from easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb rename to easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-4.0.2-gmpolf-1.4.8.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-4.0.2-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-4.0.2-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-4.0.2-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.2-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/p/ParMETIS/ParMETIS-4.0.2-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/p/ParMGridGen/ParMGridGen-1.0-ictce-4.1.13.eb 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 easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-4.1.13-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/p/pandas/pandas-0.11.0-ictce-4.1.13-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/p/parallel/parallel-20130122-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb b/easybuild/easyconfigs/__archive__/p/parallel/parallel-20130122-ictce-4.0.6.eb similarity index 100% rename from easybuild/easyconfigs/p/parallel/parallel-20130122-ictce-4.0.6.eb rename to easybuild/easyconfigs/__archive__/p/parallel/parallel-20130122-ictce-4.0.6.eb diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/p/petsc4py/petsc4py-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/p/petsc4py/petsc4py-3.3-goalf-1.1.0-no-OFED-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/__archive__/p/petsc4py/petsc4py-3.3-ictce-4.0.6-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/p/petsc4py/petsc4py-3.3-ictce-4.0.6-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/p/petsc4py/petsc4py-3.3-ictce-4.0.6-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.28.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/pixman/pixman-0.28.2-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/p/pixman/pixman-0.28.2-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/p/pixman/pixman-0.28.2-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.28.2-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/__archive__/p/pixman/pixman-0.28.2-ictce-3.2.2.u3.eb similarity index 100% rename from easybuild/easyconfigs/p/pixman/pixman-0.28.2-ictce-3.2.2.u3.eb rename to easybuild/easyconfigs/__archive__/p/pixman/pixman-0.28.2-ictce-3.2.2.u3.eb diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.28.2-ictce-4.1.13.eb b/easybuild/easyconfigs/__archive__/p/pixman/pixman-0.28.2-ictce-4.1.13.eb similarity index 100% rename from easybuild/easyconfigs/p/pixman/pixman-0.28.2-ictce-4.1.13.eb rename to easybuild/easyconfigs/__archive__/p/pixman/pixman-0.28.2-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/p/pkg-config/pkg-config-0.27.1-goalf-1.1.0-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/p/pkg-config/pkg-config-0.27.1-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-ictce-4.0.6.eb 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b/easybuild/easyconfigs/__archive__/t/TAMkin/TAMkin-1.0.0-ictce-4.1.13-Python-2.7.3.eb similarity index 100% rename from easybuild/easyconfigs/t/TAMkin/TAMkin-1.0.0-ictce-4.1.13-Python-2.7.3.eb rename to easybuild/easyconfigs/__archive__/t/TAMkin/TAMkin-1.0.0-ictce-4.1.13-Python-2.7.3.eb diff --git a/easybuild/easyconfigs/__archive__/t/TAU/TAU-2.22.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/t/TAU/TAU-2.22.2-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000000000000000000000000000000000..b8a2739b01a61c6668f79f30c4d2eab884b07c0b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/t/TAU/TAU-2.22.2-gompi-1.4.12-no-OFED.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': 'gompi', 'version': '1.4.12-no-OFED'} +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/Tar/Tar-1.26-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/t/Tar/Tar-1.26-goalf-1.1.0-no-OFED.eb similarity index 100% rename from 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a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.1.12rc1.eb similarity index 100% rename from easybuild/easyconfigs/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.1.12rc1.eb rename to easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.1.12rc1.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.2.7.eb similarity index 100% rename from easybuild/easyconfigs/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.2.7.eb rename to easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgmvolf-1.2.7.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.8.1-cgoolf-1.1.7.eb b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-cgoolf-1.1.7.eb similarity index 100% rename from easybuild/easyconfigs/v/Valgrind/Valgrind-3.8.1-cgoolf-1.1.7.eb rename to 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easybuild/easyconfigs/v/Valgrind/Valgrind-3.8.1-goalf-1.1.0-no-OFED.eb rename to easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.8.1-goalf-1.1.0-no-OFED.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.9.0-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.9.0-goalf-1.5.12-no-OFED.eb similarity index 100% rename from easybuild/easyconfigs/v/Valgrind/Valgrind-3.9.0-goalf-1.5.12-no-OFED.eb rename to easybuild/easyconfigs/__archive__/v/Valgrind/Valgrind-3.9.0-goalf-1.5.12-no-OFED.eb diff --git a/easybuild/easyconfigs/__archive__/v/VampirTrace/VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/__archive__/v/VampirTrace/VampirTrace-5.14.4-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000000000000000000000000000000000..02bc1f21cc036e2509ecf2f602c48678ebe2955b --- /dev/null +++ b/easybuild/easyconfigs/__archive__/v/VampirTrace/VampirTrace-5.14.4-gompi-1.4.12-no-OFED.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': 'gompi', 'version': '1.4.12-no-OFED'} +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/Velvet/Velvet-1.2.07-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/__archive__/v/Velvet/Velvet-1.2.07-goalf-1.1.0-no-OFED.eb similarity index 100% rename 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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 --git a/easybuild/easyconfigs/w/WRF/WRF-3.4-goalf-1.1.0-no-OFED-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WRF/WRF-3.4-goalf-1.1.0-no-OFED-dmpar.eb similarity index 100% rename from easybuild/easyconfigs/w/WRF/WRF-3.4-goalf-1.1.0-no-OFED-dmpar.eb rename to easybuild/easyconfigs/__archive__/w/WRF/WRF-3.4-goalf-1.1.0-no-OFED-dmpar.eb diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.4-ictce-3.2.2.u3-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WRF/WRF-3.4-ictce-3.2.2.u3-dmpar.eb similarity index 100% rename from easybuild/easyconfigs/w/WRF/WRF-3.4-ictce-3.2.2.u3-dmpar.eb rename to easybuild/easyconfigs/__archive__/w/WRF/WRF-3.4-ictce-3.2.2.u3-dmpar.eb diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.4.1-iqacml-3.7.3-dmpar.eb b/easybuild/easyconfigs/__archive__/w/WRF/WRF-3.4.1-iqacml-3.7.3-dmpar.eb similarity index 100% rename from easybuild/easyconfigs/w/WRF/WRF-3.4.1-iqacml-3.7.3-dmpar.eb rename to easybuild/easyconfigs/__archive__/w/WRF/WRF-3.4.1-iqacml-3.7.3-dmpar.eb diff --git 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 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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-7.6.2-foss-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..bfa5f0befa0694ec82a86b15cc06a3bb88fd165b --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2-foss-2015a.eb @@ -0,0 +1,36 @@ +easyblock = "ConfigureMake" + +name = 'ABINIT' +version = '7.6.2' + +homepage = 'http://www.abinit.org/' +description = """Abinit is a plane wave pseudopotential code for doing condensed phase electronic + structure calculations using DFT.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'ABINIT-%(version)s_named-constant.patch', + 'ABINIT-%(version)s_odamix.patch', +] + +dependencies = [ + ('netCDF', '4.3.2'), + ('netCDF-Fortran', '4.4.0'), +] + +configopts = '--enable-mpi --with-mpi-prefix="$EBROOTOPENMPI" --enable-fallbacks ' +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include -I$EBROOTNETCDFMINFORTRAN/include" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib64 -lnetcdf -L$EBROOTNETCDFMINFORTRAN/lib -lnetcdff" ' +configopts += '--with-fft-libs="-L$EBROOTFFTW/lib -lfftw3 -lfftw3f" --with-fft-flavor=fftw3 ' +configopts += '--with-trio-flavor=netcdf+etsf_io --with-dft-flavor=libxc --enable-gw-dpc' + +sanity_check_paths = { + 'files': ["bin/abinit"], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_named-constant.patch b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_named-constant.patch new file mode 100644 index 0000000000000000000000000000000000000000..bb56a05a0a36ff63d5de64fe16f01a71b41bf03f --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_named-constant.patch @@ -0,0 +1,18 @@ +# This patch fixes a 'cannot assign to a named constant' error that occurs during the build. +# Suggested fix from: https://lists.debian.org/debian-mentors/2014/08/msg00475.html +--- src/62_ctqmc/defs.h.orig 2014-02-15 21:30:20.000000000 +0000 ++++ src/62_ctqmc/defs.h 2016-08-22 13:05:09.473620286 +0100 +@@ -5,11 +5,11 @@ + + #define MALLOC(ARR,SIZE) ABI_ALLOCATE(ARR,SIZE) + #define FREE(ARR) ABI_DEALLOCATE(ARR) +-#define FREEIF(ARR) IF(ALLOCATED(ARR)) THEN NEWLINE ABI_DEALLOCATE(ARR) NEWLINE END IF ++#define FREEIF(ARR) IF(ALLOCATED(ARR)) ABI_DEALLOCATE(ARR) + + #define DT_MALLOC(ARR,SIZE) ABI_DATATYPE_ALLOCATE(ARR,SIZE) + #define DT_FREE(ARR) ABI_DATATYPE_DEALLOCATE(ARR) +-#define DT_FREEIF(ARR) IF(ALLOCATED(ARR)) THEN NEWLINE ABI_DATATYPE_DEALLOCATE(ARR) NEWLINE END IF ++#define DT_FREEIF(ARR) IF(ALLOCATED(ARR)) ABI_DATATYPE_DEALLOCATE(ARR) + + #define myWARNALL(msg) MSG_WARNING(msg) + #define myWARN(msg) call msg_hndl(msg,"WARNING","PERS") diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_odamix.patch b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_odamix.patch new file mode 100644 index 0000000000000000000000000000000000000000..2ea83d3829846a8e8eee520df802d29fac158c27 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.6.2_odamix.patch @@ -0,0 +1,12 @@ +# This fixes a build time error that is acknowledged here: http://forum.abinit.org/viewtopic.php?f=3&t=2656 +--- src/67_common/odamix.F90.orig 2016-08-22 13:27:30.289621140 +0100 ++++ src/67_common/odamix.F90 2016-08-22 13:27:40.063570238 +0100 +@@ -544,7 +544,7 @@ + do ispden=1,pawrhoij(iatom)%nspden + do irhoij=1,pawrhoij(iatom)%nrhoijsel + klmn=2*pawrhoij(iatom)%rhoijselect(irhoij)-1 +- rhoijtmp(klmn-1:klmn+1,ispden)=pawrhoij(iatom)%rhoijp(jrhoij:jrhoij+1,ispden) ++ rhoijtmp(klmn:klmn+1,ispden)=pawrhoij(iatom)%rhoijp(jrhoij:jrhoij+1,ispden) + jrhoij=jrhoij+2 + end do + end do diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-8.0.8-intel-2016a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-8.0.8-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..21aa0bf4482503e24be28f42a76aefc27297cfe6 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-8.0.8-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '8.0.8' + +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': '2016a'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7b67d9ffc6200b3bcca0db12f7c69581'] + +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$EBROOTLIBXC/lib -lxc" ' + +dependencies = [ + ('libxc', '3.0.0'), + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.4'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-8.0.8b-intel-2016b.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-8.0.8b-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..5e7c671066207276a325b5b416e43ed21abea489 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-8.0.8b-intel-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '8.0.8b' + +homepage = 'http://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, charge density and + electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional + Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['abc9e303bfa7f9f43f95598f87d84d5d'] + +configopts = "--with-mpi-prefix=$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/ADMIXTURE/ADMIXTURE-1.3.0.eb b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..1c6dbcdc1b30668bf13194dc531395f87f934a86 --- /dev/null +++ b/easybuild/easyconfigs/a/ADMIXTURE/ADMIXTURE-1.3.0.eb @@ -0,0 +1,21 @@ +easyblock = 'PackedBinary' + +name = 'ADMIXTURE' +version = '1.3.0' + +homepage = 'https://www.genetics.ucla.edu/software/admixture' +description = """ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from +multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much +more rapidly using a fast numerical optimization algorithm.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://www.genetics.ucla.edu/software/%(namelower)s/binaries/'] +sources = ['%(namelower)s_linux-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['admixture', 'admixture32'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ALADIN/ALADIN-36t1_op2bf1-intel-2016a.eb b/easybuild/easyconfigs/a/ALADIN/ALADIN-36t1_op2bf1-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e2a9d8684d86e9e1957c3b87b3266fae0242fa6e --- /dev/null +++ b/easybuild/easyconfigs/a/ALADIN/ALADIN-36t1_op2bf1-intel-2016a.eb @@ -0,0 +1,36 @@ +name = 'ALADIN' +version = '36t1_op2bf1' + +homepage = 'http://www.cnrm.meteo.fr/aladin/' +description = """ALADIN was entirely built on the notion of compatibility with its mother system, IFS/ARPEG. + The latter, a joint development between the European Centre for Medium-Range Weather Forecasts (ECMWF) and + Meteo-France, was only meant to consider global Numerical Weather Prediction applications; hence the idea, + for ALADIN, to complement the IFS/ARPEGE project with a limited area model (LAM) version, while keeping the + differences between the two softwares as small as possible.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True, 'strict': True} + +sources = [ + 'cy%(version)s.tgz', + 'gmkpack.6.5.0.tgz', + 'auxlibs_installer.2.0.tgz', +] + +patches = [ + 'ALADIN_ictce-clim_import-export.patch', + 'gmkpack_multi-lib.patch', +] + +dependencies = [ + ('JasPer', '1.900.1'), + ('grib_api', '1.16.0'), + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.4'), +] +builddependencies = [('Bison', '3.0.4')] + +# too parallel makes the build very slow +maxparallel = 3 + +moduleclass = 'geo' 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/ASE/ASE-3.11.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/a/ASE/ASE-3.11.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..7834a9fb0eeb4e86bd55c905a266466db3e4eb0c --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.11.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'ASE' +version = '3.11.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb b/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb new file mode 100644 index 0000000000000000000000000000000000000000..1e7fda13a16fd9fbb8e218c3ea48b5c3b2a98cc2 --- /dev/null +++ b/easybuild/easyconfigs/a/ASHS/ASHS-rev103_20140612.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'ASHS' +version = 'rev103_20140612' + +homepage = 'https://sites.google.com/site/hipposubfields/home' +description = """ Automatic Segmentation of Hippocampal Subfields (ASHS) """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +#You need to create an account to download the source +#from https://www.nitrc.org/frs/?group_id=370 +sources = ['ashs_Linux64_%(version)s.tgz'] + +checksums= ["07fea2883b856af8797b200212b72e71"] + +modextravars = {'ASHS_ROOT': '%(installdir)s'} + +sanity_check_paths = { + 'files': ["bin/ashs_main.sh", "bin/ashs_template_qsub.sh", "bin/ashs_train.sh", + "bin/ashs_util_makepdf.sh"], + 'dirs': ["ext"] +} + +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..22d5bebaad96415f872801708a48f949f4213876 --- /dev/null +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2017_update1.eb @@ -0,0 +1,23 @@ +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'] + +checksums = ['af87b381394be3100507827a3461b3bc'] + +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/Allinea/Allinea-4.1-32834-Redhat-5.7-x86_64.eb b/easybuild/easyconfigs/a/Allinea/Allinea-4.1-32834-Redhat-5.7-x86_64.eb index d4565683b662783826ab1a20d35b9848fe153624..e3a2bc98c49e053ce7bf05beeae56db6826142d2 100644 --- a/easybuild/easyconfigs/a/Allinea/Allinea-4.1-32834-Redhat-5.7-x86_64.eb +++ b/easybuild/easyconfigs/a/Allinea/Allinea-4.1-32834-Redhat-5.7-x86_64.eb @@ -11,7 +11,6 @@ source_urls = ['http://content.allinea.com/downloads/'] sources = ['%(namelower)s-tools-%(version)s.tar'] # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "allinea", "license.lic") +license_file = HOME + '/licenses/allinea/license.lic' moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/Allinea/Allinea-4.1-32834-Redhat-6.0-x86_64.eb b/easybuild/easyconfigs/a/Allinea/Allinea-4.1-32834-Redhat-6.0-x86_64.eb index 90466a264315cfa91c3a0a76bededc39f8e0370d..9b1ddba636864e5595f494558bf95bc1f38c148c 100644 --- a/easybuild/easyconfigs/a/Allinea/Allinea-4.1-32834-Redhat-6.0-x86_64.eb +++ b/easybuild/easyconfigs/a/Allinea/Allinea-4.1-32834-Redhat-6.0-x86_64.eb @@ -11,7 +11,6 @@ source_urls = ['http://content.allinea.com/downloads/'] sources = ['%(namelower)s-tools-%(version)s.tar'] # license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "allinea", "license.lic") +license_file = HOME + '/licenses/allinea/license.lic' moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/Allinea/Allinea-6.1.1-Ubuntu-14.04-x86_64.eb b/easybuild/easyconfigs/a/Allinea/Allinea-6.1.1-Ubuntu-14.04-x86_64.eb new file mode 100644 index 0000000000000000000000000000000000000000..9a71b607bea2787595926570ae7ddc408b9a3dd3 --- /dev/null +++ b/easybuild/easyconfigs/a/Allinea/Allinea-6.1.1-Ubuntu-14.04-x86_64.eb @@ -0,0 +1,25 @@ +name = 'Allinea' +version = '6.1.1-Ubuntu-14.04-x86_64' + +homepage = 'http://www.allinea.com' +description = """The Allinea environment is an essential toolkit for developers and computational scientists +looking to get results faster.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://content.allinea.com/downloads/'] +sources = ['%(namelower)s-forge-%(version)s.tar'] + +# Example of templates usage +#templates = [ +# 'kebnekaise.qtf', +# 'kebnekaise-gpu.qtf', +#] + +# Example of sysconfig usage +#sysconfig = 'system.config.hpc2n' + +# license file +license_file = HOME + '/licenses/allinea/license.lic' + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb b/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb new file mode 100644 index 0000000000000000000000000000000000000000..9eab720e748108f354c9cb5b97af2eeefe336b03 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-14-intel-2016a-AmberTools-15-patchlevel-13-13.eb @@ -0,0 +1,41 @@ +# +# modified by Stephane Thiell (Stanford University) for Amber v14 +# +# author: Benjamin P. Roberts (University of Auckland) +# +# based on work by Marios Constantinou (University of Cyprus) +# +name = 'Amber' +version = '14' + +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': 'intel', 'version': '2016a'} +toolchainopts = {'openmp': False, 'usempi': True} + +ambertools_ver = '15' +sources = [ + 'Amber%(version)s.tar.bz2', + 'AmberTools%s.tar.bz2' % ambertools_ver, +] +patches = [ + 'Amber-%(version)s_fix-hardcoding.patch', + 'AmberTools-%s_fix-mdgx-print-bug.patch' % ambertools_ver, +] + +dependencies = [ + ('CUDA', '7.5.18', '', True), + ('netCDF', '4.4.0'), + ('netCDF-Fortran', '4.4.4'), + ('Python', '2.7.11'), +] + +patchlevels = (13, 13) +patchruns = 1 + +versionsuffix = '-AmberTools-%s-patchlevel-%d-%d' % (ambertools_ver, patchlevels[0], patchlevels[1]) + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-14_fix-hardcoding.patch b/easybuild/easyconfigs/a/Amber/Amber-14_fix-hardcoding.patch new file mode 100644 index 0000000000000000000000000000000000000000..6f4b9b5047fb4597c09086597c706e1e0233af74 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-14_fix-hardcoding.patch @@ -0,0 +1,173 @@ +fix hardcoding of compilers & MKL lib dir, add support for separate netCDF-Fortran installation & recent CUDA +author: Stephane Thiell (Stanford University) +--- amber14/AmberTools/src/cpptraj/configure.orig 2015-11-25 21:25:27.219014394 -0800 ++++ amber14/AmberTools/src/cpptraj/configure 2015-11-25 21:26:36.935069823 -0800 +@@ -676,9 +676,9 @@ fi + if [[ $USEMPI -eq 1 ]] ; then + echo "Using MPI" + DIRECTIVES="$DIRECTIVES -DMPI" +- CC=mpicc +- CXX=mpicxx +- FC=mpif90 ++ CC=${CC} ++ CXX=${CXX} ++ FC=${F90} + SFX=".MPI" + fi + +--- amber14/AmberTools/src/configure2.orig 2015-11-25 21:18:37.473056279 -0800 ++++ amber14/AmberTools/src/configure2 2015-11-27 00:05:54.009556748 -0800 +@@ -385,6 +385,7 @@ mpinab='' + mpi='no' + mtkpp='install_mtkpp' + netcdf_dir='' ++netcdf_fort_dir='' + netcdf_flag='' + netcdfstatic='no' + noX11='false' +@@ -442,6 +443,7 @@ while [ $# -gt 0 ]; do + -lio) lio='yes' ;; + --with-python) shift; python="$1";; + --with-netcdf) shift; netcdf_dir="$1";; ++ --with-netcdf-fort) shift; netcdf_fort_dir="$1";; + -netcdfstatic) netcdfstatic='yes' ;; + -dragonegg) shift; dragonegg="$1";; + -g95) g95='yes' ;; +@@ -594,7 +596,7 @@ flibs="-larpack -llapack -lblas " + # Fortran versions, if compiled from source: + flibsf="-larpack -llapack -lblas" + # only used when the user requests a static build: +-staticflag='-static' ++staticflag='-static-intel' + omp_flag= + mpi_flag= + lex=flex +@@ -861,13 +863,13 @@ if [ "$cuda_SPFP" = 'yes' -o "$cuda_SPXP + echo "CUDA Version $cudaversion detected" + echo "Configuring for SM2.0 and SM3.0 - warning does not support Maxwell (GM200/GM204) cards [e.g. GTX970/980]" + nvccflags="$sm20flags $sm30flags" +- elif [ "$cudaversion" = "6.5" ]; then ++ elif [ "$cudaversion" = "6.5" -o "$cudaversion" = "7.0" -o "$cudaversion" = "7.5" ]; then + echo "CUDA Version $cudaversion detected" + echo "Configuring for SM2.0, SM3.0 and SM5.0" + nvccflags="$sm20flags $sm30flags $sm50flags" + else + echo "Error: Unsupported CUDA version $cudaversion detected." +- echo " AMBER requires CUDA version == 5.0 .or. 5.5 .or. 6.0 .or. 6.5" ++ echo " AMBER requires CUDA version == 5.0 .or. 5.5 .or. 6.0 .or. 6.5 .or. 7.0 .or. 7.5" + exit 1 + fi + nvcc="$nvcc $nvccflags" +@@ -1058,7 +1060,7 @@ gnu) + fi + if [ "$mpi" = 'yes' -a "$intelmpi" = 'no' ]; then + if [ "$intelmpi" = 'no' ]; 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 ", $i);}; i++;}}'` + fi + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" +@@ -1354,7 +1356,7 @@ intel) + 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="$pmemd_coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -1630,7 +1632,7 @@ EOF + nvcc="$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="$coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -1880,7 +1882,7 @@ clang) + nvcc="$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="$coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -1947,17 +1949,17 @@ if [ -n "$MKL_HOME" ]; then + 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="$MKL_HOME/mkl/lib/intel64" + mkl_processor="intel64" + mkl_procstring="intel64" + fi +@@ -2374,8 +2376,13 @@ if [ "$bintraj" = 'yes' ]; then + 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" + netcdf_flag="-L${netcdf_dir}/lib $netcdf_flag" +- netcdf=$netcdf_dir"/include/netcdf.mod" ++ netcdf=$netcdf_fort_dir"/include/netcdf.mod" + if [ ! -e "$netcdf" ]; then + echo "Error: '$netcdf' not found." + exit 1 +@@ -2385,7 +2392,7 @@ if [ "$bintraj" = 'yes' ]; then + netcdfflagc="-L${netcdf_dir}/lib -lnetcdf" + # Newer versions of NetCDF have a separate fortran library. + # If not found default to libnetcdf.a +- netcdfflagf=$netcdf_dir"/lib/libnetcdff" ++ netcdfflagf=$netcdf_fort_dir"/lib/libnetcdff" + if [ ! -e "${netcdfflagf}.a" -a ! -e "${netcdfflagf}.so" ]; then + echo "Does not exist!" + netcdfflagf=$netcdfflagc +@@ -2399,7 +2406,7 @@ if [ "$bintraj" = 'yes' ]; then + echo "Error: '$netcdfflagc' not found." + exit 1 + fi +- netcdfflagf=$netcdf_dir"/lib/libnetcdff.a" ++ netcdfflagf=$netcdf_fort_dir"/lib/libnetcdff.a" + if [ ! -e "$netcdfflagf" ]; then + netcdfflagf=$netcdfflagc + fi +@@ -2814,14 +2821,14 @@ if [ "$mpi" = 'yes' ]; then + cplusplus="CC" + mpi_flag="-DMPI " + elif [ "$intelmpi" = 'yes' ]; then +- cc="mpiicc" +- fc="mpiifort" +- cplusplus="mpiicpc" +- mpi_flag="-DMPI " ++ cc=${CC} ++ fc=${F90} ++ cplusplus=${CXX} ++ mpi_flag="-DMPI " + else +- cc="mpicc" +- cplusplus="mpicxx" +- fc="mpif90" ++ cc=${CC} ++ fc=${F90} ++ cplusplus=${CXX} + mpi_flag="-DMPI " + + # Catch a corner-case of unusually setup intel compilers. 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 && $(MAKE) test.cuda.serial) + diff --git a/easybuild/easyconfigs/a/Amber/AmberTools-15_fix-mdgx-print-bug.patch b/easybuild/easyconfigs/a/Amber/AmberTools-15_fix-mdgx-print-bug.patch new file mode 100644 index 0000000000000000000000000000000000000000..20f849b0561528690fff33a38083aae0f97511b8 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/AmberTools-15_fix-mdgx-print-bug.patch @@ -0,0 +1,16 @@ +fix for hanging mdgx test (Test.1p7e) on long installation paths, backported from AmberTools 16 +author: David Cerutti +--- amber14/AmberTools/src/mdgx/Manual.c.orig 2016-06-10 11:39:47.719576723 +0200 ++++ amber14/AmberTools/src/mdgx/Manual.c 2016-06-10 11:41:16.670677715 +0200 +@@ -142,9 +142,10 @@ + endfound = 0; + j = 0; + while (endfound == 0) { ++ vpivot = j + width; + for (i = 0; i < width; i++) { + if (vpar[j+i] == ' ') { +- i++; ++ i++; + vpivot = j+i; + } + if (vpar[j+i] == '\0') { diff --git a/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..c0ff978ea57c40c5c71d57c01576ba6ad878bd60 --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda2/Anaconda2-4.0.0.eb @@ -0,0 +1,23 @@ +# author: Jillian Rowe +easyblock = 'EB_Anaconda' + +name = 'Anaconda2' +version = '4.0.0' + +homepage = 'https://www.continuum.io/anaconda-overview' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://repo.continuum.io/archive/'] +sources = ['%(name)s-%(version)s-Linux-x86_64.sh'] +checksums = ['31ed3ef07435d7068e1e03be49381b13'] + +# a newer version of conda is required to run 'conda env create -p' +prep_env = "PATH=%(installdir)s/bin:$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/AutoDock/AutoDock-4.2.5.1-GCC-5.2.0.eb b/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.5.1-GCC-5.2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..58598fa8b43a70459a7f6180375ff8e73cb37cf3 --- /dev/null +++ b/easybuild/easyconfigs/a/AutoDock/AutoDock-4.2.5.1-GCC-5.2.0.eb @@ -0,0 +1,24 @@ +# Currently there is not an EasyBlock to unify AutoDock and AutoGrid so this is a happy medium until then +easyblock = 'ConfigureMake' + +name = 'AutoDock' +version = '4.2.5.1' + +homepage = 'http://autodock.scripps.edu/' +description = """AutoDock is a suite of automated docking tools. It is designed to + predict how small molecules, such as substrates or drug candidates, bind to + a receptor of known 3D structure.""" + +toolchain = {'name': 'GCC', 'version': '5.2.0'} + +sources = ['%(namelower)ssuite-%(version)s-src.tar.gz'] +source_urls = ['http://autodock.scripps.edu/downloads/previous-releases/autodock-4-2-5/tars/dist4251/'] + +start_dir = 'autodock' + +sanity_check_paths = { + 'files': ["bin/autodock4"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.5.1-GCC-5.2.0.eb b/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.5.1-GCC-5.2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..1cb41f8b792ef3f454ac176a79e2410cc86a78fc --- /dev/null +++ b/easybuild/easyconfigs/a/AutoGrid/AutoGrid-4.2.5.1-GCC-5.2.0.eb @@ -0,0 +1,24 @@ +# Currently there is not an EasyBlock to unify AutoDock and AutoGrid so this is a happy medium until then +easyblock = 'ConfigureMake' + +name = 'AutoGrid' +version = '4.2.5.1' + +homepage = 'http://autodock.scripps.edu/' +description = """AutoDock is a suite of automated docking tools. It is designed to + predict how small molecules, such as substrates or drug candidates, bind to + a receptor of known 3D structure.""" + +toolchain = {'name': 'GCC', 'version': '5.2.0'} + +sources = ['autodocksuite-%(version)s-src.tar.gz'] +source_urls = ['http://autodock.scripps.edu/downloads/previous-releases/autodock-4-2-5/tars/dist4251/'] + +start_dir = 'autogrid' + +sanity_check_paths = { + 'files': ["bin/autogrid4"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..a3fab7ed38073daa3a67356347092512d9a6de60 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCC-5.4.0-2.26.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': 'GCC', 'version': '5.4.0-2.26'} + +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-GCCcore-4.9.3.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..8b7fb4793d96caaf7a7046721a1b785123c234a7 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-4.9.3.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'http://www.gnu.org/software/autoconf/' +description = """Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can adapt the + packages to many kinds of UNIX-like systems without manual user intervention. Autoconf + creates a configuration script for a package from a template file that lists the + operating system features that the package can use, in the form of M4 macro calls.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.25') +] + +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-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-foss-2016b.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..4ddc61da6964ccbc17ab6a300e5962ee63cecb64 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-foss-2016b.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': '2016b'} + +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-intel-2016b.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..439e6e5e5153abfdbea6fb13e5c3fd9fe1309e29 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-intel-2016b.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': 'intel', 'version': '2016b'} + +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-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..e42ff285562e7c1784ff562473516c8f22c98a9f --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCC-5.4.0-2.26.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': 'GCC', 'version': '5.4.0-2.26'} + +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-GCCcore-4.9.3.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..5927ea856a1017088765c98659a0821800d75a1f --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GCCcore-4.9.3.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15" + +homepage = 'http://www.gnu.org/software/automake/automake.html' +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('binutils', '2.25')] +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-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-foss-2016b.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..5c1e645dea90fd635698e8c30184a1fea25d9b64 --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-foss-2016b.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': '2016b'} + +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-intel-2016b.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..2a6c1808780ceb2e145b34933aa86b398e4fef8f --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-intel-2016b.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': 'intel', 'version': '2016b'} + +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-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..1452a8b0add5fe55c46e756e5922ba722696f0c9 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCC-5.4.0-2.26.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': 'GCC', 'version': '5.4.0-2.26'} + +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-GCCcore-4.9.3.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..14abf09d3b2d974f740bd7df3170c27c908b978a --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GCCcore-4.9.3.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': 'GCCcore', 'version': '4.9.3'} + +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-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-foss-2016b.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..c3a3670b4e18f3ca123aa124cf79a07aa69215da --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-foss-2016b.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': '2016b'} + +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-intel-2016b.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..625e2b28004dda335dad5bee9e7fd8700d802f35 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-intel-2016b.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': '2016b'} + +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/ant/ant-1.9.6-Java-1.8.0_72.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb new file mode 100644 index 0000000000000000000000000000000000000000..407fa7e1c06d7edf8e51d6edb1b96f91ca75fe71 --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_72.eb @@ -0,0 +1,25 @@ +name = 'ant' +version = '1.9.6' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files + as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['apache-%(name)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] + +dependencies = [('Java', '1.8.0_72')] + +builddependencies = [('JUnit', '4.12', versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'], + 'dirs': [], +} + +modextravars = {'ANT_HOME': '%(installdir)s'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb new file mode 100644 index 0000000000000000000000000000000000000000..08bcaf86cf6b0470f2a4cd82464073fd0ca4b974 --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.8.0_77.eb @@ -0,0 +1,25 @@ +name = 'ant' +version = '1.9.6' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files + as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['apache-%(name)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] + +dependencies = [('Java', '1.8.0_77')] + +builddependencies = [('JUnit', '4.12', versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'], + 'dirs': [], +} + +modextravars = {'ANT_HOME': '%(installdir)s'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb b/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb new file mode 100644 index 0000000000000000000000000000000000000000..186bcfb543dfa7b7ca1455aa97a55cd4878f7929 --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.9.7-Java-1.8.0_92.eb @@ -0,0 +1,25 @@ +name = 'ant' +version = '1.9.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files + as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['apache-%(name)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] + +dependencies = [('Java', '1.8.0_92')] + +builddependencies = [('JUnit', '4.12', versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'], + 'dirs': [], +} + +modextravars = {'ANT_HOME': '%(installdir)s'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ec3422f1097e46cfb6167c5f2cdd4d5b7026007d --- /dev/null +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-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 +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'argtable' +version = '2.13' + +homepage = 'http://argtable.sourceforge.net/' +description = """ Argtable is an ANSI C library for parsing GNU style + command line options with a minimum of fuss. """ + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%s%s.tar.gz' % (name, version.replace('.', '-'))] + +sanity_check_paths = { + 'files': ['lib/libargtable2.so', 'lib/libargtable2.la'], + 'dirs': ['include', 'lib', 'share'], +} + +moduleclass = 'lib' 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/BCFtools/BCFtools-1.3.1-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-goolf-1.7.20.eb index 056a4ca4d8b15e63885702028f62781a1b04d084..885f9339b0f4bc2c89c9a54df246a9f353760206 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-goolf-1.7.20.eb @@ -18,8 +18,8 @@ source_urls = ['https://github.com/samtools/bcftools/releases/download/%(version sources = [SOURCELOWER_TAR_BZ2] dependencies = [ - ('zlib', '1.2.8'), - ('GSL', '1.16'), + ('zlib', '1.2.8'), + ('GSL', '1.16'), ] buildopts = " USE_GPL=1 GSL_LIBS='-lgsl -lgslcblas'" @@ -27,7 +27,7 @@ buildopts = " USE_GPL=1 GSL_LIBS='-lgsl -lgslcblas'" runtest = 'test' files_to_copy = [(["bcftools", "plot-vcfstats", "vcfutils.pl"], "bin"), - "doc", "plugins", "test", "LICENSE", "README", "AUTHORS"] + "doc", "plugins", "test", "LICENSE", "README", "AUTHORS"] sanity_check_paths = { 'files': ["bin/bcftools"], diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..47aaf73fa3241d5c495936f0d30d078e055ac2a6 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = "BEDOPS" +version = "2.4.1" + +homepage = 'https://github.com/bedops/bedops' +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.""" + +# this application requires GCC-4.8.x or higher +# be aware if you switch to a different toolchain +toolchain = {'name': 'GCC', 'version': '4.8.4'} + +source_urls = ['https://github.com/bedops/bedops/archive/'] +sources = ['v%(version)s.tar.gz'] + +buildopts = ' static && make install' + +parallel = 1 + +files_to_copy = ["bin"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bedmap", "bam2bed" , "sort-bed", + "starchcat", "vcf2bed", "wig2bed", + "gtf2bed", "bedops", "wig2bed"]], + 'dirs': [] +} + +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/BEDTools/BEDTools-2.26.0-foss-2015a.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a90d60385a6571b0ad786627694844d5a5ee5f4c --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-foss-2015a.eb @@ -0,0 +1,33 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.26.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps + and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, + and SAM/BAM.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-foss-2015b.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-foss-2015b.eb new file mode 100644 index 0000000000000000000000000000000000000000..b29f870077112fda5551bdefb9ecc7d68e871328 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-foss-2015b.eb @@ -0,0 +1,33 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.26.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps + and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, + and SAM/BAM.""" + +toolchain = {'name': 'foss', 'version': '2015b'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-foss-2016a.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b3f384512fc314449d02e103306f42813e3c7fff --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-foss-2016a.eb @@ -0,0 +1,33 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.26.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps + and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, + and SAM/BAM.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..02ae17a7fd901ef6c64bbdba38db55fd907ba3d0 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-goolf-1.7.20.eb @@ -0,0 +1,33 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.26.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps + and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, + and SAM/BAM.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-intel-2016b.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..3c9d695141470be3c80509db643dfd8470176778 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.26.0-intel-2016b.eb @@ -0,0 +1,33 @@ +# Author: Maxime Schmitt, University of Luxembourg +# Author: Adam Huffman, The Francis Crick Institute +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.26.0' + +homepage = "https://github.com/arq5x/bedtools2" +description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps + and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, + and SAM/BAM.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.26.0/bedtools-2.26.0.tar.gz +source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/'] +sources = ['bedtools-%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']], + 'dirs': files_to_copy, +} + +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+-2.3.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.3.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..c7b71288fa90b01fdffe5c8f57bb147cfdbd9dcd --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.3.0-foss-2016a-Python-2.7.11.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 , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.3.0' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +dependencies = [('Boost', '1.58.0', versionsuffix)] + +configopts = '--with-boost=$EBROOTBOOST --with-64' + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} + +moduleclass = 'bio' 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-foss-2016a.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..88e524cd9dfc39177028a262b3c02da8cac42f2a --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.15-foss-2016a.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': 'foss', 'version': '2016a'} +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/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/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb b/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..9cd875e7c60fa38c6eb4476b15a970310707c439 --- /dev/null +++ b/easybuild/easyconfigs/b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'BXH_XCEDE_TOOLS' +version = '1.11.1' + +homepage = 'http://www.nitrc.org/projects/bxh_xcede_tools/' +description = """A collection of data processing and image analysis +tools for data in BXH or XCEDE format. This includes data format +encapsulation/conversion, event-related analysis, QA tools, and more. +These tools form the basis of the fBIRN QA procedures and are also +distributed as part of the fBIRN Data Upload Scripts.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.nitrc.org/frs/download.php/7384/'] +sources = ['bxh_xcede_tools-%(version)s-lsb30.x86_64.tgz'] + +sanity_check_paths = { + 'files': ["bin/dicom2bxh", "bin/dicom2xcede"], + 'dirs': [] +} + +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/BamUtil/BamUtil-1.0.13-foss-2015b.eb b/easybuild/easyconfigs/b/BamUtil/BamUtil-1.0.13-foss-2015b.eb index 66b054ccebd90db9a6298310d0657db059fc5486..bbca7a748e4392eb67844612d09fe67a1f29a1e7 100644 --- a/easybuild/easyconfigs/b/BamUtil/BamUtil-1.0.13-foss-2015b.eb +++ b/easybuild/easyconfigs/b/BamUtil/BamUtil-1.0.13-foss-2015b.eb @@ -21,6 +21,9 @@ toolchain = {'name': 'foss', 'version': '2015b'} sources = ['%(name)sLibStatGen.%(version)s.tgz'] source_urls = ['http://genome.sph.umich.edu/w/images/7/70/'] +# make sure right compilers are used by passing them as options to 'make' (default is to use gcc/g++) +buildopts = 'CC="$CC" CXX="$CXX"' + files_to_copy = ["bamUtil/bin", "libStatGen"] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/BamUtil/BamUtil-1.0.13-intel-2016b.eb b/easybuild/easyconfigs/b/BamUtil/BamUtil-1.0.13-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ceadf51bc5831ef2d2e440501616b1bebe05fd78 --- /dev/null +++ b/easybuild/easyconfigs/b/BamUtil/BamUtil-1.0.13-intel-2016b.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute +# +# This is the version with the bundled libStatGen library + +name = 'BamUtil' +version = '1.0.13' + +easyblock = 'MakeCp' + +homepage = 'http://genome.sph.umich.edu/wiki/BamUtil' +description = """BamUtil is a repository that contains several programs + that perform operations on SAM/BAM files. All of these programs + are built into a single executable, bam.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['%(name)sLibStatGen.%(version)s.tgz'] +source_urls = ['http://genome.sph.umich.edu/w/images/7/70/'] + +# make sure right compilers are used by passing them as options to 'make' (default is to use gcc/g++) +# USER_WARNINGS needs to be emptied to avoid use of -Werror which leads to compiler errors with Intel compilers +buildopts = 'CC="$CC" CXX="$CXX" USER_WARNINGS=""' + +files_to_copy = ['bamUtil/bin', 'libStatGen'] + +sanity_check_paths = { + 'files': ['bin/bam'], + 'dirs': ['libStatGen'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BayPass/BayPass-2.1-foss-2015a.eb b/easybuild/easyconfigs/b/BayPass/BayPass-2.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..132df40d050f5826a957291adb2cfdd9fddd418c --- /dev/null +++ b/easybuild/easyconfigs/b/BayPass/BayPass-2.1-foss-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'MakeCp' + +name = 'BayPass' +version = '2.1' + +homepage = 'http://www1.montpellier.inra.fr/CBGP/software/baypass/' +description = """The package 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).""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'openmp': True} + +source_urls = ['http://www1.montpellier.inra.fr/CBGP/software/baypass/files/'] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +start_dir = 'sources' + +files_to_copy = [(['g_baypass'], 'bin'), (['BayPass_manual_2.1.pdf'], 'manual'), 'examples', 'utils'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/g_baypass'], + 'dirs': [], +} + +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/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..cd1dd2595af31e41000bba732fd8b4053ec560ec --- /dev/null +++ b/easybuild/easyconfigs/b/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'BayeScEnv' +version = '1.1' + +homepage = 'https://github.com/devillemereuil/bayescenv' +description = """BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detect +local adaptation.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/devillemereuil/bayescenv/archive/'] +sources = ['v%(version)s.tar.gz'] + +start_dir = 'source' + +files_to_copy = [(['source/bayescenv'], 'bin'), 'test', 'COPYING', 'README.md', 'ChangeLog'] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/bayescenv'], + '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} ${CXXFLAGS}/g' Makefile && " + +start_dir = 'source' + +files_to_copy = [ + (['source/bayescan_%(version)s'], 'bin'), + 'BayeScan%(version)s_manual.pdf', + 'input_examples', + 'R functions' +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/bayescan_%(version)s'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..3745f65f5f01f2dd6524bca9ec5d6f4560197c2e --- /dev/null +++ b/easybuild/easyconfigs/b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'BayeScan' +version = '2.1' + +homepage = 'http://cmpg.unibe.ch/software/BayeScan/' +description = """BayeScan aims at identifying candidate loci under natural selection from genetic data, + using differences in allele frequencies between populations.""" + +# BayeScan makefile is hardcoded to use g++. In case you want to use a non-gcc toolchain you will need to patch the makefile +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'openmp': True} + +source_urls = ['http://cmpg.unibe.ch/software/BayeScan/files/'] +sources = ['%(name)s%(version)s.zip'] + +start_dir = 'source' + +# fix the makefile which hardcodes g++ compiler +prebuildopts = "sed -i -e 's/g++/${CXX} ${CFLAGS}/g' Makefile && " + +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/Bazel/Bazel-0.3.0-CrayGNU-2016.03.eb b/easybuild/easyconfigs/b/Bazel/Bazel-0.3.0-CrayGNU-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..2490a42529e66d8b37280f1ae621bc07c94625a4 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-0.3.0-CrayGNU-2016.03.eb @@ -0,0 +1,30 @@ +# @author: Guilherme Peretti-Pezzi (CSCS) + +easyblock = "CmdCp" + +name = 'Bazel' +version = '0.3.0' + +homepage = 'http://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'CrayGNU', 'version': '2016.03'} + +dependencies = [ + ('java/jdk1.8.0_51', EXTERNAL_MODULE), +] + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/bazelbuild/bazel/archive/'] + +cmds_map = [('.*', "JAVA_VERSION=1.8 CC=gcc CXX=g++ ./compile.sh")] + +files_to_copy = [(['output/bazel'], 'bin')] + +sanity_check_paths={ + 'files': ['bin/bazel'], + 'dirs': ['bin'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb index d62e2cbb8823c0787bf2bc24c9cf66135246bc84..2661f0fe3802997d2a090e9cd5bd129b4a06a9f4 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-foss-2016a-Perl-5.22.1.eb @@ -27,8 +27,8 @@ exts_list = [ }), (name, version, { 'modulename': 'Bio::Perl', - 'source_tmpl': 'release-%s.tar.gz' % version.replace('.', '-'), - 'source_urls': ['https://github.com/bioperl/bioperl-live/archive/'], + 'source_tmpl': 'release-%s.tar.gz' % version.replace('.', '-'), + 'source_urls': ['https://github.com/bioperl/bioperl-live/archive/'], }), ] 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-3.0.1-ictce-5.5.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.1-ictce-5.5.0.eb new file mode 100755 index 0000000000000000000000000000000000000000..152bd6207af9951c3bc05ab0754f0b73d9866cf0 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.1-ictce-5.5.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.1' + +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': 'ictce', 'version': '5.5.0'} + +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-GCCcore-4.9.4.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..e81223bab29eb3722cdc76e3070fb8120230d8fa --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-4.9.4.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.4'} + +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', '2.25', '', True), +] + + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..5aa4ce571e95c66d52c0b3299346d3bf45c27fcc --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-5.4.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +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', '2.26', '', True), +] + + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bison", "yacc"]] + ["lib/liby.a"], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-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-GCCcore-6.2.0.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..e30337e6bae7275448de7447d5e28edb49f8407d --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-GCCcore-6.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.4' + +homepage = 'http://www.gnu.org/software/bison' +description = """Bison is a general-purpose parser generator that converts an annotated context-free grammar + into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.""" + +toolchain = {'name': 'GCCcore', 'version': '6.2.0'} + +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-foss-2016b.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..cf973dd271274fa904dc222d2f29bd2946296668 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-foss-2016b.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': 'foss', 'version': '2016b'} + +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-intel-2016b.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..331dd395ff8e29a7a4784ccffeb2a790f52f3ae3 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.4-intel-2016b.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': 'intel', 'version': '2016b'} + +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-2016.07.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..0c7912b766385ee10d40bdf13acf525be9464311 --- /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-1.52.0-foss-2015a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.52.0-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..68ec7366721cd71215bb058f57f5e8e542c2cc47 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.52.0-foss-2015a.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.52.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +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/Boost/Boost-1.53.0-GCC-4.7.3-serial.eb b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-GCC-4.7.3-serial.eb new file mode 100644 index 0000000000000000000000000000000000000000..98fbdcdb13e8b62c0b497dcf1d797be9f0ed254b --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.53.0-GCC-4.7.3-serial.eb @@ -0,0 +1,20 @@ +name = 'Boost' +version = '1.53.0' +versionsuffix = '-serial' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '4.7.3'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +configopts = '--with-libraries=serialization' + +sanity_check_paths = { + 'files': ["lib/libboost_serialization.a"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..6a2d69c834b7dfdf0dee333f5e34ab3f296685dd --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.55.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-GCC-4.9.2-serial.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-GCC-4.9.2-serial.eb new file mode 100644 index 0000000000000000000000000000000000000000..a23a6b98964b76fb93dc483afb29c3b7ec2032ed --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-GCC-4.9.2-serial.eb @@ -0,0 +1,29 @@ +name = 'Boost' +version = '1.58.0' +versionsuffix = '-serial' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source +libraries.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +configopts = '--with-libraries=serialization' + +toolset = 'gcc' + +sanity_check_paths = { + 'files': ["lib/libboost_serialization.a"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..d764ab9fbfd2d491569c681d9e6258a2b6247a76 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.58.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..18a7a4b74458a4b3750b6162faf0665cf40002fe --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-CrayGNU-2016.03-Python-2.7.11.eb @@ -0,0 +1,30 @@ +# @author: Luca Marsella (CSCS) +# @author: Guilherme Peretti-Pezzi (CSCS) +# @author: Petar Forai (IMP/IMBA) + +name = 'Boost' +version = "1.60.0" + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'CrayGNU', 'version': '2016.03'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.bz2' % '_'.join(version.split('.'))] + +pythonversion = '2.7.11' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6' ), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +osdependencies = [('zlib-devel','zlib1g-dev')] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015a.eb index 76d7cbc28490deed83296adbf26067f4b64a6c5d..8b079d2cebd36e70ea92b6c2294f1e15aab481ee 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015a.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015a.eb @@ -10,6 +10,8 @@ toolchainopts = {'pic': True, 'usempi': True} sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] source_urls = [SOURCEFORGE_SOURCE] +patches = ['Boost-%(version)s_fix-auto-pointer-reg.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015b.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015b.eb index 6319781076f5254aea6c6dd4989cc4b1b1469d39..ffc05c737eb8eb6a11246244defc0d65dfd5e5f1 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015b.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2015b.eb @@ -10,6 +10,8 @@ toolchainopts = {'pic': True, 'usempi': True} sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] source_urls = [SOURCEFORGE_SOURCE] +patches = ['Boost-%(version)s_fix-auto-pointer-reg.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb index a913c208499b17dd4228b65c51fbd87c3741924c..7e8085b5c4fe626abbb551660abbbb2f38e7c897 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-2.7.11.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-%(version)s_fix-auto-pointer-reg.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..0ce990c87d3655c40c9e622028037320ec67ef8c --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,28 @@ +name = 'Boost' +version = '1.60.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +patches = [ + 'Boost-%(version)s_fix-auto-pointer-reg.patch', + 'Boost-%(version)s_python3.patch', +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '3.5.1'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a.eb index c50510711dba9e3d0833c53637a8cb56915a465e..e6a66c8f3d2f27ca6610414552c8a429b7ef3222 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-foss-2016a.eb @@ -10,6 +10,8 @@ toolchainopts = {'pic': True, 'usempi': True} sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] source_urls = [SOURCEFORGE_SOURCE] +patches = ['Boost-%(version)s_fix-auto-pointer-reg.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a-Python-2.7.11.eb index 5a42251165e3c2c62dcf1d031fad3e12dd34d96e..15e0b3204eef070aca9e1e1416285088795eeaea 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a-Python-2.7.11.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-%(version)s_fix-auto-pointer-reg.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a.eb index c6b8b5f02fd21b1ef2b7a1b8a83ba9f879e6e90b..fe909ab861b69be64bd59f784854199777527bb8 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0-intel-2016a.eb @@ -10,6 +10,8 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +patches = ['Boost-%(version)s_fix-auto-pointer-reg.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.8'), diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0_fix-auto-pointer-reg.patch b/easybuild/easyconfigs/b/Boost/Boost-1.60.0_fix-auto-pointer-reg.patch new file mode 100644 index 0000000000000000000000000000000000000000..74e13d96056b08c50be1d9f149b06e6a567a80fc --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0_fix-auto-pointer-reg.patch @@ -0,0 +1,31 @@ +see https://github.com/boostorg/python/issues/56 and https://github.com/boostorg/python/pull/59 +diff --git a/include/boost/python/object/class_metadata.hpp b/include/boost/python/object/class_metadata.hpp +index c71cf67..5009c17 100644 +--- a/include/boost/python/object/class_metadata.hpp ++++ b/include/boost/python/object/class_metadata.hpp +@@ -164,7 +164,7 @@ struct class_metadata + >::type held_type; + + // Determine if the object will be held by value +- typedef is_convertible use_value_holder; ++ typedef mpl::bool_::value> use_value_holder; + + // Compute the "wrapped type", that is, if held_type is a smart + // pointer, we're talking about the pointee. +@@ -175,10 +175,12 @@ struct class_metadata + >::type wrapped; + + // Determine whether to use a "back-reference holder" +- typedef mpl::or_< +- has_back_reference +- , is_same +- , is_base_and_derived ++ typedef mpl::bool_< ++ mpl::or_< ++ has_back_reference ++ , is_same ++ , is_base_and_derived ++ >::value + > use_back_reference; + + // Select the holder. diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.60.0_python3.patch b/easybuild/easyconfigs/b/Boost/Boost-1.60.0_python3.patch new file mode 100644 index 0000000000000000000000000000000000000000..279cbfb666d75cbaef236916a2c09d5f9d5a4ee4 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.60.0_python3.patch @@ -0,0 +1,24 @@ +#Boost checks Python include in $(prefix)/include/python$(version) +#some cases it is in $(prefix)/include/python$(version)m +#see more: https://svn.boost.org/trac/boost/ticket/11120 +# Aug 27th 2016 by B. Hajgato (Free Univeristy Brussels - VUB) +--- boost_1_60_0/tools/build/src/tools/python.jam.org 2015-10-16 20:55:36.000000000 +0200 ++++ boost_1_60_0/tools/build/src/tools/python.jam 2016-07-27 16:20:52.549560154 +0200 +@@ -539,7 +539,16 @@ + } + else + { +- includes ?= $(prefix)/include/python$(version) ; ++ if not($(prefix)/include/python$(version)m) ++ { ++ debug-message "Used include path: $(prefix)/include/python$(version)m" ; ++ includes ?= $(prefix)/include/python$(version)m ; ++ } ++ else ++ { ++ debug-message "Used include path: $(prefix)/include/python$(version)" ; ++ includes ?= $(prefix)/include/python$(version) ; ++ } + + local lib = $(exec-prefix)/lib ; + libraries ?= $(lib)/python$(version)/config $(lib) ; diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..06bc1679e1bcaa7fb11979377cd5e91947532327 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-foss-2016a.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': '2016a'} +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-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-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..822d74b107331b20a796e205a66e4f05538da643 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a-Python-2.7.11.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': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.11'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7840698ed46ea38b18c1383ba8780af0f2aad86b --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016a.eb @@ -0,0 +1,21 @@ +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': '2016a'} +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'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..015aad27165b26a87deeffbb317a82fc49b8ee29 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.61.0-intel-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': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', '2.7.12'), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' 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/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..63080d8ef9d20b9ef66d6a5c02446dfb368cea2f --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.9-foss-2016a.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 +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.9' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] + +files_to_copy = [ + (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s", + "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'), + "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"], + 'dirs': [], +} + +# to add script folder to path just uncomment this line +#modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..95d2b2fb64d59d69068ce6424ce27d9083f7750e --- /dev/null +++ b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'Bullet' +version = '2.83.7' + +homepage = "http://bulletphysics.org/" +description = """Bullet professional 3D Game Multiphysics Library provides state + of the art collision detection, soft body and rigid body dynamics.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': False, 'pic': True} + +source_urls = ['https://github.com/bulletphysics/bullet3/archive/'] +sources = ["%(version)s.tar.gz"] + +builddependencies = [('CMake', '3.5.2')] + +# build shared libraries +configopts = "-DBUILD_SHARED_LIBS=ON" + +sanity_check_paths = { + 'files': ['include/bullet/btBullet%sCommon.h' % x for x in ['Collision', 'Dynamics']] + + ['lib/libBullet%s.%s' % (x,SHLIB_EXT) for x in ['Collision', 'Dynamics']], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/bullet'} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d23fa88f5772ac64dd8e2190914cfe2365747c83 --- /dev/null +++ b/easybuild/easyconfigs/b/Bullet/Bullet-2.83.7-intel-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'Bullet' +version = '2.83.7' + +homepage = "http://bulletphysics.org/" +description = """Bullet professional 3D Game Multiphysics Library provides state + of the art collision detection, soft body and rigid body dynamics.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': False, 'pic': True} + +source_urls = ['https://github.com/bulletphysics/bullet3/archive/'] +sources = ["%(version)s.tar.gz"] + +builddependencies = [('CMake', '3.5.2')] + +# build shared libraries +configopts = "-DBUILD_SHARED_LIBS=ON" + +sanity_check_paths = { + 'files': ['include/bullet/btBullet%sCommon.h' % x for x in ['Collision', 'Dynamics']] + + ['lib/libBullet%s.%s' % (x,SHLIB_EXT) for x in ['Collision', 'Dynamics']], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/bullet'} + +moduleclass = 'phys' 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-2.25-GCCcore-4.9.4.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..4eee9df8fa2b14e1008d640e7da30508aa41b0bd --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCCcore-4.9.4.eb @@ -0,0 +1,22 @@ +name = 'binutils' +version = '2.25' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '4.9.4'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('M4', '1.4.17'), + ('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/binutils/binutils-2.26-GCCcore-5.4.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..0461a3563b635b64b16313315f07388f4cb85e7c --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.26-GCCcore-5.4.0.eb @@ -0,0 +1,21 @@ +name = 'binutils' +version = '2.26' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # zlib required, but being linked instatically, 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/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/binutils/binutils-2.27-GCCcore-6.2.0.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..88e16771dff3753f0cfe8e94ae4b87e4fa98f200 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27-GCCcore-6.2.0.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': '6.2.0'} + +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/binutils/binutils-2.27.eb b/easybuild/easyconfigs/b/binutils/binutils-2.27.eb new file mode 100644 index 0000000000000000000000000000000000000000..6011a780095ddc76213da5448e5d2bfd977105c1 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.27.eb @@ -0,0 +1,19 @@ +name = 'binutils' +version = '2.27' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + # zlib required, but being linked in statically, so not a runtime dep + ('zlib', '1.2.8'), +] + +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..25c40493113031e575197107ef7287a554bf9f88 --- /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/byacc/byacc-20160324-intel-2016a.eb b/easybuild/easyconfigs/b/byacc/byacc-20160324-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a80f721d5ed5a1f94d3b86b2ed9072c8b8b080f2 --- /dev/null +++ b/easybuild/easyconfigs/b/byacc/byacc-20160324-intel-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'byacc' +version = '20160324' + +homepage = 'http://invisible-island.net/byacc/byacc.html' +description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. + In contrast to bison, it is written to avoid dependencies upon a particular compiler.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TGZ] +source_urls = ['ftp://invisible-island.net/byacc'] + +checksums = ['bde0463c6c03f059b1e6e9c5579cbe49'] + +sanity_check_paths = { + 'files': ["bin/yacc"], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/byacc/byacc-20160606-intel-2016b.eb b/easybuild/easyconfigs/b/byacc/byacc-20160606-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..981c94c528c1c490f3cb02b27c641bfe49ae624f --- /dev/null +++ b/easybuild/easyconfigs/b/byacc/byacc-20160606-intel-2016b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'byacc' +version = '20160606' + +homepage = 'http://invisible-island.net/byacc/byacc.html' +description = """Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. + In contrast to bison, it is written to avoid dependencies upon a particular compiler.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TGZ] +source_urls = ['ftp://invisible-island.net/byacc'] + +checksums = ['d527c811b360f04a8c5f5a0a90625966'] + +sanity_check_paths = { + 'files': ["bin/yacc"], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2016.03.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..276f46cd3c4dcfcbe3be8b4f767754f59ff57a93 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-2016.03.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': 'CrayGNU', 'version': '2016.03'} +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-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-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..42b488a1d63cb1af9284d9163004ce5e369bd7ba --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCC-5.4.0-2.26.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': '5.4.0-2.26'} +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-GCCcore-4.9.3.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..3f3812483e0f9b4cf50ce888659fd8d111053cfa --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-GCCcore-4.9.3.eb @@ -0,0 +1,19 @@ +name = 'bzip2' +version = '1.0.6' + +homepage = 'http://www.bzip.org/' +description = """bzip2 is a freely available, patent free, high-quality data compressor. It typically + compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical + compressors), whilst being around twice as fast at compression and six times faster at decompression.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +builddependencies = [ + ('binutils', '2.25'), +] + +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-foss-2016b.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..a1b865f0b8f771a11fb07b9906923991a171a577 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2016b.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': 'foss', 'version': '2016b'} +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-intel-2016b.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..b37807492544a920cc26a72184388e8a5befc480 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2016b.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': 'intel', 'version': '2016b'} +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-1.7.1-foss-2015a.eb b/easybuild/easyconfigs/c/CDO/CDO-1.7.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0f0ccdc37335fef465ee10434f8a6a4b73e4fb51 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-1.7.1-foss-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '1.7.1' + +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': 'foss', 'version': '2015a'} +toolchainopts = {'opt': True, 'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://code.zmaw.de/attachments/download/12070/'] + +dependencies = [ + ('HDF5', '1.8.13'), + ('netCDF', '4.3.2'), + ('YAXT', '0.4.4'), +] + +configopts = "--with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF" + +sanity_check_paths = { + 'files': ["bin/cdo"], + 'dirs': [], +} + +moduleclass = 'data' 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/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..177bb20dcc1286cb244bace7ba4155d63eefe745 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.350-ictce-5.5.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '3.350' + +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 = {'optarch': True, 'pic': True} + +srcversion = '%s' % 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/CFITSIO/CFITSIO-3.38-foss-2016a.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..654a6284e8fedce41ef4852e3ce08b399e6b750b --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.38-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '3.38' + +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': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +srcversion = '%s0' % 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/CHARMM/CHARMM-37b2-foss-2016a.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c24eb87f8589c5af6c76691ba59f10de1c70a9db --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-foss-2016a.eb @@ -0,0 +1,28 @@ +# Authors:: Ward Poelmans + +name = 'CHARMM' +version = '37b2' + +homepage = "http://www.charmm.org" +description = """CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile +and widely used molecular simulation program with broad application to many-particle systems.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +sources = ["c%(version)s.tar.gz"] + +patches = [ + "qmmm-pme-%(version)s.patch", + "use-xhost-%(version)s.patch", + "main-case-fix-%(version)s.patch", + 'CHARMM-%(version)s_fix-qgas-double-declared.patch', +] + +# MKL activated automatically when the intel toolchain is used +build_options = "FULL COLFFT PIPF +DOMDEC -CMPI" + +# Choose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce +system_size = "medium" + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CHASE/CHASE-20130626.eb b/easybuild/easyconfigs/c/CHASE/CHASE-20130626.eb new file mode 100644 index 0000000000000000000000000000000000000000..83fba54e753e54e0d6c0b5c279e956e254cd5395 --- /dev/null +++ b/easybuild/easyconfigs/c/CHASE/CHASE-20130626.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'CHASE' +version = '20130626' + +homepage = 'http://people.duke.edu/~asallen/Software.html' +description = """Case-control HAplotype Sharing analyses. +Haplotype sharing analyses for genome-wide association studies.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://people.duke.edu/~asallen/Software_files/'] +sources = ['chase_64bit_linux.tar.gz'] + +checksums = ['901ba8c71d90e49fe3e8ff325cdee464'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ["chase", "convert_to_ent"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-ictce-5.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..380b94f6c7c236a984046b0053fec8a39724a641 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.1.3.1-ictce-5.5.0.eb @@ -0,0 +1,23 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.1.3.1' + +homepage = 'http://proj-clhep.web.cern.ch/proj-clhep/' +description = """The CLHEP project is intended to be a set of HEP-specific foundation and + utility classes such as random generators, physics vectors, geometry and linear algebra. + CLHEP is structured in a set of packages independent of any external package.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] + +builddependencies = [('CMake', '2.8.12')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=Release' + +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-3.5.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..c7cd4a579a0fe1ef1143b43f99f52c26067d9e4c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2015.11.eb @@ -0,0 +1,23 @@ +# Contributed by Luca Marsella (CSCS) +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.0' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2016.03.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..f9e868c77a7d018860f5ff43b6614fb56bb02632 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.0-CrayGNU-2016.03.eb @@ -0,0 +1,23 @@ +# Contributed by Luca Marsella (CSCS) +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.0' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'CrayGNU', 'version': '2016.03'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..42e9b3b3bdba0019e6715258f9e557f63d0cfff4 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-foss-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.2' + +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', '1.0.1s'), +] + +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-3.5.2-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..b68274e5b4bf4d24e8945a31d3df4c4ca653bb1a --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.5.2-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.5.2' + +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', '1.0.1s'), +] + +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-3.6.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..97b2282312fdb2dc386f319eb008d3f7ab5c60c3 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCC-5.4.0-2.26.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.6.1' + +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': 'GCC', 'version': '5.4.0-2.26'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1s'), +] + +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-3.6.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..d5ca429e05c505cb75fa5bd613bb898ff5121bce --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-GCCcore-4.9.3.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.6.1' + +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': 'GCCcore', 'version': '4.9.3'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +builddependencies = [ + ('binutils', '2.25'), +] + +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-3.6.1-foss-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..c1386c78f896d8dc07fb578f87f9d3f0253b1a5e --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-foss-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.6.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1s'), +] + +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-3.6.1-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..40d915d152ffed6606ba6cd6a87ebb9e652c2944 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-intel-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.6.1' + +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': 'intel', 'version': '2016b'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['%(name)s-%(version)s-use-gnu11.patch'] + +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', '1.0.1s'), +] + +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-3.6.1-use-gnu11.patch b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-use-gnu11.patch new file mode 100644 index 0000000000000000000000000000000000000000..361f38b0b3faa10732edf1ccc36e48c7ee5173b2 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.1-use-gnu11.patch @@ -0,0 +1,17 @@ +# Using -std=c11 lets the build fail with very weird errors (with icc). Switching to +# gnu11 makes it pass. +# Ward Poelmans +diff -ur cmake-3.6.1.orig/Modules/Compiler/Intel-C.cmake cmake-3.6.1/Modules/Compiler/Intel-C.cmake +--- cmake-3.6.1.orig/Modules/Compiler/Intel-C.cmake 2016-07-22 15:50:22.000000000 +0200 ++++ cmake-3.6.1/Modules/Compiler/Intel-C.cmake 2016-08-31 17:32:38.594401777 +0200 +@@ -15,8 +15,8 @@ + endif() + + if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 15.0.0) +- set(CMAKE_C11_STANDARD_COMPILE_OPTION "${_std}=c11") +- set(CMAKE_C11_EXTENSION_COMPILE_OPTION "${_std}=c11") ++ set(CMAKE_C11_STANDARD_COMPILE_OPTION "${_std}=gnu11") ++ set(CMAKE_C11_EXTENSION_COMPILE_OPTION "${_std}=gnu11") + endif() + + if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 12.1) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..aa63de70da721013fc93e04d1b4e4f1999961539 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.6.2-GCCcore-5.4.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.6.2' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +builddependencies = [ + ('binutils', '2.26'), +] + + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.1.0c'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' 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/CMake/CMake-3.7.1-GCCcore-5.4.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..5b3221d0bf7e2c9e09c6d665aee8474b1aa3f8cf --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-5.4.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.7.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +builddependencies = [ + ('binutils', '2.26'), +] + + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.1.0c'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..b364332ea03c7dc74cfe573fcdba9bbe21b4cc92 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-GCCcore-6.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.7.1' +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': 'GCCcore', 'version': '6.2.0'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +builddependencies = [ + ('binutils', '2.27'), +] + + +dependencies = [ + ('ncurses', '6.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.1.0c'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['cmake', 'cpack', 'ctest']], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..0464c9024de4e98f9916c5b7400d9a2a9e92d14a --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.7.1-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.7.1' + +homepage = 'http://www.cmake.org' +description = """CMake, the cross-platform, open-source build system. + CMake is a family of tools designed to build, test and package software.""" + +toolchain = {'name': '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/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-proteins.eb b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-proteins.eb new file mode 100644 index 0000000000000000000000000000000000000000..b60083b2b25384326d5e375064d468eeafb77621 --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-proteins.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 = 'MakeCp' + +name = 'CONTRAlign' +version = '2.01' +versionsuffix = '-proteins' + +homepage = 'http://contra.stanford.edu/contralign/' +description = """CONditional TRAining for Protein Sequence Alignment""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [homepage] +sources = ['%%(namelower)s_v%s.tar.gz' % version.replace('.', '_')] + +patches = ['CONTRAlign-%(version)s_gcc47.patch'] + +start_dir = 'src' + +# this option determines whether the program is being compiled for protein or RNA sequence input. +# Here we are compiling for protein input. Check docs for details +buildopts = 'MODEL_TYPE="-DRNA=0"' + +files_to_copy = [(['contralign', 'score_directory.pl', 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] + +sanity_check_paths = { + 'files': ['bin/contralign'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-rna.eb b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-rna.eb new file mode 100644 index 0000000000000000000000000000000000000000..41ffea3e50b9484c18167e39191d078fbf5bb66e --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01-goolf-1.4.10-rna.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 = 'MakeCp' + +name = 'CONTRAlign' +version = '2.01' +versionsuffix = '-rna' + +homepage = 'http://contra.stanford.edu/contralign/' +description = """CONditional TRAining for Protein Sequence Alignment""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [homepage] +sources = ['%%(namelower)s_v%s.tar.gz' % version.replace('.', '_')] + +patches = ['CONTRAlign-%(version)s_gcc47.patch'] + +start_dir = 'src' + +# this option determines whether the program is being compiled for protein or RNA sequence input. +# Here we are compiling for RNA input. Check docs for details +buildopts = 'MODEL_TYPE="-DRNA=1"' + +files_to_copy = [(['contralign', 'score_directory.pl', 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] + +sanity_check_paths = { + 'files': ['bin/contralign'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01_gcc47.patch b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01_gcc47.patch new file mode 100644 index 0000000000000000000000000000000000000000..f2647d776330dda1cc76fb92a776b81287c18b09 --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAlign/CONTRAlign-2.01_gcc47.patch @@ -0,0 +1,24 @@ +this patch adds flag -fpermissive which is needed to build with GCC-4.7.x +and also adds a missing include +Pablo Escobar - sciCORE +--- contralign.orig/src/Makefile 2008-08-15 03:06:30.000000000 +0200 ++++ contralign/src/Makefile 2014-02-04 17:25:31.364788280 +0100 +@@ -23,7 +23,7 @@ + -ffast-math -funroll-all-loops -funsafe-math-optimizations \ + -fpeel-loops -Winline --param large-function-growth=100000 \ + --param max-inline-insns-single=100000 \ +- --param inline-unit-growth=100000 ++ --param inline-unit-growth=100000 -fpermissive + + OTHER_FLAGS = + +--- contralign.orig/src/Utilities.cpp 2008-08-14 02:08:30.000000000 +0200 ++++ contralign/src/Utilities.cpp 2014-02-04 17:25:05.483971266 +0100 +@@ -2,6 +2,7 @@ + // Utilities.cpp + ////////////////////////////////////////////////////////////////////// + ++#include + #include "Utilities.hpp" + + bool toggle_error = false; diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06.eb index 428626aef1f0a454e076498929067aeb1cdc9c55..3b5ab3bb9d0c5d4ab77ab9b4a8bf980814c8eb83 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.06.eb @@ -24,6 +24,7 @@ dependencies = [ ] builddependencies = [ + ('fftw/3.3.4.3', EXTERNAL_MODULE), ('flex', '2.5.39'), ('Bison', '3.0.2'), ] diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11.eb index 1b2b44d855a3c9c4abcfccb015719ef6cfaa115f..4d855a0429cebbab4606523f13c12feab5720208 100644 --- a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11.eb +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-2015.11.eb @@ -19,6 +19,7 @@ patches = [ ] dependencies = [ + ('fftw/3.3.4.3', EXTERNAL_MODULE), ('Libint', '1.1.4'), ('libxc', '2.2.1'), ] diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0d4b88847698e17f484531db6e557e13126a53a0 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016a.eb @@ -0,0 +1,41 @@ +name = 'CP2K' +version = '3.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.4'), + ('libxc', '2.2.3'), + ('PLUMED', '2.2.2'), + ('libxsmm', '1.4'), +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True +plumed = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b-psmp.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b-psmp.eb new file mode 100644 index 0000000000000000000000000000000000000000..70102c177eacc4d112a76f7c857b32c6cbaed858 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b-psmp.eb @@ -0,0 +1,45 @@ +name = 'CP2K' +version = '3.0' +versionsuffix = '-psmp' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.6'), + ('libxc', '2.2.3'), + ('PLUMED', '2.2.3'), + ('libxsmm', '1.4.4'), +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +type = 'psmp' + +# regression test reports failures +ignore_regtest_fails = True + +plumed = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b.eb b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..edd1ebec094a6985529b7027d59a114055f88583 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-3.0-intel-2016b.eb @@ -0,0 +1,42 @@ +name = 'CP2K' +version = '3.0' + +homepage = 'http://www.cp2k.org/' +description = """CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular + simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different + methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and + classical pair and many-body potentials. """ + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = [ + 'CP2K-2.6.0-ifort-compiler-bug-fix.patch', + 'CP2K-2.4.0-fix_compile_date_lastsvn.patch', +] + +dependencies = [ + ('Libint', '1.1.6'), + ('libxc', '2.2.3'), + ('PLUMED', '2.2.3'), + ('libxsmm', '1.4.4'), +] + +builddependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +# regression test reports failures +ignore_regtest_fails = True + +plumed = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3-ictce-5.5.0.eb b/easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3-ictce-5.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..7d9e83529184c681cc75561bef7591189cecde31 --- /dev/null +++ b/easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3-ictce-5.5.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'CRPropa' +version = '2.0.3' + +homepage = 'https://crpropa.desy.de' +description = """CRPropa is a publicly available code to study the propagation of ultra high energy nuclei up to iron + on their voyage through an extra galactic environment.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['https://github.com/CRPropa/CRPropa2/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = ['CRPropa-%(version)s_no-docs.patch'] + +dependencies = [ + ('CLHEP', '2.1.3.1'), + ('CFITSIO', '3.350'), + ('ROOT', 'v5.34.13'), + ('FFTW', '3.3.3'), +] +builddependencies = [('Doxygen', '1.8.5')] + +configopts = '--with-clhep-path=$EBROOTCLHEP/bin' +configopts += '--with-cfitsio-include=$EBROOTCFITSIO/include --with-cfitsio-library=$EBROOTCFITSIO/lib ' +configopts += '--with-root=$EBROOTROOT/lib' + +# download and install the photo disintegration data package +prebuildopts = './GetPDCrossSections.sh && ' + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/CRPropa"], + 'dirs': ["lib", "share"], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3_no-docs.patch b/easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3_no-docs.patch new file mode 100644 index 0000000000000000000000000000000000000000..98c5588397252a252578618dc710865229da307a --- /dev/null +++ b/easybuild/easyconfigs/c/CRPropa/CRPropa-2.0.3_no-docs.patch @@ -0,0 +1,13 @@ +skip building of docs +author: Kenneth Hoste (HPC-UGent) +--- Makefile.in.orig 2014-03-26 17:18:53.474997093 +0100 ++++ Makefile.in 2014-03-26 17:19:18.844596386 +0100 +@@ -291,7 +291,7 @@ + AM_CPPFLAGS = $(GNL_CPPFLAGS) + + #SUBDIRS = External doc sophia dint src +-SUBDIRS = External sophia sibyll dint src doc ++SUBDIRS = External sophia sibyll dint src # doc + EXTRA_DIST = sophia/src/sophia.h sibyll/sibyll.h src/Interactions/proton_f77 src/Interactions/proton_sophia dint/src/tables sysdep.h get_externals.sh GetPDCrossSections.sh HalfLifeTable doc/Doxyfile COPYRIGHT doc/UserGuide.tex doc/precision_traj.ps doc/PhotonDensityCollection2.eps doc/crpdetector.eps doc/AllIRBzEvolutionModelsCan.eps IRBzRedshiftEvol_Kneiske examples/GettingStarted Plot + all: config.h + $(MAKE) $(AM_MAKEFLAGS) all-recursive 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/CUDA/CUDA-8.0.44.eb b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44.eb new file mode 100644 index 0000000000000000000000000000000000000000..9407a6399ef7ef14f54055fdc14fcc962d13f60e --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-8.0.44.eb @@ -0,0 +1,18 @@ +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': 'dummy', 'version': 'dummy'} + +source_urls = ['https://developer.nvidia.com/compute/cuda/%(version_major_minor)s/prod/local_installers/'] + +sources = ['%(namelower)s_%(version)s_linux-run'] + +modextravars = { 'CUDA_HOME': '%(installdir)s' } + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-4.9.3.eb b/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..e9bbed8bb408f80f991a353e8ed09453e22b2d0d --- /dev/null +++ b/easybuild/easyconfigs/c/CVS/CVS-1.11.23-GCCcore-4.9.3.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +## + +easyblock = 'ConfigureMake' + +name = 'CVS' +version = '1.11.23' + +homepage = 'https://savannah.nongnu.org/projects/cvs' +description = """CVS is a version control system, an important component of + Source Configuration Management (SCM).""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +source_urls = [' http://ftp.gnu.org/non-gnu/cvs/source/stable/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['CVS-1.11.23-zlib-1.patch', 'CVS-1.11.23-getline.patch'] + +builddependencies = [('binutils', '2.25')] +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': ['bin/cvs', 'bin/cvsbug', 'bin/rcs2log'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/Cantera/Cantera-2.2.1-intel-2016b-Python-2.7.12.eb 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/CastXML/CastXML-20160617-foss-2016a.eb b/easybuild/easyconfigs/c/CastXML/CastXML-20160617-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..553587edc64960c94294604b15c4fcf79aa78b9a --- /dev/null +++ b/easybuild/easyconfigs/c/CastXML/CastXML-20160617-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'CastXML' +version = '20160617' +commit_id = 'd5934bd' + +homepage = 'https://github.com/CastXML/CastXML' +description = """CastXML is a C-family abstract syntax tree XML output tool.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/CastXML/CastXML/archive'] +sources = ['%s.tar.gz' % commit_id] + +builddependencies = [ + ('CMake', '3.4.3'), +] + +dependencies = [ + ('Clang', '3.7.1'), + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ["bin/castxml"], + 'dirs': ["share/castxml"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7.1-intel-2016a.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7.1-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5f43a0c1f4b82e8260100bc1627eae3ab6f729d9 --- /dev/null +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7.1-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'CheMPS2' +version = '1.7.1' + +homepage = 'https://github.com/SebWouters/CheMPS2' +description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the +density matrix renormalization group (DMRG) for ab initio quantum chemistry.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] + +builddependencies = [('CMake', '3.5.2')] + +dependencies = [ + ('HDF5', '1.8.17') +] + +runtest = 'test' + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'], + 'dirs': ['include/chemps2'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7.2-intel-2016a.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7.2-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4d4c3350be7dd549809740aa514058b4c19c7ff2 --- /dev/null +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.7.2-intel-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'CheMPS2' +version = '1.7.2' + +homepage = 'https://github.com/SebWouters/CheMPS2' +description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the +density matrix renormalization group (DMRG) for ab initio quantum chemistry.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] + +builddependencies = [('CMake', '3.5.2')] + +dependencies = [ + ('HDF5', '1.8.17') +] + +runtest = 'test' + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'], + 'dirs': ['include/chemps2'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8-intel-2016b.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..f566c1ab13646dce3d167e758063c93a9815b966 --- /dev/null +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8-intel-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'CheMPS2' +version = '1.8' + +homepage = 'https://github.com/SebWouters/CheMPS2' +description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the +density matrix renormalization group (DMRG) for ab initio quantum chemistry.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] + +builddependencies = [('CMake', '3.5.2')] + +dependencies = [ + ('HDF5', '1.8.17') +] + +runtest = 'test' + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'], + 'dirs': ['include/chemps2'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/Circos/Circos-0.69-2-ictce-5.5.0-Perl-5.18.2.eb b/easybuild/easyconfigs/c/Circos/Circos-0.69-2-ictce-5.5.0-Perl-5.18.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..6c93e5f90f003a228b0cdfbc379f9bf172c66c6c --- /dev/null +++ b/easybuild/easyconfigs/c/Circos/Circos-0.69-2-ictce-5.5.0-Perl-5.18.2.eb @@ -0,0 +1,33 @@ +easyblock = "Tarball" + +name = 'Circos' +version = '0.69-2' + +homepage = 'http://www.circos.ca/' +description = """Circos is a software package for visualizing data and information. + It visualizes data in a circular layout - this makes Circos ideal for exploring + relationships between objects or positions.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://circos.ca/distribution/'] +sources = [SOURCELOWER_TGZ] + +perl = 'Perl' +perlver = '5.18.2' +versionsuffix = '-%s-%s' % (perl, perlver) +dependencies = [ + (perl, perlver), + ('GD', '2.52', versionsuffix), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/%(name)s'], +} + +modextrapaths = {'PERL5LIB': 'lib'} + +sanity_check_commands = [('perl', '-e "use Circos"')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.7.1-foss-2016a.eb b/easybuild/easyconfigs/c/Clang/Clang-3.7.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9037365bc8267644191599bf3a1f9a87d774e81c --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.7.1-foss-2016a.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = "Clang" +version = "3.7.1" + +homepage = "http://clang.llvm.org/" +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'foss', 'version': '2016a'} +# Do not set optarch to True: it will cause the build to fail +toolchainopts = {'optarch': False} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = [ + "llvm-%(version)s.src.tar.xz", + "cfe-%(version)s.src.tar.xz", + "compiler-rt-%(version)s.src.tar.xz", + "polly-%(version)s.src.tar.xz", +] + +dependencies = [ + ('GMP', '6.1.0'), + ('ISL', '0.17'), +] + +builddependencies = [ + ('CMake', '3.4.3'), + ('Python', '2.7.11'), + ('libxml2', '2.9.3'), +] + +assertions = True + +usepolly = True + +build_targets = ['X86'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.8.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/c/Clang/Clang-3.8.1-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..3c6cb72c88a688d2ab94ee9989c9e2add70eeb57 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.8.1-GCC-5.4.0-2.26.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = "Clang" +version = "3.8.1" + +homepage = "http://clang.llvm.org/" +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} +# Do not set optarch to True: it will cause the build to fail +toolchainopts = {'optarch': False} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = [ + "llvm-%(version)s.src.tar.xz", + "cfe-%(version)s.src.tar.xz", + "compiler-rt-%(version)s.src.tar.xz", + "polly-%(version)s.src.tar.xz", + "openmp-%(version)s.src.tar.xz", +] + +dependencies = [ + ('GMP', '6.1.1'), +] + +builddependencies = [ + ('CMake', '3.6.1'), + ('Python', '2.7.12', '-bare'), + ('libxml2', '2.9.4'), +] + +assertions = True + +usepolly = True + +build_targets = ['X86'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-foss-2016b.eb b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..06226cf0b0a0ffc84b6aa27a0b262f226b8a0a87 --- /dev/null +++ b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.0-foss-2016b.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by Adam Huffman +# Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Clustal-Omega' +version = '1.2.0' + +homepage = 'http://www.clustal.org/omega/' +description = """ Clustal Omega is a multiple sequence alignment + program for proteins. It produces biologically meaningful multiple + sequence alignments of divergent sequences. Evolutionary relationships + can be seen via viewing Cladograms or Phylograms """ + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('argtable', '2.13')] + +sanity_check_paths = { + 'files': ['bin/clustalo'], + 'dirs': [], +} + +moduleclass = 'bio' 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/Cluster-Buster/Cluster-Buster-20160106-intel-2016a.eb b/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20160106-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..009a6c205795e637c8f16f9f2f2d4f9e3313d2ec --- /dev/null +++ b/easybuild/easyconfigs/c/Cluster-Buster/Cluster-Buster-20160106-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'CmdCp' + +name = 'Cluster-Buster' +version = '20160106' + +homepage = 'https://github.com/weng-lab/cluster-buster/' +description = """Cluster-Buster: Finding dense clusters of motifs in DNA sequences""" + +source_urls = ['https://github.com/weng-lab/cluster-buster/archive/'] +sources = ['a343491.tar.gz'] + +toolchain = {'name': 'intel', 'version': '2016a'} + +start_dir = 'cbust-src' + +cmds_map = [('.*', "$CXX $CXXFLAGS -DNDEBUG -o cbust *.cpp")] + +files_to_copy = [(['cbust'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/cbust'], + '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..6a2974e5b4d07e2ea3e33a194cd7409d59d9eb2b --- /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/CppUnit/CppUnit-1.12.1-foss-2016a.eb b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.12.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f0709a3154d0b8541aa75babc8a00739bb0004c3 --- /dev/null +++ b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.12.1-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'CppUnit' +version = '1.12.1' + +homepage = 'http://sourceforge.net/projects/cppunit/' +description = """CppUnit is the C++ port of the famous JUnit framework for unit testing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libcppunit.a', 'lib/libcppunit.%s' % SHLIB_EXT, 'lib/pkgconfig/cppunit.pc'], + 'dirs': ['bin', 'include/cppunit', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.03.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..eeedf98b762503c576fdeeaf47d9e5505f7858c4 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.03.eb @@ -0,0 +1,19 @@ +easyblock = 'CrayToolchain' + +name = 'CrayGNU' +version = '2016.03' + +homepage = 'http://docs.cray.com/books/S-9408-1603/' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: March 2016).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version + ('PrgEnv-gnu', EXTERNAL_MODULE), + ('gcc/4.9.3', EXTERNAL_MODULE), + ('cray-libsci/16.03.1', EXTERNAL_MODULE), + ('cray-mpich/7.3.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.04.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..19027f6d87150885c43b6276eb6cbf7dcbe7651a --- /dev/null +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.04.eb @@ -0,0 +1,19 @@ +easyblock = 'CrayToolchain' + +name = 'CrayGNU' +version = '2016.04' + +homepage = 'http://docs.cray.com/books/S-9408-1604/' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: April 2016).\n""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version + ('PrgEnv-gnu', EXTERNAL_MODULE), + ('gcc/4.9.3', EXTERNAL_MODULE), + ('cray-libsci/16.03.1', EXTERNAL_MODULE), + ('cray-mpich/7.3.3', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.06.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..306310f5af24ccb42eefa82a6ee902e74a563a3c --- /dev/null +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-2016.06.eb @@ -0,0 +1,19 @@ +easyblock = 'CrayToolchain' + +name = 'CrayGNU' +version = '2016.06' + +homepage = 'http://docs.cray.com/books/S-9408-1606/' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: June 2016).\n""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version + ('PrgEnv-gnu', EXTERNAL_MODULE), + ('gcc/4.9.3', EXTERNAL_MODULE), + ('cray-libsci/16.06.1', EXTERNAL_MODULE), + ('cray-mpich/7.4.0', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2016.06.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2016.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..bb3bd926daba0bfdf58c1270f551ae55ac49f7b3 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-2016.06.eb @@ -0,0 +1,19 @@ +easyblock = 'CrayToolchain' + +name = 'CrayIntel' +version = '2016.06' + +homepage = 'http://docs.cray.com/books/S-9407-1606' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module (PE release: June 2016).\n""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + # PrgEnv version is not pinned, as Cray recommends to use the latest (default) version + ('PrgEnv-intel', EXTERNAL_MODULE), + ('intel/16.0.1.150', EXTERNAL_MODULE), + ('cray-libsci/16.06.1', EXTERNAL_MODULE), + ('cray-mpich/7.4.0', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CryptoMiniSat/CryptoMiniSat-5.0.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/CryptoMiniSat/CryptoMiniSat-5.0.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..28c7775c76cf1297cdf641f7b5e339fe4c3057fd --- /dev/null +++ b/easybuild/easyconfigs/c/CryptoMiniSat/CryptoMiniSat-5.0.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'CryptoMiniSat' +version = '5.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/msoos/cryptominisat' +description = "CryptoMiniSat is an advanced SAT solver" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/msoos/cryptominisat/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['CryptoMiniSat-%(version)s_fix-python-prefix.patch'] + +dependencies = [ + ('Python', '2.7.12'), + ('Boost', '1.61.0', versionsuffix), +] +builddependencies = [('CMake', '3.7.1')] + +separate_build_dir = True + +configopts = "-DPYTHON_PACKAGES_PATH=%(installdir)s/lib/python%(pyshortver)s/site-packages" + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/cryptominisat%(version_major)s', 'lib/libcryptominisat%%(version_major)s.%s' % SHLIB_EXT], + 'dirs': ['include/cryptominisat%(version_major)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import pycryptosat'"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CryptoMiniSat/CryptoMiniSat-5.0.1_fix-python-prefix.patch b/easybuild/easyconfigs/c/CryptoMiniSat/CryptoMiniSat-5.0.1_fix-python-prefix.patch new file mode 100644 index 0000000000000000000000000000000000000000..27de192b0154292ece0ce160d438531bb19905a8 --- /dev/null +++ b/easybuild/easyconfigs/c/CryptoMiniSat/CryptoMiniSat-5.0.1_fix-python-prefix.patch @@ -0,0 +1,13 @@ +install Python bindings into same CryptoMiniSat-specific installation directory rather than in Python installation directory +author: Kenneth Hoste (HPC-UGent) +--- cryptominisat-5.0.1/python/CMakeLists.txt.orig 2016-12-20 14:29:51.756760945 +0100 ++++ cryptominisat-5.0.1/python/CMakeLists.txt 2016-12-20 14:29:59.786688501 +0100 +@@ -14,7 +14,7 @@ + + add_custom_target(python_interface ALL DEPENDS ${OUTPUT}/timestamp) + +-install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${SETUP_PY} install --record files.txt)") ++install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${SETUP_PY} install --prefix ${CMAKE_INSTALL_PREFIX} --record files.txt)") + + if (ENABLE_TESTING) + add_test (NAME pytest 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-2016a.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b2f95877ad35c0733f3cc00e38275ce46861f7ec --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2016a.eb @@ -0,0 +1,29 @@ +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': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] + +dependencies = [ + # issues with boost > 1.55, see https://github.com/cole-trapnell-lab/cufflinks/issues/3 + ('Boost', '1.55.0', '-Python-2.7.11'), + ('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/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=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.49.1-foss-2016a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.49.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..72e01a54b40f817ce138e9eebfd30981a86056d0 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.49.1-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.49.1' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1t')] +# configopts = "--with-ssl=$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-7.49.1-foss-2016b.eb b/easybuild/easyconfigs/c/cURL/cURL-7.49.1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..c1e4c831e02bf17fa6670befce14c924c8c5aabe --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.49.1-foss-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.49.1' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1t')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.49.1-intel-2016a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.49.1-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4acaead8d9ea550fe290c50b940a2b4a17006a4f --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.49.1-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.49.1' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1t')] +# configopts = "--with-ssl=$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-7.49.1-intel-2016b.eb b/easybuild/easyconfigs/c/cURL/cURL-7.49.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..26bcff067d01f63faa6c24b0d69966080ff074f4 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.49.1-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.49.1' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1t')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..92598548412db0b63dc7ad0646c9ba909214283e --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.14.6-foss-2016a-GLib-2.48.0.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.14.6' +glibver = '2.48.0' +versionsuffix = '-GLib-%s' % glibver + +homepage = 'http://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.21'), + ('freetype', '2.6.3'), + ('pixman', '0.34.0'), + ('fontconfig', '2.11.95'), + ('expat', '2.1.1'), + ('libX11', '1.6.3'), + ('libxcb', '1.11.1'), + ('libXrender', '0.9.9'), + ('libXext', '1.3.3'), + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), + ('GLib', glibver), +] +builddependencies = [ + ('renderproto', '0.11'), + ('xproto', '7.0.28'), + ('xextproto', '7.3.0'), +] + +# 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 " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.so', 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo-gobject.so', 'lib/libcairo-script-interpreter.so', 'lib/libcairo.so'] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.14.6-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-3.2.5.eb b/easybuild/easyconfigs/c/ccache/ccache-3.2.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..3880874512c56ff4d63b4adddc28775cfa39b8f0 --- /dev/null +++ b/easybuild/easyconfigs/c/ccache/ccache-3.2.5.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 = '3.2.5' + +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-3.3.1.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-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..8172078525f96c03663a1beea13b87ada0cd6e0c --- /dev/null +++ b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'configparser' +version = '3.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://docs.python.org/3/library/configparser.html' +description = "configparser is a Python library that brings the updated configparser from Python 3.5 to Python 2.6-3.5" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://pypi.python.org/packages/7c/69/c2ce7e91c89dc073eb1aa74c0621c3eefbffe8216b3f9af9d3885265c01c/'] +sources = ['configparser-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.11'), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/configparser.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/backports/configparser'], +} + +# XXX: hack! for some reason the sanity check imports fail, even though the +# PYTHONPATH seems to point to the right directory?!? Creating the __init__.py +# in backports makes it pass and hopefully does not break anything. +postinstallcmds = ['touch %(installdir)s/lib/python%(pyshortver)s/site-packages/backports/__init__.py'] + +sanity_check_commands = [ + ('python', "-c 'import configparser'"), + ('python', "-c 'from backports import configparser'"), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..10fc57629790cf1dc3e8f3dbcc5c8fb3e6bbf443 --- /dev/null +++ b/easybuild/easyconfigs/c/configparser/configparser-3.5.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,40 @@ +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', '2.7.12'), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/configparser.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/backports/configparser'], +} + +# XXX: hack! for some reason the sanity check imports fail, even though the +# PYTHONPATH seems to point to the right directory?!? Creating the __init__.py +# in backports makes it pass and hopefully does not break anything. +postinstallcmds = ['touch %(installdir)s/lib/python%(pyshortver)s/site-packages/backports/__init__.py'] + +sanity_check_commands = [ + ('python', "-c 'import configparser'"), + ('python', "-c 'from backports import configparser'"), +] + +moduleclass = 'lib' 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/configurable-http-proxy/configurable-http-proxy-1.3.0-foss-2016a-nodejs-4.4.7.eb b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-1.3.0-foss-2016a-nodejs-4.4.7.eb new file mode 100644 index 0000000000000000000000000000000000000000..049f03862b48bbf3d0fb14b4a3158d1ab9d50657 --- /dev/null +++ b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-1.3.0-foss-2016a-nodejs-4.4.7.eb @@ -0,0 +1,30 @@ +easyblock = 'PackedBinary' + +name = 'configurable-http-proxy' +version = '1.3.0' +nodejsver = '4.4.7' +versionsuffix = '-nodejs-%s' % nodejsver + +homepage = 'https://github.com/jupyterhub/configurable-http-proxy' +description = """HTTP proxy for node.js including a REST API for updating the routing table. + Developed as a part of the Jupyter Hub multi-user server.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/jupyterhub/configurable-http-proxy/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('nodejs', nodejsver), +] + +preinstallopts = 'cd %(name)s-%(version)s && ' +install_cmd = 'npm install --prefix %(installdir)s -g' + +sanity_check_paths = { + 'files': ['bin/configurable-http-proxy'], + 'dirs': ['lib/node_modules/configurable-http-proxy'], +} +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'tools' 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/c/cuDNN/cuDNN-5.0-CUDA-7.5.18.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-CUDA-7.5.18.eb new file mode 100644 index 0000000000000000000000000000000000000000..aaab290dcfb394320a21e904a5c2c4c088167ec7 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.0-CUDA-7.5.18.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '5.0' +cuda_version = '7.5.18' + +versionsuffix = '-CUDA-%s' % cuda_version + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for + deep neural networks.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +sources = ['%(namelower)s-7.5-linux-x64-v%(version)s-ga.tgz'] + +checksums = [ + '6f9110f66c8a48e15766b1f8c2a1baf3', # cudnn-7.5-linux-x64-v5.0-ga.tgz +] + +dependencies = [('CUDA', cuda_version)] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb new file mode 100644 index 0000000000000000000000000000000000000000..0cbdeea8a4b08547d57e18988bf612673de6fcec --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1-CUDA-8.0.44.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '5.1' +cuda_version = '8.0.44' + +versionsuffix = '-CUDA-%s' % cuda_version + +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for + deep neural networks.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +sources = ['%(namelower)s-8.0-linux-x64-v%(version)s.tgz'] + +dependencies = [('CUDA', cuda_version)] + +checksums = [ + '099ca6a9b21b35e32f3408eff2a1c06d', # cudnn-8.0-linux-x64-v5.1.tgz +] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..63398f9cb069861aa85ee45a47c1a2c570026f23 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.9.1-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.9.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://opensource.scilifelab.se/projects/cutadapt/' +description = """ Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads. """ + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cutadapt/'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2016a-Perl-5.22.2.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2016a-Perl-5.22.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..6491ebe755614488ed5bca43b4265b1e3da6b7f6 --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.032-intel-2016a-Perl-5.22.2.eb @@ -0,0 +1,36 @@ +easyblock = 'PerlModule' + +name = 'DBD-mysql' +version = '4.032' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://search.cpan.org/~capttofu/DBD-mysql-%(version)s/' +description = """Perl binding for MySQL""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://cpan.metacpan.org/authors/id/C/CA/CAPTTOFU/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.22.2'), + ('MariaDB', '10.1.13'), + ('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/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/DCA++/DCA++-1.0-CrayGNU-2015.11-cpu.eb b/easybuild/easyconfigs/d/DCA++/DCA++-1.0-CrayGNU-2015.11-cpu.eb new file mode 100644 index 0000000000000000000000000000000000000000..86590d12e7f7a59c61b0a857466a07c87a4e8fa6 --- /dev/null +++ b/easybuild/easyconfigs/d/DCA++/DCA++-1.0-CrayGNU-2015.11-cpu.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'DCA++' +version = '1.0' +versionsuffix = '-cpu' + +homepage = 'http://www.itp.phys.ethz.ch/research/comp/computation.html' + +description = """The DCA++ software project is a C++ implementation of the dynamical cluster +approximation (DCA) and its DCA+ extension. It aims to solve lattice models of strongly +correlated electron systems. This module bundles all the dependencies for the CPU-only version.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +dependencies = [ + ('CMake', '3.5.0'), + ('spglib', '1.7.3'), + ('NFFT', '3.3.0'), + ('GSL', '2.1'), + ('gtest', '1.7.0'), + ('cray-hdf5/1.8.13', EXTERNAL_MODULE), +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/d/DCA++/DCA++-1.0-CrayGNU-2015.11-cuda.eb b/easybuild/easyconfigs/d/DCA++/DCA++-1.0-CrayGNU-2015.11-cuda.eb new file mode 100644 index 0000000000000000000000000000000000000000..231148074a75ee35be224392b89c4639fc238f33 --- /dev/null +++ b/easybuild/easyconfigs/d/DCA++/DCA++-1.0-CrayGNU-2015.11-cuda.eb @@ -0,0 +1,26 @@ +easyblock = 'Bundle' + +name = 'DCA++' +version = '1.0' +versionsuffix = '-cuda' + +homepage = 'http://www.itp.phys.ethz.ch/research/comp/computation.html' + +description = """The DCA++ software project is a C++ implementation of the dynamical cluster +approximation (DCA) and its DCA+ extension. It aims to solve lattice models of strongly correlated +electron systems. This module bundles all the dependencies for the CPU+GPU version.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +dependencies = [ + ('CMake', '3.5.0'), + ('spglib', '1.7.3'), + ('NFFT', '3.3.0'), + ('GSL', '2.1'), + ('gtest', '1.7.0'), + ('cray-hdf5/1.8.13', EXTERNAL_MODULE), + ('cudatoolkit/7.0.28-1.0502.10742.5.1', EXTERNAL_MODULE), + ('magma', '2.0.0'), +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb index 0edd0228ed665f100ce875affd1624aff6992c73..1a6bd6a25d96476b8b2125f7a6f21f84afd559c9 100644 --- a/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb +++ b/easybuild/easyconfigs/d/DIAL/DIAL-2011.06.06-foss-2016a.eb @@ -20,10 +20,10 @@ dependencies = [ ('LASTZ', '1.02.00'), ] -binaries = [ 'assemble', 'assemble1', 'assemble_illumina', 'build_sff_index', 'convertFastqFasta', - 'cull_components', 'DIAL', 'filter', 'filter_clusters', 'fish_clusters', 'make_template', - 'masker', 'partition', 'remove_clones', 'remove_clusters', 'update', 'update_clusters', - 'update_status',] +binaries = ['assemble', 'assemble1', 'assemble_illumina', 'build_sff_index', 'convertFastqFasta', + 'cull_components', 'DIAL', 'filter', 'filter_clusters', 'fish_clusters', 'make_template', + 'masker', 'partition', 'remove_clones', 'remove_clusters', 'update', 'update_clusters', + 'update_status'] sanity_check_paths = { 'files': ['bin/%s' % binfile for binfile in binaries], 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/DMTCP/DMTCP-2.4.5.eb b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..597de0792e7d546c3e3d1d78dcf9857d0fadbb7e --- /dev/null +++ b/easybuild/easyconfigs/d/DMTCP/DMTCP-2.4.5.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = 'ConfigureMake' + +name = 'DMTCP' +version = '2.4.5' + +homepage = "http://dmtcp.sourceforge.net/index.html" +description = """DMTCP (Distributed MultiThreaded Checkpointing) +transparently checkpoints a single-host or distributed computation +in user-space -- with no modifications to user code or to the O/S.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/dmtcp/dmtcp/archive/'] +sources = ['%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/dmtcp_command', 'bin/dmtcp_discover_rm', 'bin/dmtcp_nocheckpoint', 'bin/dmtcp_srun_helper', + 'bin/dmtcp_sshd', 'bin/dmtcp_coordinator', 'bin/dmtcp_launch', 'bin/dmtcp_restart', 'bin/dmtcp_ssh'], + 'dirs': [], +} + +moduleclass = 'tools' + diff --git a/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb b/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.eb new file mode 100644 index 0000000000000000000000000000000000000000..295844b8bab62326fe432853ee68d7d20fb9bd1a --- /dev/null +++ b/easybuild/easyconfigs/d/DicomBrowser/DicomBrowser-1.7.0b5-Java-1.7.0_80.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 = 'JAR' + +name = "DicomBrowser" +version = "1.7.0b5" +versionsuffix = "-Java-%(javaver)s" + +homepage = 'http://nrg.wustl.edu/software/dicom-browser/' +description = """DicomBrowser is an application for inspecting and modifying DICOM metadata in many files at once.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['https://bitbucket.org/nrg/dicombrowser/downloads/'] +sources = ['%(name)s-%(version)s-bin-with-dependencies.jar'] + +dependencies = [ + ('Java', '1.7.0_80', '', True), +] + +sanity_check_paths = { + 'files': ['%(name)s-%(version)s-bin-with-dependencies.jar'], + 'dirs': [], +} + +modloadmsg = """To execute run: java -jar \\$EBROOTDICOMBROWSER/%(name)s-%(version)s-bin-with-dependencies.jar""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016b.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..00e90a1e4094868e3b91d2a9e1df407b74fc5e8a --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-foss-2016b.eb @@ -0,0 +1,21 @@ +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': 'foss', 'version': '2016b'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('CMake', '3.5.2'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +parallel = 1 + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016b.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..038f6a11a2f4c5ed359832f976d094947eafc856 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.11-intel-2016b.eb @@ -0,0 +1,21 @@ +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': 'intel', 'version': '2016b'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('CMake', '3.5.2'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), +] + +parallel = 1 + +moduleclass = 'devel' 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/Doxygen/Doxygen-1.8.5-ictce-5.5.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.5-ictce-5.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..e87a654b014227c0b97575144e44c4ddce8ca031 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.5-ictce-5.5.0.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.5' + +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': 'ictce', 'version': '5.5.0'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +dependencies = [ + ('flex', '2.5.37'), + ('Bison', '3.0.1'), +] + +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/damageproto/damageproto-1.2.1-foss-2016a.eb b/easybuild/easyconfigs/d/damageproto/damageproto-1.2.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..13810699c6e9bb01bec4bb547d6bfa55c89bd18c --- /dev/null +++ b/easybuild/easyconfigs/d/damageproto/damageproto-1.2.1-foss-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'damageproto' +version = '1.2.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers for xinerama" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +builddependencies = [('xorg-macros', '1.19.0')] + +sanity_check_paths = { + 'files': ['include/X11/extensions/damageproto.h'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/damageproto/damageproto-1.2.1-intel-2016a.eb b/easybuild/easyconfigs/d/damageproto/damageproto-1.2.1-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5d7b16e6f251330ad6449c948e70ef7c20c6ca43 --- /dev/null +++ b/easybuild/easyconfigs/d/damageproto/damageproto-1.2.1-intel-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'damageproto' +version = '1.2.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers for xinerama" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +builddependencies = [('xorg-macros', '1.19.0')] + +sanity_check_paths = { + 'files': ['include/X11/extensions/damageproto.h'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..27c5d182f4f47dfdbaa071604984566eac6cd2f0 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'dask' +version = '0.11.0' +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'} + +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 = 'data' diff --git a/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..1b19e5cf3849107a2281b3cd74fda9d0a9658a61 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-0.11.0-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'dask' +version = '0.11.0' +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'} + +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 = 'data' 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..c1c0d704374c238698e031660b63d594142c8a74 --- /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..198de40465b8b8a294510b264a683ac2d3cbbef6 --- /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/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..6b962c6687fcb9fc2d126c2ae6372045a8536d8f --- /dev/null +++ b/easybuild/easyconfigs/e/EIGENSOFT/EIGENSOFT-6.1.1-goolf-1.7.20.eb @@ -0,0 +1,37 @@ +# 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 = 'Tarball' + +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': 'goolf', 'version': '1.7.20'} + +dependencies = [ + ('GSL', '1.16'), +] + +source_urls = [ + 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/', + 'https://data.broadinstitute.org/alkesgroup/EIGENSOFT/OLD/'] +sources = ['EIG%(version)s.tar.gz'] + +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-2.8.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..f166a5d5875478d6a27faba9136d6e4ddb18fc34 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.1.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.8.1' + +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/18/7a/c983e61bb91687ad74faab0edd7471b5e78f12cf3c71087581eedc6dd9e5/', + # vsc-base + 'https://pypi.python.org/packages/c2/b9/8686ca09c21d59d49ce5964cea035d158d84447fdd0c7d1bfc1d2701c17d/', + # easybuild-framework + 'https://pypi.python.org/packages/22/66/21c21c0f1770ba240a3ef37ed7ba20eb0af0ff08be1f522c849310444ee3/', + # easybuild-easyblocks + 'https://pypi.python.org/packages/93/7a/0d89cfde1530fc6932b9a474bd23808fef40ffcce03b99a7907700612371/', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/22/22/ecabee7c42a676a195301251bdc486c8b25fb4422963a0daab2184afed8f/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.6.tar.gz', + 'vsc-base-2.5.1.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-2.8.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..b0edd36c9663cddb7eaecc34b4a8677864b16b4a --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.8.2.eb @@ -0,0 +1,38 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.8.2' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # vsc-install + 'https://pypi.python.org/packages/03/d0/291da76d7da921cf8e70dd7db79b0838e0f633655e8f2dd06093d99ce851/', + # vsc-base + 'https://pypi.python.org/packages/c2/b9/8686ca09c21d59d49ce5964cea035d158d84447fdd0c7d1bfc1d2701c17d/', + # easybuild-framework + 'https://pypi.python.org/packages/cf/3f/9f485d534e78aec24d75d2e0c17a6136bb477c8a3972c670827d5f973cf2/', + # easybuild-easyblocks + 'https://pypi.python.org/packages/d7/e1/a0ac4227297b66dc9527dbb93c2e8083ec604ce8b00b3a3676cd40620383/', + # easybuild-easyconfigs + 'https://pypi.python.org/packages/d5/80/aab7243f47f15eb2a61bcbb4a5d772c3864407f41f1bd0bd2978f6b6259e/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-install-0.10.11.tar.gz', + 'vsc-base-2.5.1.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-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-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9d490e4cb31525f29bfd54a6fc836f34a2458ba0 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2016a.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': '2016a'} + +source_urls = [BITBUCKET_SOURCE] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' 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/Eigen/Eigen-3.2.8-foss-2016a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..99e9f6bd5181ba4519b2827f00f5e52639fff8d3 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8-foss-2016a.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.2.8' + +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': '2016a'} + +source_urls = [BITBUCKET_SOURCE] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..34ee5e6ea4967b1a07773ba7de18fedf49c50b7a --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.8.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.2.8' + +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': 'dummy', 'version': ''} + +source_urls = [BITBUCKET_SOURCE] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-intel-2016b.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..887c3a69f79050c4ff4df69f52c384ef5573d3f1 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.9-intel-2016b.eb @@ -0,0 +1,13 @@ +name = 'Eigen' +version = '3.2.9' + +homepage = 'http://eigen.tuxfamily.org/index.php?title=Main_Page' +description = """Eigen is a C++ template library for linear algebra: + matrices, vectors, numerical solvers, and related algorithms.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://bitbucket.org/%(namelower)s/%(namelower)s/get'] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/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/Emacs/Emacs-24.5-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/e/Emacs/Emacs-24.5-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..0e7922786cd81fdadc60dc6835b9aa71ec451c96 --- /dev/null +++ b/easybuild/easyconfigs/e/Emacs/Emacs-24.5-GCC-4.9.3-2.25.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Emacs' +version = '24.5' + +homepage = 'http://www.gnu.org/software/emacs/' +description = """GNU Emacs is an extensible, customizable text editor—and more. + At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language + with extensions to support text editing.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('ncurses', '6.0'), +] + +configopts = '--with-gif=no --with-tiff=no --with-x-toolkit=no --with-xpm=no --with-jpeg=no' + +sanity_check_paths = { + 'files': ["bin/emacs", "bin/emacs-%(version)s", "bin/emacsclient", "bin/etags"], + 'dirs': [] +} + +moduleclass = 'tools' 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/Extrae/Extrae-2.4.1_configure-no-shared-binutils.patch b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1_configure-no-shared-binutils.patch new file mode 100644 index 0000000000000000000000000000000000000000..c2fc719e06365bdccd09363a17b28186f01f51c6 --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-2.4.1_configure-no-shared-binutils.patch @@ -0,0 +1,16 @@ +fix configure tests for libbfd.a +author: Bernd Mohr (Juelich Supercomputing Centre, Germany) +--- configure.orig 2013-11-11 16:38:11.872367495 +0100 ++++ configure 2013-11-11 16:38:32.872767289 +0100 +@@ -27477,9 +27477,9 @@ + BFD_LIBSDIR="${binutils_home_dir}/lib${BITS}" + elif test -r "${binutils_home_dir}/lib/libbfd.so" ; then + BFD_LIBSDIR="${binutils_home_dir}/lib" +- elif test -r "${binutils_home_dir}/lib${BITS}/libbfd.a" -a "${binutils_require_shared}" = "no" ; then ++ elif test -r "${binutils_home_dir}/lib${BITS}/libbfd.a"; then #-a "${binutils_require_shared}" = "no" ; then + BFD_LIBSDIR="${binutils_home_dir}/lib${BITS}" +- elif test -r "${binutils_home_dir}/lib/libbfd.a" -a "${binutils_require_shared}" = "no" ; then ++ elif test -r "${binutils_home_dir}/lib/libbfd.a"; then # -a "${binutils_require_shared}" = "no" ; then + BFD_LIBSDIR="${binutils_home_dir}/lib" + else + if test -d ${binutils_home_dir}/lib${BITS} ; then diff --git a/easybuild/easyconfigs/e/Extrae/Extrae-3.0.1-foss-2015a.eb b/easybuild/easyconfigs/e/Extrae/Extrae-3.0.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4e0f98d635d634fa4cf2aa3a64bd778789ccea6f --- /dev/null +++ b/easybuild/easyconfigs/e/Extrae/Extrae-3.0.1-foss-2015a.eb @@ -0,0 +1,40 @@ +# 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 = 'Extrae' +version = '3.0.1' + +homepage = 'http://www.bsc.es/computer-sciences/performance-tools' +description = """Extrae is the core instrumentation package developed by the Performance Tools + group at BSC. Extrae is capable of instrumenting applications based on MPI, OpenMP, pthreads, + CUDA1, OpenCL1, and StarSs1 using different instrumentation approaches. The information gathered + by Extrae typically includes timestamped events of runtime calls, performance counters and source + code references. Besides, Extrae provides its own API to allow the user to manually instrument his + or her application.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'usempi': True} + +# http://www.bsc.es/computer-sciences/performance-tools/downloads +# Requires input of email address for download +sources = [SOURCELOWER_TAR_BZ2] + +compname = 'GCC' +compver = '4.9.2' + +# compiler toolchain depencies +dependencies = [ + ('zlib', '1.2.8', '', (compname, compver)), + ('Boost', '1.58.0', '-serial', (compname, compver)), + ('libunwind', '1.1', '', (compname, compver)), + ('libxml2', '2.9.2', '', (compname, compver)), + ('libdwarf', '20150310', '', (compname, compver)), + ('PAPI', '5.4.1'), +] + +moduleclass = 'perf' 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-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..ed854e0191c45ef4793342efe3446bf596947572 --- /dev/null +++ b/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'entrypoints' +version = '0.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/takluyver/entrypoints' +description = """Entry points are a way for Python packages to advertise objects with some common interface.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://pypi.python.org/packages/f8/ad/0e77a853c745a15981ab51fa9a0cb4eca7a7a007b4c1970106ee6ba01e0c/'] +sources = ['entrypoints-0.2.2-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '2.7.11'), + ('configparser', '3.5.0', versionsuffix), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/entrypoints.py'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..a804dca9840f4db186d238b26d7049ca65f72062 --- /dev/null +++ b/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'entrypoints' +version = '0.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/takluyver/entrypoints' +description = """Entry points are a way for Python packages to advertise objects with some common interface.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://pypi.python.org/packages/f8/ad/0e77a853c745a15981ab51fa9a0cb4eca7a7a007b4c1970106ee6ba01e0c/'] +sources = ['entrypoints-0.2.2-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '3.5.1'), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/entrypoints.py'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..7345e0bb2fa5bbf9203f069142d227576de2ce57 --- /dev/null +++ b/easybuild/easyconfigs/e/entrypoints/entrypoints-0.2.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,31 @@ +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', '2.7.12'), + ('configparser', '3.5.0', versionsuffix), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/entrypoints.py'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/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/e/eudev/eudev-3.2-GCCcore-4.9.3.eb b/easybuild/easyconfigs/e/eudev/eudev-3.2-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..82f14302a61c9030cf283d617fc6246fa8a8c791 --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.2-GCCcore-4.9.3.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'eudev' +version = '3.2' + +homepage = 'https://wiki.gentoo.org/wiki/Project:Eudev' +description = """eudev is a fork of systemd-udev with the goal of obtaining + better compatibility with existing software such as + OpenRC and Upstart, older kernels, various toolchains + and anything else required by users and various distributions.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] +patches = ['%(name)s-3.1.2_pre-2.6.34_kernel.patch'] + +builddependencies = [ + ('binutils', '2.25'), + ('gperf', '3.0.4'), +] + +osdependencies = [('kernel-headers', 'linux-libc-dev')] + +configopts = '--disable-blkid --disable-selinux --disable-manpages ' +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/udevadm', 'include/libudev.h', 'include/udev.h', 'lib/libudev.so.1'], + 'dirs': [], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..cb60566c9f6779cc9823d6ce91ddaeb2e8af7b18 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.2.0-GCCcore-4.9.3.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.2.0' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +builddependencies = [ + ('binutils', '2.25'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/e/expat/expat-2.2.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..cae54fdf71836fcc3effd733a74dc5ef81bf66c4 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.2.0-foss-2016a.eb @@ -0,0 +1,16 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.2.0' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.0-foss-2016b.eb b/easybuild/easyconfigs/e/expat/expat-2.2.0-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..f32fbc7e2c152e9df6396dc9a02a6f9f81c5517d --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.2.0-foss-2016b.eb @@ -0,0 +1,16 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.2.0' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/expat/expat-2.2.0-intel-2016b.eb b/easybuild/easyconfigs/e/expat/expat-2.2.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..9f9b279d3b2b837c37ce62d7d08d0ca76b5d9427 --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.2.0-intel-2016b.eb @@ -0,0 +1,16 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.2.0' + +homepage = 'http://expat.sourceforge.net/' +description = """Expat is an XML parser library written in C. It is a stream-oriented parser in which an application + registers handlers for things the parser might find in the XML document (like start tags)""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' 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-6.3.0-intel-2015b.eb b/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb index 7278d23d80b703dd82a2dec30188728b4ed9bf53..f3aacd25ad010c1b3a1553d376a3fb8e02c09953 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-6.3.0-intel-2015b.eb @@ -23,7 +23,10 @@ start_dir = 'FDS_Compilation' skipsteps = ['configure', 'install'] buildininstalldir = True -prebuildopts = 'env FFLAGS="$FFLAGS -fpp"' +target = 'mpi_intel_linux_64' +buildopts = '%s FFLAGS="$FFLAGS -fpp" FCOMPL="$FC"' % target + +postinstallcmds = ["ln -s %%(installdir)s/FDS_Compilation/fds_%s %%(installdir)s/FDS_Compilation/fds" % target] modextrapaths = {'PATH': 'FDS_Compilation'} @@ -31,4 +34,7 @@ sanity_check_paths = { 'files': ['FDS_Compilation/fds'], 'dirs': [], } + +sanity_check_commands = [("fds 2>&1 | grep 'MPI Enabled;'", '')] + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.5.2-intel-2016b.eb b/easybuild/easyconfigs/f/FDS/FDS-6.5.2-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..477d5d84f28f6a947e5624d2aa89e75426214146 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.5.2-intel-2016b.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = '6.5.2' + +homepage = 'https://pages.nist.gov/fds-smv/' +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/firemodels/fds/archive/'] +sources = ['Git-r21.tar.gz'] + +patches = ['FDS-r18915_makefile.patch'] + +unpack_options = '--strip-components=1' + +start_dir = 'FDS_Compilation' + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +target = 'mpi_intel_linux_64' +buildopts = '%s FFLAGS="$FFLAGS -fpp" FCOMPL="$FC"' % target + +postinstallcmds = ["ln -s %%(installdir)s/FDS_Compilation/fds_%s %%(installdir)s/FDS_Compilation/fds" % target] + +modextrapaths = {'PATH': 'FDS_Compilation'} + +sanity_check_paths = { + 'files': ['FDS_Compilation/fds'], + 'dirs': [], +} + +sanity_check_commands = [("fds 2>&1 | grep 'MPI Enabled;'", '')] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb b/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb index 2779e0ddd8dcfc2b1f6f16dba1b0d6f8d6d306ca..6addd713dcaa31ff90454b8f7011c8fba23ef05a 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb @@ -23,6 +23,11 @@ parallel = 1 skipsteps = ['configure', 'install'] buildininstalldir = True +target = 'mpi_intel_linux_64' +buildopts = '%s FFLAGS="$FFLAGS -fpp" FCOMPL="$FC"' % target + +postinstallcmds = ["ln -s %%(installdir)s/FDS_Compilation/fds_%s %%(installdir)s/FDS_Compilation/fds" % target] + modextrapaths = {'PATH': 'FDS_Compilation'} sanity_check_paths = { @@ -30,4 +35,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [("fds 2>&1 | grep 'MPI Enabled;'", '')] + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb index cefbd7a7f6cef12102aae7c3d5e263372764febc..aa1cadabd32a28a11fb238193cb7fd0aa6925460 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb @@ -17,6 +17,11 @@ patches = ['FDS-%(version)s_makefile.patch'] skipsteps = ['configure', 'install'] buildininstalldir = True +target = 'mpi_gnu_linux' +buildopts = '%s FFLAGS="$FFLAGS" FCOMPL="$FC"' % target + +postinstallcmds = ["ln -s %%(installdir)s/FDS_Source/fds_%s %%(installdir)s/FDS_Source/fds" % target] + modextrapaths = {'PATH': 'FDS_Source'} sanity_check_paths = { @@ -24,4 +29,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [("fds 2>&1 | grep 'MPI Enabled;'", '')] + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb index bbf4065638c714cf5260fbb8ac836ed68ce1adde..25ed6f846acce8689155ab39aa326a2da1cc8eda 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb @@ -17,6 +17,11 @@ patches = ['FDS-%(version)s_makefile.patch'] skipsteps = ['configure', 'install'] buildininstalldir = True +target = 'mpi_intel_linux_64' +buildopts = '%s FFLAGS="$FFLAGS" FCOMPL="$FC"' % target + +postinstallcmds = ["ln -s %%(installdir)s/FDS_Source/fds_%s %%(installdir)s/FDS_Source/fds" % target] + modextrapaths = {'PATH': 'FDS_Source'} sanity_check_paths = { @@ -24,4 +29,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [("fds 2>&1 | grep 'MPI Enabled;'", '')] + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb b/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb index e4ac832f81e11d32813be60afdf010fc329b8138..001132efa24d71094a0610ba012fade9ad16f0fc 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-intel-2015a.eb @@ -17,6 +17,11 @@ patches = ['FDS-%(version)s_makefile.patch'] skipsteps = ['configure', 'install'] buildininstalldir = True +target = 'mpi_intel_linux_64' +buildopts = '%s FFLAGS="$FFLAGS" FCOMPL="$FC"' % target + +postinstallcmds = ["ln -s %%(installdir)s/FDS_Source/fds_%s %%(installdir)s/FDS_Source/fds" % target] + modextrapaths = {'PATH': 'FDS_Source'} sanity_check_paths = { @@ -24,4 +29,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [("fds 2>&1 | grep 'MPI Enabled;'", '')] + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb b/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb index 75d4dcf42fd11d409e6ec785c94713ab826783e4..6f8589d3e9253ca75be573e9ae5e35feb47482d0 100644 --- a/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb +++ b/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb @@ -21,6 +21,11 @@ start_dir = 'FDS_Compilation' skipsteps = ['configure', 'install'] buildininstalldir = True +target = 'mpi_intel_linux_64' +buildopts = '%s FFLAGS="$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 = { @@ -28,4 +33,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = [("fds 2>&1 | grep 'MPI Enabled;'", '')] + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.06.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..274c8d2e7c9dc742b757f1d8d0580420029af148 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016.06.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': '2016.06'} +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-3.3.4-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-gompi-2016b.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..005a4be826cc84c49c2c7b17a4ba1a0e77a9f148 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2016b.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': '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-3.3.4-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="$CXX" ' @@ -23,7 +25,7 @@ configopts += '--enable-libx264' sanity_check_paths = { 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', - 'swresample', 'swscale', 'avutil'] for y in ['so', 'a']], + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], 'dirs': ['include'] } diff --git a/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..0744eae109c4a859e10e10a188cebb3f7c912b95 --- /dev/null +++ b/easybuild/easyconfigs/f/FFmpeg/FFmpeg-3.1.3-intel-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'FFmpeg' +version = '3.1.3' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +dependencies = [ + ('NASM', '2.12.02'), + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('x264', '20160614'), + ('X11', '20160819'), +] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX" ' +configopts += '--enable-libx264' + +sanity_check_paths = { + 'files': ['bin/ff%s' % x for x in ['mpeg', 'probe', 'server']] + + ['lib/lib%s.%s' % (x, y) for x in ['avdevice', 'avfilter', 'avformat', 'avcodec', 'postproc', + 'swresample', 'swscale', 'avutil'] for y in [SHLIB_EXT, 'a']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/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/FIAT/FIAT-1.6.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..d231b285fd30ef3fd7c0fb43ea933b5db6c0fcdb --- /dev/null +++ b/easybuild/easyconfigs/f/FIAT/FIAT-1.6.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'FIAT' +version = '1.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/fenics-project/fiat' +description = """The FInite element Automatic Tabulator FIAT supports generation of arbitrary order + instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating + arbitrary order instances of Jacobi-type quadrature rules on the same element shapes.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://bitbucket.org/fenics-project/fiat/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('sympy', '1.0', versionsuffix), +] + +options = {'modulename': name} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' 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/FSL/FSL-5.0.9-centos6_64.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-centos6_64.eb new file mode 100644 index 0000000000000000000000000000000000000000..a98d2244dbe0b45d845451bf8044aa9fe03c645d --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.9-centos6_64.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'FSL' +version = '5.0.9' +versionsuffix = '-centos6_64' + +homepage = 'http://www.fmrib.ox.ac.uk/fsl/' +description = """FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://fsl.fmrib.ox.ac.uk/fsldownloads/'] +sources = ['fsl-%(version)s%(versionsuffix)s.tar.gz'] + +modextravars = {'FSLDIR': '%(installdir)s'} + +# eddy_openmp is not available anymore when compiling FSL 5.0.9 from source +# fslview (& others incl. atlasquery) are more difficult via compiling from source due to required dependencies +sanity_check_paths = { + 'files': ['bin/atlasquery', 'bin/basil', 'bin/bet', 'bin/eddy_openmp', 'bin/fabber', 'bin/fast', 'bin/Fdt', + 'bin/feat', 'bin/first', 'bin/flirt', 'bin/fnirt', 'bin/fsl', 'bin/fsl_anat', 'bin/fslview', + 'bin/melodic', 'bin/pngappend', 'bin/siena', 'bin/tbss_fill', 'bin/topup'], + 'dirs': ['data', 'etc', 'extras', 'include', 'lib'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb b/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb index 21da1fddad55a1d15559dcf2430a828f3becf94e..59de3272db0df7ae24fdb6b256e976d343422e17 100644 --- a/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb +++ b/easybuild/easyconfigs/f/Firefox/Firefox-44.0.2.eb @@ -25,7 +25,7 @@ sanity_check_paths = { # add the installation dir to PATH modextrapaths = { - 'PATH': "", + 'PATH': '', } moduleclass = 'tools' 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/FreeSurfer/FreeSurfer-5.3.0-centos6_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-5.3.0-centos6_x86_64.eb new file mode 100644 index 0000000000000000000000000000000000000000..8d5cb684a594838ea06955541177f3fbd3ff391a --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-5.3.0-centos6_x86_64.eb @@ -0,0 +1,21 @@ +name = 'FreeSurfer' +version = '5.3.0' +versionsuffix = '-centos6_x86_64' + +homepage = 'http://freesurfer.net/' +description = """FreeSurfer is a software package for the analysis and visualization of structural and functional + neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational + Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(namelower)s-Linux%(versionsuffix)s-stable-pub-v%(version)s.tar.gz'] +source_urls = ['ftp://surfer.nmr.mgh.harvard.edu/pub/dist/%(namelower)s/%(version)s'] + +patches = ['FreeSurfer-5.3.0-matlab-2013.patch'] + +license_text = """email@example.com +00000 +g1bb3r1sh""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-5.3.0-matlab-2013.patch b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-5.3.0-matlab-2013.patch new file mode 100644 index 0000000000000000000000000000000000000000..a713512b021beb4b701223103b9bf4ef6241ee32 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-5.3.0-matlab-2013.patch @@ -0,0 +1,17 @@ +this patch fixes an issue when using MATLAB 2013 or higher. +Details in https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-March/044183.html +--- freesurfer.orig/matlab/SearchProjectionOnPial.m 2013-05-13 23:34:06.000000000 +0200 ++++ freesurfer/matlab/SearchProjectionOnPial.m 2016-12-20 21:37:40.732901000 +0100 +@@ -4,7 +4,11 @@ + % limit redundancies in the resulting path file. + + verticeslist=[]; +-for t=1:step:size(perim,2) ++% this file has been patched as described in ++% https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-March/044183.html ++%for t=1:step:size(perim,2) ++si=max(size(perim)); ++for t=1:step:si + [nearestIndexMT,nearestValuesMT]=mesh_vertex_nearest(mesh_total.vertices,mesh_outer.vertices(perim(t),:)); + verticeslist= [verticeslist nearestIndexMT]; + end 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/fastPHASE/fastPHASE-1.4.8.eb b/easybuild/easyconfigs/f/fastPHASE/fastPHASE-1.4.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..189d668ffd8668cb7aaaa4145a6bcea15cada575 --- /dev/null +++ b/easybuild/easyconfigs/f/fastPHASE/fastPHASE-1.4.8.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 = "BinariesTarball" + +name = 'fastPHASE' +version = '1.4.8' + +homepage = 'http://stephenslab.uchicago.edu/software.html#fastphase' +description = """ fastPHASE: software for haplotype reconstruction, +and estimating missing genotypes from population data +Documentation: http://scheet.org/code/fastphase_doc_1.4.pdf""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://scheet.org/code/'] +sources = ['Linuxfp.tar.gz'] + +checksums = ['b48731eed9b8d0a5a321f970c5c20d8c'] + +sanity_check_paths = { + 'files': ["bin/fastPHASE"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb b/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb new file mode 100644 index 0000000000000000000000000000000000000000..7eeaa4c1a4e9d1d76ef9ef00352410c5e0a66b05 --- /dev/null +++ b/easybuild/easyconfigs/f/fastQValidator/fastQValidator-0.1.1a-20151214-goolf-1.7.20-aadc6f9.eb @@ -0,0 +1,55 @@ +# 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 = 'fastQValidator' +version = '0.1.1a-20151214' +fastqvalidator_git_commit = 'aadc6f9' +libstatgen_git_commit = '8246906' +versionsuffix = '-%s' % fastqvalidator_git_commit + +homepage = 'http://genome.sph.umich.edu/wiki/FastQValidator' +description = """Validate FastQ Files""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +# we download latest source available in github for fastQValidator and libStatGen (dependency) +# using latest release tags doesn't work +# https://github.com/statgen/fastQValidator/issues/9 +source_urls = [ + 'https://github.com/statgen/fastQValidator/archive/', + 'https://github.com/statgen/libStatGen/archive/' +] + +sources = [ + '%s.tar.gz' % fastqvalidator_git_commit, + '%s.tar.gz' % libstatgen_git_commit +] + +dependencies = [ + ('zlib', '1.2.8'), +# ('OpenSSL', '1.0.1q'), # OS dependency should be preferred if the os version is more recent then this version, it's +# nice to have an up to date openssl for security reasons +] + +# openssl required by libStatgen +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +prebuildopts = 'CFLAGS="$CFLAGS -L${EBROOTZLIB}/lib" && ' +prebuildopts += 'mv %(builddir)s/libStatGen-* %(builddir)s/libStatGen && ' + +buildopts = ' LIB_PATH_GENERAL=../libStatGen ' + +files_to_copy = [(['bin/fastQValidator'], 'bin')] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/fastQValidator'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fdstools/fdstools-20160322-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/fdstools/fdstools-20160322-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..3ab45b46b599837d23571158d1ee8fb1999b0265 --- /dev/null +++ b/easybuild/easyconfigs/f/fdstools/fdstools-20160322-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'fdstools' +version = '20160322' +versionsuffix = '-Python-%(pyver)s' +commit = '3a495653' + +homepage = 'https://git.lumc.nl/jerryhoogenboom/fdstools' +description = """Forensic DNA Sequencing Tools +Tools for characterisation and filtering of PCR stutter artefacts +and other systemic noise in Next Generation Sequencing data of forensic STR markers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [('https://git.lumc.nl/jerryhoogenboom/%(name)s/repository', '?ref=%s' % commit)] +sources = ['archive.tar.gz'] + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': ['bin/fdstools'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/ffnet/ffnet-0.8.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/f/ffnet/ffnet-0.8.3-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..f19794fdc6a20a8c08c0a189fb7ca356e93f8e93 --- /dev/null +++ b/easybuild/easyconfigs/f/ffnet/ffnet-0.8.3-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,37 @@ +easyblock = 'Bundle' + +name = 'ffnet' +version = '0.8.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ffnet.sourceforge.net/' +description = """Feed-forward neural network solution for python""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [('Python', '2.7.11')] + +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/f/ffnet/'], + }), +] + +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 = '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/fixesproto/fixesproto-5.0-foss-2016a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb index b04efa3b3acc51b4f2b283745cf71e6db42672ce..a697c14eb7985ddeaa81dd716f56884dbd101067 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-foss-2016a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] +builddependencies = [('xorg-macros', '1.19.0')] + sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], 'dirs': ['lib/pkgconfig'], diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb index f26ed2df7ac7bb5e12118867ec0c210a1827721c..93a258a7af0384d7e4eafd421c1d96014c4e9d1d 100644 --- a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2016a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] +builddependencies = [('xorg-macros', '1.19.0')] + sanity_check_paths = { 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], 'dirs': ['lib/pkgconfig'], 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 new file mode 100644 index 0000000000000000000000000000000000000000..73279c6d88cda5d1c4c3718ac303fc9c8411b714 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-4.9.4.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': '4.9.4'} +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', '2.25', '', 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 new file mode 100644 index 0000000000000000000000000000000000000000..ee9b4ed94d327a92a7790ff9c4a29749d6fd7022 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-5.4.0.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': '5.4.0'} +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', '2.26', '', 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 new file mode 100644 index 0000000000000000000000000000000000000000..43cfdfac42c2c9b7aba940b18f55419747ae4864 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-GCCcore-6.2.0.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': '6.2.0'} +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-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 new file mode 100644 index 0000000000000000000000000000000000000000..626ebe5d467e8970022cfc467f89bfb3440f634e --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-foss-2016b.eb @@ -0,0 +1,21 @@ +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': 'foss', 'version': '2016b'} +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')] + +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 new file mode 100644 index 0000000000000000000000000000000000000000..1dc06e55c18c1bac16123fb3ece39831dd5ea2c1 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.6.0-intel-2016b.eb @@ -0,0 +1,21 @@ +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': 'intel', 'version': '2016b'} +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')] + +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/fontconfig/fontconfig-2.12.1-intel-2016b.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..a2cd748981ec6c6592ecb8ba73536ed99301d0ac --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.12.1-intel-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': 'intel', '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/fontsproto/fontsproto-2.1.3-foss-2016a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb index 1fbffb27588efc6c82d37f505ba0e96a0ed0aef6..f29659fb130c06531205705098e24a5427c89e5b 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-foss-2016a.eb @@ -12,6 +12,8 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] +builddependencies = [('xorg-macros', '1.19.0')] + sanity_check_paths = { 'files': [], 'dirs': ['include/X11/fonts'], diff --git a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb index 9c00b32506d3366db2c62d0738c75afeb56cfc02..f5229cc8c366b7d7eeb147f82dd6921fbd504577 100644 --- a/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/f/fontsproto/fontsproto-2.1.3-intel-2016a.eb @@ -12,6 +12,8 @@ toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] +builddependencies = [('xorg-macros', '1.19.0')] + sanity_check_paths = { 'files': [], 'dirs': ['include/X11/fonts'], diff --git a/easybuild/easyconfigs/f/foss/foss-2016.06.eb b/easybuild/easyconfigs/f/foss/foss-2016.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..66d73ecb4aeba0d724a19ca014ec642d261df9b7 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2016.06.eb @@ -0,0 +1,35 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2016.06' + +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 = '5.4.0-2.26' + +blaslib = 'OpenBLAS' +blasver = '0.2.18' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.6.0' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# compiler toolchain depencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds +dependencies = [ + ('GCC', gccver), + ('OpenMPI', '1.10.3', '', ('GCC', gccver)), + (blaslib, blasver, blassuff, ('GCC', gccver)), + ('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-2016.07.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/foss/foss-2016b.eb b/easybuild/easyconfigs/f/foss/foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..57e96f0ec9758ce67de82e52c6300717292ef20c --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2016b.eb @@ -0,0 +1,35 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2016b' + +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 = '5.4.0-2.26' + +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', gccver), + ('OpenMPI', '1.10.3', '', ('GCC', gccver)), + (blaslib, blasver, blassuff, ('GCC', gccver)), + ('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/freeglut/freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb index 1965349120d771320ee1751d89bbd458efd15b57..c44a62753bf62a2166c5863467560fc87f7e5a52 100644 --- a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a-Mesa-11.2.1.eb @@ -21,6 +21,7 @@ dependencies = [ ('libXext', '1.3.3'), ('libXrandr', '1.5.0'), ('libXi', '1.7.6'), + ('libGLU', '9.0.0', versionsuffix), ('Mesa', mesa_ver), ] diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a.eb index aa4fa34ea22d6438c43103e1a29f66429bf0e9b6..0c095217cc721d5b35ddf1225527471bbd706fd2 100644 --- a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-foss-2016a.eb @@ -18,6 +18,7 @@ dependencies = [ ('libXext', '1.3.3'), ('libXrandr', '1.5.0'), ('libXi', '1.7.6'), + ('libGLU', '9.0.0'), ('Mesa', '11.1.2'), ] diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a-Mesa-11.2.1.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a-Mesa-11.2.1.eb index fceaa15cbb9c99657d6bf9a720f0267c437d4731..325b61b0da2ca0b19e452da542ee9b7d1c83e247 100644 --- a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a-Mesa-11.2.1.eb +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a-Mesa-11.2.1.eb @@ -21,6 +21,7 @@ dependencies = [ ('libXext', '1.3.3'), ('libXrandr', '1.5.0'), ('libXi', '1.7.6'), + ('libGLU', '9.0.0', versionsuffix), ('Mesa', mesa_ver), ] diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb index fe4a731eff1482dd4507ef6d199073fc6a07febf..96cd6a9c812b1a939640db68f39477aadbe8cc67 100644 --- a/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016a.eb @@ -18,6 +18,7 @@ dependencies = [ ('libXext', '1.3.3'), ('libXrandr', '1.5.0'), ('libXi', '1.7.6'), + ('libGLU', '9.0.0'), ('Mesa', '11.1.2'), ] 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..531932c8dd2f9f2ac1be20e8a75830426673c928 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-3.0.0-intel-2016b.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'freeglut' +version = '3.0.0' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +builddependencies = [('CMake', '3.6.1')] + +dependencies = [ + ('X11', '20160819'), + ('libGLU', '9.0.0'), + ('Mesa', '12.0.2'), +] + +configopts = ' -DX11_X11_LIB="$EBROOTX11/lib/libX11.so" ' +configopts += ' -DX11_X11_INCLUDE_PATH="$EBROOTX11/include/X11" ' +configopts += ' -DX11_Xext_LIB="$EBROOTX11/lib/libXext.so" ' +configopts += ' -DX11_Xrandr_LIB="$EBROOTX11/lib/libXrandr.so" ' +configopts += ' -DX11_Xrandr_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' +configopts += ' -DX11_Xi_LIB="$EBROOTX11/lib/libXrandr.so" ' +configopts += ' -DX11_Xi_INCLUDE_PATH="$EBROOTX11/include/X11/extensions/" ' + +sanity_check_paths = { + 'files': [('lib/libglut.a', 'lib64/libglut.a'), ('lib/libglut.%s' % SHLIB_EXT, 'lib64/libglut.%s' % SHLIB_EXT)], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..7f9b603bc65faa52d8b46126a50bcee29ffc269e --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-CrayGNU-2015.11.eb @@ -0,0 +1,22 @@ +name = 'freetype' +version = '2.6.2' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.21')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb index 3111a314be1d335be306892eb54230a67e4fb812..932824a17e8271f228be46c473c0fdc28d90538c 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-foss-2016a.eb @@ -11,10 +11,15 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [('libpng', '1.6.21')] +dependencies = [ + ('libpng', '1.6.21'), + ('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'], + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, + 'lib/pkgconfig/freetype2.pc'], 'dirs': ['include/freetype2'], } diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2016a.eb index ce2c31a36a9264bd5baca5decec58f728241497a..60b3db5452598527e1b53c024f1a279c28a0daa1 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.2-intel-2016a.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [('libpng', '1.6.21')] +dependencies = [ + ('libpng', '1.6.21'), + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb index bc610c637e09e0c08336acbbe80fe5837022c229..d267c83653d1046fbd645c03dea04132187158c9 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-foss-2016a.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [('libpng', '1.6.21')] +dependencies = [ + ('libpng', '1.6.21'), + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb index 6245460dc23afc9577f6deaf6f3f21d4296c981d..3d89e4bbb1d7e3dcfb354d5c80485da0b16f7682 100644 --- a/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.3-intel-2016a.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -dependencies = [('libpng', '1.6.21')] +dependencies = [ + ('libpng', '1.6.21'), + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] sanity_check_paths = { 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-4.9.3.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..2c7c4b34eebe3d82ba4b6ac7160bd1d817f4dc1a --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-GCCcore-4.9.3.eb @@ -0,0 +1,32 @@ +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': 'GCCcore', 'version': '4.9.3'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('binutils', '2.25'), +] + +dependencies = [ + ('libpng', '1.6.24'), + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), +] + +configopts = '--with-harfbuzz=no' + +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-2.6.5-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-2.6.5-intel-2016b.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..bf9e0cfc01c3ed31e70e7042a11033f8a36033e2 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6.5-intel-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': 'intel', '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/GATK/GATK-3.6-Java-1.8.0_92.eb b/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb new file mode 100644 index 0000000000000000000000000000000000000000..3bbed9824ebf1b0498d618f5ff2d55d8ca2d9ef0 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-3.6-Java-1.8.0_92.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman +# The Francis Crick Institute +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '3.6' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download manually from http://www.broadinstitute.org/gatk/download +sources = ['GenomeAnalysisTK-%(version)s.tar.bz2'] + +dependencies = [('Java', '1.8.0_92')] + +modloadmsg = """To execute GATK run: java -jar \\$EBROOTGATK/GenomeAnalysisTK.jar""" + +sanity_check_paths = { + 'files': ["GenomeAnalysisTK.jar"], + 'dirs': ["resources"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb index a6eca83b67fce672084ff2f27f46bed0f56700a8..8837e39f57616abfeb480449932240077669d4cc 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb @@ -9,6 +9,8 @@ description = """GC3Pie is a Python package for running large job campaigns on d toolchain = {'name': 'dummy', 'version': 'dummy'} +osdependencies = [('python-devel', 'python-dev')] + # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb index 84677a51423eb42376059f32ed600acc1a4b3acd..4cfb618383c0d72cc2d1751fd704faed38b37322 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -9,6 +9,8 @@ description = """GC3Pie is a Python package for running large job campaigns on d toolchain = {'name': 'dummy', 'version': 'dummy'} +osdependencies = [('python-devel', 'python-dev')] + # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb index 55217f87b712186b917315b4e0b6a3decde47e2e..70eb5b0a10886b9e2a07d899ba857371fb48867a 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb @@ -9,6 +9,8 @@ description = """GC3Pie is a Python package for running large job campaigns on d toolchain = {'name': 'dummy', 'version': 'dummy'} +osdependencies = [('python-devel', 'python-dev')] + # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb index dbc732d1791f5df3629f7d962b8f9518f1d7bdbf..477760c3c0eb75e91a9900cf3509af9dc45df2e0 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb @@ -9,6 +9,8 @@ description = """GC3Pie is a Python package for running large job campaigns on d toolchain = {'name': 'dummy', 'version': 'dummy'} +osdependencies = [('python-devel', 'python-dev')] + # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb index 0e7690c9c0d9995445f6a93dea23d58e755e9e27..d952c146712437564ff20215d92ecee2cd7bb276 100644 --- a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -9,6 +9,8 @@ description = """GC3Pie is a Python package for running large job campaigns on d toolchain = {'name': 'dummy', 'version': 'dummy'} +osdependencies = [('python-devel', 'python-dev')] + # this is a bundle of Python packages exts_defaultclass = 'PythonPackage' 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-4.9.4-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.4-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..cb99659c2bbb2ef7ff8f3c447232b32224d34b5c --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.4-2.25.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '4.9.4' + +binutilsver = '2.25' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-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-5.4.0-2.26.eb b/easybuild/easyconfigs/g/GCC/GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..5be824a1d7d6291807c148b8d5d400fea253096b --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.4.0-2.26.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '5.4.0' + +binutilsver = '2.26' +versionsuffix = '-%s' % binutilsver + +homepage = 'http://gcc.gnu.org/' +description = """The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, + as well as libraries for these languages (libstdc++, libgcj,...).""" + +toolchain = {'name': 'dummy', 'version': ''} + +dependencies = [ + ('GCCcore', version), + # binutils built on top of GCCcore, which was built on top of (dummy-built) binutils + ('binutils', binutilsver, '', ('GCCcore', version)), +] + +altroot = 'GCCcore' +altversion = 'GCCcore' + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-6.1.0-2.27.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/GCC/GCC-6.2.0-2.27.eb b/easybuild/easyconfigs/g/GCC/GCC-6.2.0-2.27.eb new file mode 100644 index 0000000000000000000000000000000000000000..645cbb031445d38ae1c0dad8e981bc486490e1af --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-6.2.0-2.27.eb @@ -0,0 +1,25 @@ +easyblock = 'Bundle' + +name = 'GCC' +version = '6.2.0' + +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 new file mode 100644 index 0000000000000000000000000000000000000000..9a01aa75efb41c142b97c6e3b04ab782731b4dcb --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-4.9.4.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '4.9.4' + +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/gcc/gcc-%s' % version, # 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 +] +sources = [ + 'gcc-%(version)s.tar.bz2', + 'gmp-6.1.1.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', +] + +builddependencies = [ + ('Autotools', '20150215'), + ('binutils', '2.25'), +] + +patches = [('mpfr-%s-allpatches-20160601.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + '87c24a4090c1577ba817ec6882602491', # gcc-4.9.4.tar.bz2 + '4c175f86e11eb32d8bf9872ca3a8e11d', # gmp-6.1.1.tar.bz2 + '482ab3c120ffc959f631b4ba9ec59a46', # mpfr-3.1.4.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + '22164533561142b70fda09af4e775acc', # mpfr-3.1.4-allpatches-20160601.patch +] + +languages = ['c', 'c++', 'fortran'] + +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 new file mode 100644 index 0000000000000000000000000000000000000000..2a3fe7ab858abc680f75b5682a17e7da6b2573ec --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-5.4.0.eb @@ -0,0 +1,52 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '5.4.0' + +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/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL +] + +sources = [ + 'gcc-%(version)s.tar.bz2', + 'gmp-6.1.0.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.15.tar.bz2', +] + +patches = [('mpfr-%s-allpatches-20160601.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +builddependencies = [ + ('binutils', '2.26'), + ('M4', '1.4.17'), +] + +checksums = [ + '4c626ac2a83ef30dfb9260e6f59c2b30', # gcc-5.4.0.tar.bz2 + '86ee6e54ebfc4a90b643a65e402c4048', # gmp-6.1.0.tar.bz2 + '482ab3c120ffc959f631b4ba9ec59a46', # mpfr-3.1.4.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + '8428efbbc6f6e2810ce5c1ba73ecf98c', # isl-0.15.tar.bz2 + '22164533561142b70fda09af4e775acc', # mpfr-3.1.4-allpatches-20150603.patch +] + +languages = ['c', 'c++', 'fortran'] + +withisl = True + +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-fix-find-isl.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0-fix-find-isl.patch new file mode 100644 index 0000000000000000000000000000000000000000..6334b6be3527921cba381caf0277f360482d93cf --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0-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 new file mode 100644 index 0000000000000000000000000000000000000000..5b1200a09b5adb9149160ef4f7b7b90839d8cc4c --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-6.2.0.eb @@ -0,0 +1,54 @@ +easyblock = 'EB_GCC' + +name = 'GCCcore' +version = '6.2.0' + +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/gcc/gcc-%(version)s', # GCC auto-resolving HTTP mirror + 'http://ftpmirror.gnu.org/gmp', # idem for GMP + 'http://ftpmirror.gnu.org/mpfr', # idem for MPFR + 'http://www.multiprecision.org/mpc/download', # MPC official + 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies + 'http://gcc.cybermirror.org/infrastructure/', # HTTP mirror for GCC dependencies + 'http://isl.gforge.inria.fr/', # original HTTP source for ISL +] + +sources = [ + 'gcc-%(version)s.tar.bz2', + 'gmp-6.1.1.tar.bz2', + 'mpfr-%s.tar.bz2' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.16.1.tar.bz2', +] + +builddependencies = [ + ('M4', '1.4.17'), + ('binutils', '2.27'), +] + +patches = [ + ('mpfr-%s-allpatches-20160804.patch' % mpfr_version, '../mpfr-%s' % mpfr_version), + '%(name)s-%(version)s-fix-find-isl.patch', +] + +checksums = [ + '9768625159663b300ae4de2f4745fcc4', # gcc-6.2.0.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/mpfr-3.1.4-allpatches-20160601.patch b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.4-allpatches-20160601.patch new file mode 100644 index 0000000000000000000000000000000000000000..042e73d766f811adcdc00bf989dd329ecfa42185 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.4-allpatches-20160601.patch @@ -0,0 +1,358 @@ +downloaded from https://gforge.inria.fr/scm/viewvc.php/mpfr/misc/www/mpfr-3.1.4/allpatches?revision=10393&view=co +on June 3rd 2016 (last change: 2016-06-01) +diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES +--- mpfr-3.1.4-a/PATCHES 2016-04-13 21:22:23.720604013 +0000 ++++ mpfr-3.1.4-b/PATCHES 2016-04-13 21:22:23.744603677 +0000 +@@ -0,0 +1 @@ ++unix-check +diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION +--- mpfr-3.1.4-a/VERSION 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/VERSION 2016-04-13 21:22:23.744603677 +0000 +@@ -1 +1 @@ +-3.1.4 ++3.1.4-p1 +diff -Naurd mpfr-3.1.4-a/src/mpfr-impl.h mpfr-3.1.4-b/src/mpfr-impl.h +--- mpfr-3.1.4-a/src/mpfr-impl.h 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/src/mpfr-impl.h 2016-04-13 21:22:23.736603789 +0000 +@@ -252,19 +252,6 @@ + # define MPFR_WIN_THREAD_SAFE_DLL 1 + #endif + +-/* Detect some possible inconsistencies under Unix. */ +-#if defined(__unix__) +-# if defined(_WIN32) +-# error "Both __unix__ and _WIN32 are defined" +-# endif +-# if __GMP_LIBGMP_DLL +-# error "__unix__ is defined and __GMP_LIBGMP_DLL is true" +-# endif +-# if defined(MPFR_WIN_THREAD_SAFE_DLL) +-# error "Both __unix__ and MPFR_WIN_THREAD_SAFE_DLL are defined" +-# endif +-#endif +- + #if defined(__MPFR_WITHIN_MPFR) || !defined(MPFR_WIN_THREAD_SAFE_DLL) + extern MPFR_THREAD_ATTR unsigned int __gmpfr_flags; + extern MPFR_THREAD_ATTR mpfr_exp_t __gmpfr_emin; +diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h +--- mpfr-3.1.4-a/src/mpfr.h 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/src/mpfr.h 2016-04-13 21:22:23.744603677 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 4 +-#define MPFR_VERSION_STRING "3.1.4" ++#define MPFR_VERSION_STRING "3.1.4-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c +--- mpfr-3.1.4-a/src/version.c 2016-03-06 11:33:05.000000000 +0000 ++++ mpfr-3.1.4-b/src/version.c 2016-04-13 21:22:23.744603677 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.4"; ++ return "3.1.4-p1"; + } +diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES +--- mpfr-3.1.4-a/PATCHES 2016-05-22 19:59:43.838399677 +0000 ++++ mpfr-3.1.4-b/PATCHES 2016-05-22 19:59:43.866399168 +0000 +@@ -0,0 +1 @@ ++add-sub-ui-flags +diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION +--- mpfr-3.1.4-a/VERSION 2016-04-13 21:22:23.744603677 +0000 ++++ mpfr-3.1.4-b/VERSION 2016-05-22 19:59:43.866399168 +0000 +@@ -1 +1 @@ +-3.1.4-p1 ++3.1.4-p2 +diff -Naurd mpfr-3.1.4-a/src/add_ui.c mpfr-3.1.4-b/src/add_ui.c +--- mpfr-3.1.4-a/src/add_ui.c 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/src/add_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -49,6 +49,7 @@ + MPFR_SAVE_EXPO_MARK (expo); + MPFR_SET_EXP (uu, GMP_NUMB_BITS - cnt); + inex = mpfr_add(y, x, uu, rnd_mode); ++ MPFR_SAVE_EXPO_UPDATE_FLAGS (expo, __gmpfr_flags); + MPFR_SAVE_EXPO_FREE (expo); + return mpfr_check_range(y, inex, rnd_mode); + } +diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h +--- mpfr-3.1.4-a/src/mpfr.h 2016-04-13 21:22:23.744603677 +0000 ++++ mpfr-3.1.4-b/src/mpfr.h 2016-05-22 19:59:43.862399241 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 4 +-#define MPFR_VERSION_STRING "3.1.4-p1" ++#define MPFR_VERSION_STRING "3.1.4-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.4-a/src/sub_ui.c mpfr-3.1.4-b/src/sub_ui.c +--- mpfr-3.1.4-a/src/sub_ui.c 2016-03-06 11:33:05.000000000 +0000 ++++ mpfr-3.1.4-b/src/sub_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -52,6 +52,7 @@ + MPFR_SAVE_EXPO_MARK (expo); + MPFR_SET_EXP (uu, GMP_NUMB_BITS - cnt); + inex = mpfr_sub (y, x, uu, rnd_mode); ++ MPFR_SAVE_EXPO_UPDATE_FLAGS (expo, __gmpfr_flags); + MPFR_SAVE_EXPO_FREE (expo); + return mpfr_check_range (y, inex, rnd_mode); + } +diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c +--- mpfr-3.1.4-a/src/version.c 2016-04-13 21:22:23.744603677 +0000 ++++ mpfr-3.1.4-b/src/version.c 2016-05-22 19:59:43.866399168 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.4-p1"; ++ return "3.1.4-p2"; + } +diff -Naurd mpfr-3.1.4-a/tests/tadd_ui.c mpfr-3.1.4-b/tests/tadd_ui.c +--- mpfr-3.1.4-a/tests/tadd_ui.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tadd_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -69,7 +69,9 @@ + + /* nan + 2394875 == nan */ + mpfr_set_nan (x); ++ mpfr_clear_nanflag (); + mpfr_add_ui (y, x, 2394875L, MPFR_RNDN); ++ MPFR_ASSERTN (mpfr_nanflag_p ()); + MPFR_ASSERTN (mpfr_nan_p (y)); + + /* +inf + 2394875 == +inf */ +diff -Naurd mpfr-3.1.4-a/tests/tsub_ui.c mpfr-3.1.4-b/tests/tsub_ui.c +--- mpfr-3.1.4-a/tests/tsub_ui.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tsub_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -96,7 +96,9 @@ + + /* nan - 1 == nan */ + mpfr_set_nan (x); ++ mpfr_clear_nanflag (); + mpfr_sub_ui (y, x, 1L, MPFR_RNDN); ++ MPFR_ASSERTN (mpfr_nanflag_p ()); + MPFR_ASSERTN (mpfr_nan_p (y)); + + /* +inf - 1 == +inf */ +diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES +--- mpfr-3.1.4-a/PATCHES 2016-06-01 13:00:30.748711490 +0000 ++++ mpfr-3.1.4-b/PATCHES 2016-06-01 13:00:30.772711162 +0000 +@@ -0,0 +1 @@ ++sub1-overflow +diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION +--- mpfr-3.1.4-a/VERSION 2016-05-22 19:59:43.866399168 +0000 ++++ mpfr-3.1.4-b/VERSION 2016-06-01 13:00:30.772711162 +0000 +@@ -1 +1 @@ +-3.1.4-p2 ++3.1.4-p3 +diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h +--- mpfr-3.1.4-a/src/mpfr.h 2016-05-22 19:59:43.862399241 +0000 ++++ mpfr-3.1.4-b/src/mpfr.h 2016-06-01 13:00:30.772711162 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 4 +-#define MPFR_VERSION_STRING "3.1.4-p2" ++#define MPFR_VERSION_STRING "3.1.4-p3" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.4-a/src/sub1.c mpfr-3.1.4-b/src/sub1.c +--- mpfr-3.1.4-a/src/sub1.c 2016-03-06 11:33:05.000000000 +0000 ++++ mpfr-3.1.4-b/src/sub1.c 2016-06-01 13:00:30.760711326 +0000 +@@ -96,16 +96,15 @@ + /* A = S*ABS(B) +/- ulp(a) */ + MPFR_SET_EXP (a, MPFR_GET_EXP (b)); + MPFR_RNDRAW_EVEN (inexact, a, MPFR_MANT (b), MPFR_PREC (b), +- rnd_mode, MPFR_SIGN (a), +- if (MPFR_UNLIKELY ( ++MPFR_EXP (a) > __gmpfr_emax)) +- inexact = mpfr_overflow (a, rnd_mode, MPFR_SIGN (a))); +- /* inexact = mpfr_set4 (a, b, rnd_mode, MPFR_SIGN (a)); */ ++ rnd_mode, MPFR_SIGN (a), ++ MPFR_EXP (a)); + if (inexact == 0) + { + /* a = b (Exact) + But we know it isn't (Since we have to remove `c') + So if we round to Zero, we have to remove one ulp. + Otherwise the result is correctly rounded. */ ++ /* An overflow is not possible. */ ++ MPFR_ASSERTD (MPFR_EXP (a) <= __gmpfr_emax); + if (MPFR_IS_LIKE_RNDZ (rnd_mode, MPFR_IS_NEG (a))) + { + mpfr_nexttozero (a); +@@ -136,9 +135,14 @@ + i.e. inexact= MPFR_EVEN_INEX */ + if (MPFR_UNLIKELY (inexact == MPFR_EVEN_INEX*MPFR_INT_SIGN (a))) + { +- mpfr_nexttozero (a); ++ if (MPFR_UNLIKELY (MPFR_EXP (a) > __gmpfr_emax)) ++ mpfr_setmax (a, __gmpfr_emax); ++ else ++ mpfr_nexttozero (a); + inexact = -MPFR_INT_SIGN (a); + } ++ else if (MPFR_UNLIKELY (MPFR_EXP (a) > __gmpfr_emax)) ++ inexact = mpfr_overflow (a, rnd_mode, MPFR_SIGN (a)); + MPFR_RET (inexact); + } + } +diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c +--- mpfr-3.1.4-a/src/version.c 2016-05-22 19:59:43.866399168 +0000 ++++ mpfr-3.1.4-b/src/version.c 2016-06-01 13:00:30.772711162 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.4-p2"; ++ return "3.1.4-p3"; + } +diff -Naurd mpfr-3.1.4-a/tests/tsub.c mpfr-3.1.4-b/tests/tsub.c +--- mpfr-3.1.4-a/tests/tsub.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tsub.c 2016-06-01 13:00:30.760711326 +0000 +@@ -630,6 +630,135 @@ + } + } + ++static void ++check_max_almosteven (void) ++{ ++ mpfr_exp_t old_emin, old_emax; ++ mpfr_exp_t emin[2] = { MPFR_EMIN_MIN, -1000 }; ++ mpfr_exp_t emax[2] = { MPFR_EMAX_MAX, 1000 }; ++ int i; ++ ++ old_emin = mpfr_get_emin (); ++ old_emax = mpfr_get_emax (); ++ ++ for (i = 0; i < 2; i++) ++ { ++ mpfr_t a1, a2, b, c; ++ mpfr_prec_t p; ++ int neg, j, rnd; ++ ++ set_emin (emin[i]); ++ set_emax (emax[i]); ++ ++ p = MPFR_PREC_MIN + randlimb () % 70; ++ mpfr_init2 (a1, p); ++ mpfr_init2 (a2, p); ++ mpfr_init2 (b, p+1); ++ mpfr_init2 (c, MPFR_PREC_MIN); ++ ++ mpfr_setmax (b, 0); ++ mpfr_set_ui (c, 1, MPFR_RNDN); ++ ++ for (neg = 0; neg < 2; neg++) ++ { ++ for (j = 1; j >= 0; j--) ++ { ++ mpfr_set_exp (b, __gmpfr_emax - j); ++ RND_LOOP (rnd) ++ { ++ unsigned int flags1, flags2; ++ int inex1, inex2; ++ ++ flags1 = MPFR_FLAGS_INEXACT; ++ if (rnd == MPFR_RNDN || MPFR_IS_LIKE_RNDZ (rnd, neg)) ++ { ++ inex1 = neg ? 1 : -1; ++ mpfr_setmax (a1, __gmpfr_emax - j); ++ } ++ else ++ { ++ inex1 = neg ? -1 : 1; ++ if (j == 0) ++ { ++ flags1 |= MPFR_FLAGS_OVERFLOW; ++ mpfr_set_inf (a1, 1); ++ } ++ else ++ { ++ mpfr_setmin (a1, __gmpfr_emax); ++ } ++ } ++ MPFR_SET_SIGN (a1, neg ? -1 : 1); ++ ++ mpfr_clear_flags (); ++ inex2 = mpfr_sub (a2, b, c, (mpfr_rnd_t) rnd); ++ flags2 = __gmpfr_flags; ++ ++ if (! (flags1 == flags2 && SAME_SIGN (inex1, inex2) && ++ mpfr_equal_p (a1, a2))) ++ { ++ printf ("Error 1 in check_max_almosteven for %s," ++ " i = %d, j = %d, neg = %d\n", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) rnd), ++ i, j, neg); ++ printf (" b = "); ++ mpfr_dump (b); ++ printf ("Expected "); ++ mpfr_dump (a1); ++ printf (" with inex = %d, flags =", inex1); ++ flags_out (flags1); ++ printf ("Got "); ++ mpfr_dump (a2); ++ printf (" with inex = %d, flags =", inex2); ++ flags_out (flags2); ++ exit (1); ++ } ++ ++ if (i == 0) ++ break; ++ ++ mpfr_clear_flags (); ++ set_emin (MPFR_EMIN_MIN); ++ set_emax (MPFR_EMAX_MAX); ++ inex2 = mpfr_sub (a2, b, c, (mpfr_rnd_t) rnd); ++ set_emin (emin[i]); ++ set_emax (emax[i]); ++ inex2 = mpfr_check_range (a2, inex2, (mpfr_rnd_t) rnd); ++ flags2 = __gmpfr_flags; ++ ++ if (! (flags1 == flags2 && SAME_SIGN (inex1, inex2) && ++ mpfr_equal_p (a1, a2))) ++ { ++ printf ("Error 2 in check_max_almosteven for %s," ++ " i = %d, j = %d, neg = %d\n", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) rnd), ++ i, j, neg); ++ printf (" b = "); ++ mpfr_dump (b); ++ printf ("Expected "); ++ mpfr_dump (a1); ++ printf (" with inex = %d, flags =", inex1); ++ flags_out (flags1); ++ printf ("Got "); ++ mpfr_dump (a2); ++ printf (" with inex = %d, flags =", inex2); ++ flags_out (flags2); ++ exit (1); ++ } ++ } ++ } /* j */ ++ ++ mpfr_neg (b, b, MPFR_RNDN); ++ mpfr_neg (c, c, MPFR_RNDN); ++ } /* neg */ ++ ++ mpfr_clears (a1, a2, b, c, (mpfr_ptr) 0); ++ } /* i */ ++ ++ set_emin (old_emin); ++ set_emax (old_emax); ++} ++ + #define TEST_FUNCTION test_sub + #define TWO_ARGS + #define RAND_FUNCTION(x) mpfr_random2(x, MPFR_LIMB_SIZE (x), randlimb () % 100, RANDS) +@@ -647,6 +776,7 @@ + check_rounding (); + check_diverse (); + check_inexact (); ++ check_max_almosteven (); + bug_ddefour (); + for (p=2; p<200; p++) + for (i=0; i<50; i++) diff --git a/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.4-allpatches-20160804.patch b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.4-allpatches-20160804.patch new file mode 100644 index 0000000000000000000000000000000000000000..5823cecfe6cc3957094dd17f4a07f65391efac5c --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/mpfr-3.1.4-allpatches-20160804.patch @@ -0,0 +1,455 @@ +# All mpfr patches as of 2016-08-04 +# taken from their website: http://www.mpfr.org/mpfr-current/#download +diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES +--- mpfr-3.1.4-a/PATCHES 2016-04-13 21:22:23.720604013 +0000 ++++ mpfr-3.1.4-b/PATCHES 2016-04-13 21:22:23.744603677 +0000 +@@ -0,0 +1 @@ ++unix-check +diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION +--- mpfr-3.1.4-a/VERSION 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/VERSION 2016-04-13 21:22:23.744603677 +0000 +@@ -1 +1 @@ +-3.1.4 ++3.1.4-p1 +diff -Naurd mpfr-3.1.4-a/src/mpfr-impl.h mpfr-3.1.4-b/src/mpfr-impl.h +--- mpfr-3.1.4-a/src/mpfr-impl.h 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/src/mpfr-impl.h 2016-04-13 21:22:23.736603789 +0000 +@@ -252,19 +252,6 @@ + # define MPFR_WIN_THREAD_SAFE_DLL 1 + #endif + +-/* Detect some possible inconsistencies under Unix. */ +-#if defined(__unix__) +-# if defined(_WIN32) +-# error "Both __unix__ and _WIN32 are defined" +-# endif +-# if __GMP_LIBGMP_DLL +-# error "__unix__ is defined and __GMP_LIBGMP_DLL is true" +-# endif +-# if defined(MPFR_WIN_THREAD_SAFE_DLL) +-# error "Both __unix__ and MPFR_WIN_THREAD_SAFE_DLL are defined" +-# endif +-#endif +- + #if defined(__MPFR_WITHIN_MPFR) || !defined(MPFR_WIN_THREAD_SAFE_DLL) + extern MPFR_THREAD_ATTR unsigned int __gmpfr_flags; + extern MPFR_THREAD_ATTR mpfr_exp_t __gmpfr_emin; +diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h +--- mpfr-3.1.4-a/src/mpfr.h 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/src/mpfr.h 2016-04-13 21:22:23.744603677 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 4 +-#define MPFR_VERSION_STRING "3.1.4" ++#define MPFR_VERSION_STRING "3.1.4-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c +--- mpfr-3.1.4-a/src/version.c 2016-03-06 11:33:05.000000000 +0000 ++++ mpfr-3.1.4-b/src/version.c 2016-04-13 21:22:23.744603677 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.4"; ++ return "3.1.4-p1"; + } +diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES +--- mpfr-3.1.4-a/PATCHES 2016-05-22 19:59:43.838399677 +0000 ++++ mpfr-3.1.4-b/PATCHES 2016-05-22 19:59:43.866399168 +0000 +@@ -0,0 +1 @@ ++add-sub-ui-flags +diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION +--- mpfr-3.1.4-a/VERSION 2016-04-13 21:22:23.744603677 +0000 ++++ mpfr-3.1.4-b/VERSION 2016-05-22 19:59:43.866399168 +0000 +@@ -1 +1 @@ +-3.1.4-p1 ++3.1.4-p2 +diff -Naurd mpfr-3.1.4-a/src/add_ui.c mpfr-3.1.4-b/src/add_ui.c +--- mpfr-3.1.4-a/src/add_ui.c 2016-03-06 11:33:04.000000000 +0000 ++++ mpfr-3.1.4-b/src/add_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -49,6 +49,7 @@ + MPFR_SAVE_EXPO_MARK (expo); + MPFR_SET_EXP (uu, GMP_NUMB_BITS - cnt); + inex = mpfr_add(y, x, uu, rnd_mode); ++ MPFR_SAVE_EXPO_UPDATE_FLAGS (expo, __gmpfr_flags); + MPFR_SAVE_EXPO_FREE (expo); + return mpfr_check_range(y, inex, rnd_mode); + } +diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h +--- mpfr-3.1.4-a/src/mpfr.h 2016-04-13 21:22:23.744603677 +0000 ++++ mpfr-3.1.4-b/src/mpfr.h 2016-05-22 19:59:43.862399241 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 4 +-#define MPFR_VERSION_STRING "3.1.4-p1" ++#define MPFR_VERSION_STRING "3.1.4-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.4-a/src/sub_ui.c mpfr-3.1.4-b/src/sub_ui.c +--- mpfr-3.1.4-a/src/sub_ui.c 2016-03-06 11:33:05.000000000 +0000 ++++ mpfr-3.1.4-b/src/sub_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -52,6 +52,7 @@ + MPFR_SAVE_EXPO_MARK (expo); + MPFR_SET_EXP (uu, GMP_NUMB_BITS - cnt); + inex = mpfr_sub (y, x, uu, rnd_mode); ++ MPFR_SAVE_EXPO_UPDATE_FLAGS (expo, __gmpfr_flags); + MPFR_SAVE_EXPO_FREE (expo); + return mpfr_check_range (y, inex, rnd_mode); + } +diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c +--- mpfr-3.1.4-a/src/version.c 2016-04-13 21:22:23.744603677 +0000 ++++ mpfr-3.1.4-b/src/version.c 2016-05-22 19:59:43.866399168 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.4-p1"; ++ return "3.1.4-p2"; + } +diff -Naurd mpfr-3.1.4-a/tests/tadd_ui.c mpfr-3.1.4-b/tests/tadd_ui.c +--- mpfr-3.1.4-a/tests/tadd_ui.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tadd_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -69,7 +69,9 @@ + + /* nan + 2394875 == nan */ + mpfr_set_nan (x); ++ mpfr_clear_nanflag (); + mpfr_add_ui (y, x, 2394875L, MPFR_RNDN); ++ MPFR_ASSERTN (mpfr_nanflag_p ()); + MPFR_ASSERTN (mpfr_nan_p (y)); + + /* +inf + 2394875 == +inf */ +diff -Naurd mpfr-3.1.4-a/tests/tsub_ui.c mpfr-3.1.4-b/tests/tsub_ui.c +--- mpfr-3.1.4-a/tests/tsub_ui.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tsub_ui.c 2016-05-22 19:59:43.854399385 +0000 +@@ -96,7 +96,9 @@ + + /* nan - 1 == nan */ + mpfr_set_nan (x); ++ mpfr_clear_nanflag (); + mpfr_sub_ui (y, x, 1L, MPFR_RNDN); ++ MPFR_ASSERTN (mpfr_nanflag_p ()); + MPFR_ASSERTN (mpfr_nan_p (y)); + + /* +inf - 1 == +inf */ +diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES +--- mpfr-3.1.4-a/PATCHES 2016-06-01 13:00:30.748711490 +0000 ++++ mpfr-3.1.4-b/PATCHES 2016-06-01 13:00:30.772711162 +0000 +@@ -0,0 +1 @@ ++sub1-overflow +diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION +--- mpfr-3.1.4-a/VERSION 2016-05-22 19:59:43.866399168 +0000 ++++ mpfr-3.1.4-b/VERSION 2016-06-01 13:00:30.772711162 +0000 +@@ -1 +1 @@ +-3.1.4-p2 ++3.1.4-p3 +diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h +--- mpfr-3.1.4-a/src/mpfr.h 2016-05-22 19:59:43.862399241 +0000 ++++ mpfr-3.1.4-b/src/mpfr.h 2016-06-01 13:00:30.772711162 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 4 +-#define MPFR_VERSION_STRING "3.1.4-p2" ++#define MPFR_VERSION_STRING "3.1.4-p3" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.4-a/src/sub1.c mpfr-3.1.4-b/src/sub1.c +--- mpfr-3.1.4-a/src/sub1.c 2016-03-06 11:33:05.000000000 +0000 ++++ mpfr-3.1.4-b/src/sub1.c 2016-06-01 13:00:30.760711326 +0000 +@@ -96,16 +96,15 @@ + /* A = S*ABS(B) +/- ulp(a) */ + MPFR_SET_EXP (a, MPFR_GET_EXP (b)); + MPFR_RNDRAW_EVEN (inexact, a, MPFR_MANT (b), MPFR_PREC (b), +- rnd_mode, MPFR_SIGN (a), +- if (MPFR_UNLIKELY ( ++MPFR_EXP (a) > __gmpfr_emax)) +- inexact = mpfr_overflow (a, rnd_mode, MPFR_SIGN (a))); +- /* inexact = mpfr_set4 (a, b, rnd_mode, MPFR_SIGN (a)); */ ++ rnd_mode, MPFR_SIGN (a), ++ MPFR_EXP (a)); + if (inexact == 0) + { + /* a = b (Exact) + But we know it isn't (Since we have to remove `c') + So if we round to Zero, we have to remove one ulp. + Otherwise the result is correctly rounded. */ ++ /* An overflow is not possible. */ ++ MPFR_ASSERTD (MPFR_EXP (a) <= __gmpfr_emax); + if (MPFR_IS_LIKE_RNDZ (rnd_mode, MPFR_IS_NEG (a))) + { + mpfr_nexttozero (a); +@@ -136,9 +135,14 @@ + i.e. inexact= MPFR_EVEN_INEX */ + if (MPFR_UNLIKELY (inexact == MPFR_EVEN_INEX*MPFR_INT_SIGN (a))) + { +- mpfr_nexttozero (a); ++ if (MPFR_UNLIKELY (MPFR_EXP (a) > __gmpfr_emax)) ++ mpfr_setmax (a, __gmpfr_emax); ++ else ++ mpfr_nexttozero (a); + inexact = -MPFR_INT_SIGN (a); + } ++ else if (MPFR_UNLIKELY (MPFR_EXP (a) > __gmpfr_emax)) ++ inexact = mpfr_overflow (a, rnd_mode, MPFR_SIGN (a)); + MPFR_RET (inexact); + } + } +diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c +--- mpfr-3.1.4-a/src/version.c 2016-05-22 19:59:43.866399168 +0000 ++++ mpfr-3.1.4-b/src/version.c 2016-06-01 13:00:30.772711162 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.4-p2"; ++ return "3.1.4-p3"; + } +diff -Naurd mpfr-3.1.4-a/tests/tsub.c mpfr-3.1.4-b/tests/tsub.c +--- mpfr-3.1.4-a/tests/tsub.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tsub.c 2016-06-01 13:00:30.760711326 +0000 +@@ -630,6 +630,135 @@ + } + } + ++static void ++check_max_almosteven (void) ++{ ++ mpfr_exp_t old_emin, old_emax; ++ mpfr_exp_t emin[2] = { MPFR_EMIN_MIN, -1000 }; ++ mpfr_exp_t emax[2] = { MPFR_EMAX_MAX, 1000 }; ++ int i; ++ ++ old_emin = mpfr_get_emin (); ++ old_emax = mpfr_get_emax (); ++ ++ for (i = 0; i < 2; i++) ++ { ++ mpfr_t a1, a2, b, c; ++ mpfr_prec_t p; ++ int neg, j, rnd; ++ ++ set_emin (emin[i]); ++ set_emax (emax[i]); ++ ++ p = MPFR_PREC_MIN + randlimb () % 70; ++ mpfr_init2 (a1, p); ++ mpfr_init2 (a2, p); ++ mpfr_init2 (b, p+1); ++ mpfr_init2 (c, MPFR_PREC_MIN); ++ ++ mpfr_setmax (b, 0); ++ mpfr_set_ui (c, 1, MPFR_RNDN); ++ ++ for (neg = 0; neg < 2; neg++) ++ { ++ for (j = 1; j >= 0; j--) ++ { ++ mpfr_set_exp (b, __gmpfr_emax - j); ++ RND_LOOP (rnd) ++ { ++ unsigned int flags1, flags2; ++ int inex1, inex2; ++ ++ flags1 = MPFR_FLAGS_INEXACT; ++ if (rnd == MPFR_RNDN || MPFR_IS_LIKE_RNDZ (rnd, neg)) ++ { ++ inex1 = neg ? 1 : -1; ++ mpfr_setmax (a1, __gmpfr_emax - j); ++ } ++ else ++ { ++ inex1 = neg ? -1 : 1; ++ if (j == 0) ++ { ++ flags1 |= MPFR_FLAGS_OVERFLOW; ++ mpfr_set_inf (a1, 1); ++ } ++ else ++ { ++ mpfr_setmin (a1, __gmpfr_emax); ++ } ++ } ++ MPFR_SET_SIGN (a1, neg ? -1 : 1); ++ ++ mpfr_clear_flags (); ++ inex2 = mpfr_sub (a2, b, c, (mpfr_rnd_t) rnd); ++ flags2 = __gmpfr_flags; ++ ++ if (! (flags1 == flags2 && SAME_SIGN (inex1, inex2) && ++ mpfr_equal_p (a1, a2))) ++ { ++ printf ("Error 1 in check_max_almosteven for %s," ++ " i = %d, j = %d, neg = %d\n", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) rnd), ++ i, j, neg); ++ printf (" b = "); ++ mpfr_dump (b); ++ printf ("Expected "); ++ mpfr_dump (a1); ++ printf (" with inex = %d, flags =", inex1); ++ flags_out (flags1); ++ printf ("Got "); ++ mpfr_dump (a2); ++ printf (" with inex = %d, flags =", inex2); ++ flags_out (flags2); ++ exit (1); ++ } ++ ++ if (i == 0) ++ break; ++ ++ mpfr_clear_flags (); ++ set_emin (MPFR_EMIN_MIN); ++ set_emax (MPFR_EMAX_MAX); ++ inex2 = mpfr_sub (a2, b, c, (mpfr_rnd_t) rnd); ++ set_emin (emin[i]); ++ set_emax (emax[i]); ++ inex2 = mpfr_check_range (a2, inex2, (mpfr_rnd_t) rnd); ++ flags2 = __gmpfr_flags; ++ ++ if (! (flags1 == flags2 && SAME_SIGN (inex1, inex2) && ++ mpfr_equal_p (a1, a2))) ++ { ++ printf ("Error 2 in check_max_almosteven for %s," ++ " i = %d, j = %d, neg = %d\n", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) rnd), ++ i, j, neg); ++ printf (" b = "); ++ mpfr_dump (b); ++ printf ("Expected "); ++ mpfr_dump (a1); ++ printf (" with inex = %d, flags =", inex1); ++ flags_out (flags1); ++ printf ("Got "); ++ mpfr_dump (a2); ++ printf (" with inex = %d, flags =", inex2); ++ flags_out (flags2); ++ exit (1); ++ } ++ } ++ } /* j */ ++ ++ mpfr_neg (b, b, MPFR_RNDN); ++ mpfr_neg (c, c, MPFR_RNDN); ++ } /* neg */ ++ ++ mpfr_clears (a1, a2, b, c, (mpfr_ptr) 0); ++ } /* i */ ++ ++ set_emin (old_emin); ++ set_emax (old_emax); ++} ++ + #define TEST_FUNCTION test_sub + #define TWO_ARGS + #define RAND_FUNCTION(x) mpfr_random2(x, MPFR_LIMB_SIZE (x), randlimb () % 100, RANDS) +@@ -647,6 +776,7 @@ + check_rounding (); + check_diverse (); + check_inexact (); ++ check_max_almosteven (); + bug_ddefour (); + for (p=2; p<200; p++) + for (i=0; i<50; i++) +diff -Naurd mpfr-3.1.4-a/PATCHES mpfr-3.1.4-b/PATCHES +--- mpfr-3.1.4-a/PATCHES 2016-08-04 20:41:14.097592781 +0000 ++++ mpfr-3.1.4-b/PATCHES 2016-08-04 20:41:14.121592350 +0000 +@@ -0,0 +1 @@ ++c++11-compat +diff -Naurd mpfr-3.1.4-a/VERSION mpfr-3.1.4-b/VERSION +--- mpfr-3.1.4-a/VERSION 2016-06-01 13:00:30.772711162 +0000 ++++ mpfr-3.1.4-b/VERSION 2016-08-04 20:41:14.121592350 +0000 +@@ -1 +1 @@ +-3.1.4-p3 ++3.1.4-p4 +diff -Naurd mpfr-3.1.4-a/src/mpfr.h mpfr-3.1.4-b/src/mpfr.h +--- mpfr-3.1.4-a/src/mpfr.h 2016-06-01 13:00:30.772711162 +0000 ++++ mpfr-3.1.4-b/src/mpfr.h 2016-08-04 20:41:14.121592350 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 4 +-#define MPFR_VERSION_STRING "3.1.4-p3" ++#define MPFR_VERSION_STRING "3.1.4-p4" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.4-a/src/version.c mpfr-3.1.4-b/src/version.c +--- mpfr-3.1.4-a/src/version.c 2016-06-01 13:00:30.772711162 +0000 ++++ mpfr-3.1.4-b/src/version.c 2016-08-04 20:41:14.121592350 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.4-p3"; ++ return "3.1.4-p4"; + } +diff -Naurd mpfr-3.1.4-a/tests/tpow_z.c mpfr-3.1.4-b/tests/tpow_z.c +--- mpfr-3.1.4-a/tests/tpow_z.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tpow_z.c 2016-08-04 20:41:14.113592494 +0000 +@@ -26,7 +26,7 @@ + + #include "mpfr-test.h" + +-#define ERROR(str) do { printf("Error for "str"\n"); exit (1); } while (0) ++#define ERROR(str) do { printf ("Error for " str "\n"); exit (1); } while (0) + + static void + check_special (void) +diff -Naurd mpfr-3.1.4-a/tests/tset_si.c mpfr-3.1.4-b/tests/tset_si.c +--- mpfr-3.1.4-a/tests/tset_si.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tset_si.c 2016-08-04 20:41:14.113592494 +0000 +@@ -26,7 +26,7 @@ + + #include "mpfr-test.h" + +-#define ERROR(str) {printf("Error for "str"\n"); exit(1);} ++#define ERROR(str) do { printf ("Error for " str "\n"); exit (1); } while (0) + + static void + test_2exp (void) +diff -Naurd mpfr-3.1.4-a/tests/tset_sj.c mpfr-3.1.4-b/tests/tset_sj.c +--- mpfr-3.1.4-a/tests/tset_sj.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tset_sj.c 2016-08-04 20:41:14.113592494 +0000 +@@ -42,7 +42,7 @@ + + #else + +-#define ERROR(str) {printf("Error for "str"\n"); exit(1);} ++#define ERROR(str) do { printf ("Error for " str "\n"); exit (1); } while (0) + + static int + inexact_sign (int x) +diff -Naurd mpfr-3.1.4-a/tests/tsi_op.c mpfr-3.1.4-b/tests/tsi_op.c +--- mpfr-3.1.4-a/tests/tsi_op.c 2016-03-06 11:33:03.000000000 +0000 ++++ mpfr-3.1.4-b/tests/tsi_op.c 2016-08-04 20:41:14.113592494 +0000 +@@ -26,14 +26,16 @@ + + #include "mpfr-test.h" + +-#define ERROR1(s, i, z, exp) \ +-{\ +- printf("Error for "s" and i=%d\n", i);\ +- printf("Expected %s\n", exp);\ +- printf("Got "); mpfr_out_str (stdout, 16, 0, z, MPFR_RNDN);\ +- putchar ('\n');\ +- exit(1);\ +-} ++#define ERROR1(s,i,z,exp) \ ++ do \ ++ { \ ++ printf ("Error for " s " and i=%d\n", i); \ ++ printf ("Expected %s\n", exp); \ ++ printf ("Got "); mpfr_out_str (stdout, 16, 0, z, MPFR_RNDN); \ ++ putchar ('\n'); \ ++ exit(1); \ ++ } \ ++ while (0) + + const struct { + const char * op1; 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-2.1.0-foss-2016a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c02be486fa7beeb2a0a991c39a109f2dc2b61a16 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.0-foss-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.0' + +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', '4.4.1'), + ('expat', '2.2.0'), + ('libxml2', '2.9.4'), + ('zlib', '1.2.8'), + ('SQLite', '3.13.0'), +] + +sanity_check_paths = { + 'files': ['lib/libgdal.%s' % SHLIB_EXT, 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.0-foss-2016b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.0-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..0ed850751b4be861268b23f0c0198d42f1aa1499 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.0-foss-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.0' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('netCDF', '4.4.1'), + ('expat', '2.2.0'), + ('libxml2', '2.9.4'), + ('zlib', '1.2.8'), + ('SQLite', '3.13.0'), +] + +sanity_check_paths = { + 'files': ['lib/libgdal.%s' % SHLIB_EXT, 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.1.0-intel-2016b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..794261db7ff7e4f21cf69e970fd20f1e6881e5b8 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.0-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.0' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('netCDF', '4.4.1'), + ('expat', '2.2.0'), + ('libxml2', '2.9.4'), + ('zlib', '1.2.8'), + ('SQLite', '3.13.0'), +] + +sanity_check_paths = { + 'files': ['lib/libgdal.%s' % SHLIB_EXT, 'lib/libgdal.a'], + 'dirs': ['bin', 'include'] +} + +moduleclass = 'data' 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/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..6355e7d5d7130a05f7e5efb81ce96f824ad04a29 --- /dev/null +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.1.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'GDAL' +version = '2.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gdal.org/' +description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style + Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model + to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for + data translation and processing.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://download.osgeo.org/gdal/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] + +dependencies = [ + ('Python', '2.7.12'), + ('netCDF', '4.4.1'), + ('expat', '2.2.0'), + ('GEOS', '3.5.0', versionsuffix), + ('SQLite', '3.13.0'), + ('libxml2', '2.9.4'), + ('libpng', '1.6.24'), + ('libjpeg-turbo', '1.5.0'), + ('JasPer', '1.900.1'), + ('LibTIFF', '4.0.6'), + ('zlib', '1.2.8'), + ('cURL', '7.49.1'), + ('PCRE', '8.39'), +] + +configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' +configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGTURBO' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' +# there is a bug in the build system causing the build with libtool to fail for the moment +# (static library is also missing because of this) +configopts += ' --without-libtool' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libgdal.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.11-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/g/GDB/GDB-7.11-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..f98a09c22edd0cd9ed9035e004ea87c2645846af --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-7.11-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '7.11' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +patches = ['GDB-7.9-missing-makeinfo.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('expat', '2.1.0'), + ('Python', '2.7.11'), +] + +configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' +configopts += '--with-system-readline --enable-tui --enable-plugins' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GDB/GDB-7.11.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GDB/GDB-7.11.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..ad51f8adce6ed100c32b88850007cbece82b094f --- /dev/null +++ b/easybuild/easyconfigs/g/GDB/GDB-7.11.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'GDB' +version = '7.11.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.gnu.org/software/gdb/gdb.html' +description = "The GNU Project Debugger" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +patches = ['GDB-7.9-missing-makeinfo.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('expat', '2.2.0'), + ('Python', '2.7.12'), +] + +configopts = '--with-system-zlib --with-python=$EBROOTPYTHON/bin/python --with-expat=$EBROOTEXPAT ' +configopts += '--with-system-readline --enable-tui --enable-plugins' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/gdb', 'bin/gdbserver'], + 'dirs': [], +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..e5b4060a66bb0315b7298b10378e7ddfc9936f0f --- /dev/null +++ b/easybuild/easyconfigs/g/GEOS/GEOS-3.5.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'GEOS' +version = '3.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://trac.osgeo.org/geos' +description = """GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://download.osgeo.org/geos/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('Python', '2.7.12')] + +builddependencies = [('SWIG', '3.0.10', versionsuffix)] + +configopts = '--enable-python' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/geos-config', 'lib/libgeos.%s' % SHLIB_EXT, 'lib/libgeos.a', 'include/geos.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/geos'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/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/GLib/GLib-2.49.5-intel-2016b.eb b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..cabfe78d325876f0484af882c23960b55c41cdef --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.49.5-intel-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': 'intel', '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-CrayGNU-2015.11.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..6658db36ac96658b371159a7b25a752a7ec9ecc1 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2015.11.eb @@ -0,0 +1,25 @@ +# contributed by Luca Marsella (CSCS) +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': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'lowopt': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [GNU_SOURCE] + +preconfigopts = 'export CFLAGS="$CFLAGS -mcmodel=large" && ' +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-CrayGNU-2016.03.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..0f388ec38b6ef8a140107cecb538c8b7f8966eda --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.0-CrayGNU-2016.03.eb @@ -0,0 +1,25 @@ +# contributed by Luca Marsella (CSCS) and gppezzi +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': 'CrayGNU', 'version': '2016.03'} +toolchainopts = {'lowopt': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [GNU_SOURCE] + +preconfigopts = 'export CFLAGS="$CFLAGS -mcmodel=large" && ' +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-2016.07.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-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..e32606963803c7464924313578d22c0da36ae019 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-GCC-5.4.0-2.26.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': 'GCC', 'version': '5.4.0-2.26'} +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/GMP/GMP-6.1.1-foss-2016a.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8758c0fea08a2ec320fffeab1e40b70a3024b3dc --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-foss-2016a.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': '2016a'} +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-2016b.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..418ae20a6095d69c592c03c3d3e3ef9236d40856 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-foss-2016b.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': '2016b'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.1.1-intel-2016b.eb b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..cc91fe4582eb55b895ebbbeb902bc69f327f85ba --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.1.1-intel-2016b.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': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'precise': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/gmp'] + +builddependencies = [ + ('Autotools', '20150215'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libgmp.%s' % SHLIB_EXT, 'include/gmp.h'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-foss-2016a.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e8ddb76e89b7d35653bafb683713c3bb253736ef --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.48.0-foss-2016a.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'GObject-Introspection' +version = '1.48.0' + +homepage = 'https://wiki.gnome.org/GObjectIntrospection/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] + +glibver = '2.48.0' +dependencies = [ + ('Python', '2.7.11'), + ('GLib', glibver), + ('libffi', '3.2.1'), +] + +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('cairo', '1.14.6', '-GLib-%s' % glibver), +] + +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/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/GP2C/GP2C-0.0.9pl5-foss-2016a.eb b/easybuild/easyconfigs/g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e78f2ba765ca13f54160f88355d201e8564fec05 --- /dev/null +++ b/easybuild/easyconfigs/g/GP2C/GP2C-0.0.9pl5-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'GP2C' +version = '0.0.9pl5' + +homepage = 'http://pari.math.u-bordeaux.fr/pub/pari/manuals/gp2c/gp2c.html' +description = """The gp2c compiler is a package for translating GP routines into the C programming language, so that + they can be compiled and used with the PARI system or the GP calculator. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pari.math.u-bordeaux.fr/pub/pari/GP2C/'] + +dependencies = [ + ('PARI-GP', '2.7.6'), +] + +configopts = '--with-paricfg=$EBROOTPARIMINGP/lib/pari/pari.cfg' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/%s' % binfile for binfile in ['gp2c', 'gp2c-run',]], + 'dirs': ['bin'] +} + +moduleclass = 'math' 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-3.3.3-goolf-1.5.14.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..6cbe4c8289014f42fac1b191849a94f64d2930d4 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-3.3.3-goolf-1.5.14.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, 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 +## +name = 'GROMACS' +version = '3.3.3' + +homepage = 'http://www.gromacs.org' +description = """GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'openmp': False, 'usempi': True} + +# eg. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.tar.gz +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', # GROMACS sources + 'http://gerrit.gromacs.org/download/', # regression tests sources +] +sources = [SOURCELOWER_TAR_GZ] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.7-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.7-intel-2015a-hybrid.eb new file mode 100644 index 0000000000000000000000000000000000000000..69bf5a5d408861adbf96d633d707b818b1167c81 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.7-intel-2015a-hybrid.eb @@ -0,0 +1,34 @@ +## +# 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 +## +name = 'GROMACS' +version = '5.0.7' +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': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.2.2'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.58.0', '-Python-2.7.9')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.1-intel-2015b-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.1-intel-2015b-hybrid.eb new file mode 100644 index 0000000000000000000000000000000000000000..327b4714267942d1528d9806e7e031ad25ad808e --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.1-intel-2015b-hybrid.eb @@ -0,0 +1,34 @@ +## +# 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 +## +name = 'GROMACS' +version = '5.1.1' +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': 'intel', 'version': '2015b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.3.2'), + ('libxml2', '2.9.2') +] + +dependencies = [('Boost', '1.59.0', '-Python-2.7.10')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-CrayGNU-2016.03-cuda-7.0.28-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-CrayGNU-2016.03-cuda-7.0.28-hybrid.eb new file mode 100644 index 0000000000000000000000000000000000000000..a5ac227312277d1f4bdf0440cc4a8463a1f7825b --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-CrayGNU-2016.03-cuda-7.0.28-hybrid.eb @@ -0,0 +1,42 @@ +# Contributed by +# Luca Marsella (CSCS) +# Guilherme Peretti-Pezzi (CSCS) +# +# 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 + +name = 'GROMACS' +version = "5.1.2" +cudaversion = '7.0.28' +versionsuffix = '-cuda-%s-hybrid' % cudaversion + +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': 'CrayGNU', 'version': '2016.03'} +toolchainopts = {'usempi': True, 'openmp': True, 'pic': True, 'verbose': False} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-DCUDA_NVCC_FLAGS="-arch sm_35"' + +builddependencies = [ + ('CMake', '3.5.0'), + ('cudatoolkit/%s-1.0502.10742.5.1' % cudaversion, EXTERNAL_MODULE), + ('fftw/3.3.4.3', EXTERNAL_MODULE), + ('Boost', '1.60.0', '-Python-2.7.11'), + ('libxml2', '2.9.3'), +] + +# skip tests as they call the MPI executable gmx_mpi and would fail on the login nodes +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-mt.eb new file mode 100644 index 0000000000000000000000000000000000000000..3c8fdff8cfc702fb737d846008bef3fc75111f16 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-foss-2016a-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 5.1.2 +# Author: Adam Huffman +# The Francis Crick Institute +## + +name = 'GROMACS' +version = '5.1.2' +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': '2016a'} +toolchainopts = {'openmp': True, 'usempi': False} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.4.1'), + ('libxml2', '2.9.3') +] + +dependencies = [('Boost', '1.60.0')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.eb new file mode 100644 index 0000000000000000000000000000000000000000..f8d1e53e321d52ef5e4afce53990049bf834ff15 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-goolf-1.7.20-mt.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 / 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 +## +name = 'GROMACS' +version = '5.1.2' +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': 'goolf', 'version': '1.7.20'} +toolchainopts = {'openmp': True, 'usempi': False} + +source_urls = [ + 'ftp://ftp.gromacs.org/pub/gromacs/', + 'http://gerrit.gromacs.org/download/', +] + +sources = [ + SOURCELOWER_TAR_GZ, +# seems to have disappeared? +# 'regressiontests-5.0.2.tar.gz', +] + +builddependencies = [ + ('CMake', '2.8.12'), + ('libxml2', '2.9.3') +] + +dependencies = [('Boost', '1.53.0')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid-dp.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid-dp.eb new file mode 100644 index 0000000000000000000000000000000000000000..e85182e185cfee1d3320dd3cbad7d468c23af9b9 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.1.2-intel-2016a-hybrid-dp.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg / 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 5.1.2 +# Author: Adam Huffman +# The Francis Crick Institute +## + +name = 'GROMACS' +version = '5.1.2' +versionsuffix = '-hybrid-dp' + +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': 'intel', 'version': '2016a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.5.2'), + ('libxml2', '2.9.3') +] + +dependencies = [('Boost', '1.60.0')] + +double_precision = True + +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-CrayGNU-2015.11.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-CrayGNU-2015.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..378ea5f63e4b90d37463e1638d2f31f3bd42c885 --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-CrayGNU-2015.11.eb @@ -0,0 +1,24 @@ +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 = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths={ + 'files': ['lib/libgsl.so', 'lib/libgsl.a'], + 'dirs': ['include'], +} + +moduleclass = 'numlib' 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-2.1-intel-2016b.eb b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..5018bf16a60f8a8c6436fbe89723847500cb1eee --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.1-intel-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 = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/g/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-1.6.4-foss-2016a.eb b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6d1390515a07aec8efaebd5658224d96f885b2cf --- /dev/null +++ b/easybuild/easyconfigs/g/GST-plugins-base/GST-plugins-base-1.6.4-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'GST-plugins-base' +version = '1.6.4' + +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', '1.6.4')] + +builddependencies = [ + ('Bison', '3.0.4', '', True), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['discoverer', 'play']] + + ['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/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-1.6.4-foss-2016a.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..05dfd4ddef23d01518146e3cd8b0b7622d7973d9 --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.6.4-foss-2016a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'GStreamer' +version = '1.6.4' + +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', '', True), +] + +sanity_check_paths = { + 'files': ['bin/gst-%s-1.0' % x for x in ['inspect', 'typefind', 'launch']] + + ['lib/libgst%s-1.0.%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/GTS/GTS-0.7.6-intel-2016b.eb b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..53f710cecee47179cc8c87293f2e693286a9f3c3 --- /dev/null +++ b/easybuild/easyconfigs/g/GTS/GTS-0.7.6-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GTS' +version = '0.7.6' + +homepage = 'http://gts.sourceforge.net/' +description = """GTS stands for the GNU Triangulated Surface Library. + It is an Open Source Free Software Library intended to provide a set of useful + functions to deal with 3D surfaces meshed with interconnected triangles.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('GLib', '2.49.5'), +] + +sanity_check_paths = { + 'files': ['lib/libgts.%s' % SHLIB_EXT, 'bin/gts2oogl', 'bin/gtscheck'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/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/Geant4/Geant4-10.01.p01-intel-2015a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb index 468e4e32f471c29166b7c10b44110996d3ddbde1..4bde20b26061ad1e977d088bbfaf1d24f5fd1c96 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '3.2.2')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p03-intel-2016a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p03-intel-2016a.eb index f30dcb1a76ada8386470ee7c3ce829bcdef09fc3..60a8b5c5407b98d0757df863e598fcb6572eaf63 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p03-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p03-intel-2016a.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '3.4.3')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-10.02.p01-intel-2016a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.02.p01-intel-2016a.eb index 300557f7e0dc8f56feddd1af5f9ad742244d0c20..9f9a3a4002cda0ba837dd004bb71173968ecc8d1 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-10.02.p01-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.02.p01-intel-2016a.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '3.4.3')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goolf-1.4.10.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goolf-1.4.10.eb index 59a0ae794e5047217f700e55b63a2da7699afabf..a91fcca1a09fb2455a4ffa93547f0223929744ee 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-goolf-1.4.10.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '2.8.4')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-5.3.0.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-5.3.0.eb index ec559378298f63be5e0ccc20dde61140947ea78a..73e7a955586fb1eceb9bc78830fb227406bcaa53 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-ictce-5.3.0.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '2.8.4')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2015a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2015a.eb index 5a4e622db868fad18144f63ed37b82f00458cac8..fa0df53df2078cf49721591f4f91a7685e6984b2 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2015a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p01-intel-2015a.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '2.8.4')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p02-intel-2016a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p02-intel-2016a.eb index b790b2a3f8cc7ed3325fe488c0ceb459e50382ba..cfa9e5761c52495ebde37a74dc7bbe21a736176b 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p02-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.5.p02-intel-2016a.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '3.4.3')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2015a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2015a.eb index e8b5782036b6729d8a3c6e58707fcbc3e1ebcf78..f342971a264a92a5b75c6caa528c37a1774b1a69 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2015a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2015a.eb @@ -20,6 +20,6 @@ dependencies = [ builddependencies = [('CMake', '3.1.3')] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb index 554b9825d7df496a231e8e60385c5459d355f22f..ca80a8a174baf00fb7c990a4ce2b888bd8e23d7e 100644 --- a/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Geant4/Geant4-9.6.p04-intel-2016a.eb @@ -21,6 +21,6 @@ builddependencies = [ ] configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" -configopts += "-DGEANT4_INSTALL_DATA=OFF" +configopts += " -DGEANT4_INSTALL_DATA=OFF" moduleclass = 'phys' 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/gnutls/gnutls-3.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.1.8-goolf-1.4.10.eb similarity index 91% rename from easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb rename to easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.1.8-goolf-1.4.10.eb index f7c7021f17c8dbd48a4fa1c34d2d9ff6d9d3de1f..80b639f6e354f9faec6c75790063b782511e621b 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.1.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.1.8-goolf-1.4.10.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'gnutls' +name = 'GnuTLS' version = '3.1.8' homepage = 'http://www.gnutls.org/' @@ -8,12 +8,12 @@ description = "gnutls-3.0.22: GNU Transport Layer Security library" toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = ['ftp://ftp.gnutls.org/pub/gnutls/'] -sources = [SOURCE_TAR_XZ] +sources = [SOURCELOWER_TAR_XZ] dependencies = [ ('GMP', '5.0.5'), ('nettle', '2.6'), - ('guile', '1.8.8'), + ('Guile', '1.8.8'), ] configopts = "--with-guile-site-dir=$EBROOTGUILE" diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.3.21-intel-2016a.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.3.21-intel-2016a.eb similarity index 95% rename from easybuild/easyconfigs/g/gnutls/gnutls-3.3.21-intel-2016a.eb rename to easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.3.21-intel-2016a.eb index 62fd6a4ca6ee045b24bfda22d479a3cd6d036908..dcf1712871080bd2bba6fbfbadbc11ccafdb58a6 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.3.21-intel-2016a.eb +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.3.21-intel-2016a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'gnutls' +name = 'GnuTLS' version = '3.3.21' homepage = 'http://www.gnutls.org/' @@ -14,14 +14,14 @@ description = """GnuTLS is a secure communications library implementing the SSL, toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['ftp://ftp.gnutls.org/gcrypt/gnutls/v%(version_major_minor)s'] -sources = [SOURCE_TAR_XZ] +sources = [SOURCELOWER_TAR_XZ] guilever = '1.8.8' guileshortver = '.'.join(guilever.split('.')[:2]) dependencies = [ ('GMP', '6.1.0'), ('nettle', '3.1.1'), - ('guile', guilever), + ('Guile', guilever), ('libtasn1', '4.7'), ('libidn', '1.32'), ('p11-kit', '0.23.2'), diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.4.11-foss-2016a.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.4.11-foss-2016a.eb similarity index 95% rename from easybuild/easyconfigs/g/gnutls/gnutls-3.4.11-foss-2016a.eb rename to easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.4.11-foss-2016a.eb index fbf5215dd85dac343dcf3b29bea87c86122734b1..b1ec96f981e9b27f2d0f4d01f6b22d1f46953421 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.4.11-foss-2016a.eb +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.4.11-foss-2016a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'gnutls' +name = 'GnuTLS' version = '3.4.11' homepage = 'http://www.gnutls.org/' @@ -14,14 +14,14 @@ description = """GnuTLS is a secure communications library implementing the SSL, toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['ftp://ftp.gnutls.org/gcrypt/gnutls/v%(version_major_minor)s'] -sources = [SOURCE_TAR_XZ] +sources = [SOURCELOWER_TAR_XZ] guilever = '1.8.8' guileshortver = '.'.join(guilever.split('.')[:2]) dependencies = [ ('GMP', '6.1.0'), ('nettle', '3.1.1'), - ('guile', guilever), + ('Guile', guilever), ('libtasn1', '4.7'), ('libidn', '1.32'), ('p11-kit', '0.23.2'), diff --git a/easybuild/easyconfigs/g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.4.7-GNU-4.9.3-2.25.eb similarity index 95% rename from easybuild/easyconfigs/g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb rename to easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.4.7-GNU-4.9.3-2.25.eb index d883037773378e2bb3bb4587b6e5cebf29b0cf34..89d42e526683a041728eea0f7bbc6e019323f4c0 100644 --- a/easybuild/easyconfigs/g/gnutls/gnutls-3.4.7-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.4.7-GNU-4.9.3-2.25.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'gnutls' +name = 'GnuTLS' version = '3.4.7' homepage = 'http://www.gnutls.org/' @@ -14,14 +14,14 @@ description = """GnuTLS is a secure communications library implementing the SSL, toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} source_urls = ['ftp://ftp.gnutls.org/gcrypt/gnutls/v%(version_major_minor)s'] -sources = [SOURCE_TAR_XZ] +sources = [SOURCELOWER_TAR_XZ] guilever = '1.8.8' guileshortver = '.'.join(guilever.split('.')[:2]) dependencies = [ ('GMP', '6.0.0a'), ('nettle', '3.1.1'), - ('guile', guilever), + ('Guile', guilever), ('libtasn1', '4.7'), ('libidn', '1.32'), ('p11-kit', '0.23.2'), 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/Greenlet/Greenlet-0.4.11-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.11-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..93d3caf46d5ffb7579fae40021fa45db498bbbfe --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.11-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'Greenlet' +version = '0.4.11' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/python-greenlet/greenlet' +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_ZIP] + +patches = ['Greenlet-0.4.2_icc_no_amd64_predefined_in_prepocessor.patch'] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': ['include/python%(pyshortver)s/greenlet/greenlet.h', + 'lib/python%(pyshortver)s/site-packages/greenlet.so'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GNU-4.9.3-2.25.eb similarity index 98% rename from easybuild/easyconfigs/g/guile/guile-1.8.8-GNU-4.9.3-2.25.eb rename to easybuild/easyconfigs/g/Guile/Guile-1.8.8-GNU-4.9.3-2.25.eb index 65946ec224e68fda099e06b38735290f6b2ba104..d2f316742ea045e92bd2c82dcf0099cad924686b 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-GNU-4.9.3-2.25.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'guile' +name = 'Guile' version = '1.8.8' homepage = 'http://www.gnu.org/software/guile' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2015b.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2015b.eb similarity index 98% rename from easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2015b.eb rename to easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2015b.eb index 8e2c6a3db096ee7443693005d5851547afd0c7f3..26c0164e83ae987d194f79a15d782ae99b28706f 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2015b.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2015b.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'guile' +name = 'Guile' version = '1.8.8' homepage = 'http://www.gnu.org/software/guile' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2016a.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2016a.eb similarity index 98% rename from easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2016a.eb rename to easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2016a.eb index 132fe56abfc7e866b853a4eaec1542c5df9c9117..becfe06582f74693d89187d686bff8631b140879 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-foss-2016a.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-foss-2016a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'guile' +name = 'Guile' version = '1.8.8' homepage = 'http://www.gnu.org/software/guile' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-goolf-1.4.10.eb similarity index 98% rename from easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb rename to easybuild/easyconfigs/g/Guile/Guile-1.8.8-goolf-1.4.10.eb index 1ff3a6fc786dc4a56adb72b583124c5613f6aabd..d9813aabe25a4b94197034110662ba566f8fcd13 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-goolf-1.4.10.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'guile' +name = 'Guile' version = '1.8.8' homepage = 'http://www.gnu.org/software/guile' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-ictce-5.3.0.eb similarity index 98% rename from easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb rename to easybuild/easyconfigs/g/Guile/Guile-1.8.8-ictce-5.3.0.eb index 0ed91b303989983b225ddc1d5c671b51bf1fd813..e72e93b14b8bec4f1aff1d6e34957f4d70b0e362 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-ictce-5.3.0.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'guile' +name = 'Guile' version = '1.8.8' homepage = 'http://www.gnu.org/software/guile' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2015a.eb similarity index 98% rename from easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb rename to easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2015a.eb index d10a3259ca1441faf4d7906c0ba5534603b4aa5d..4e4bf543c3dc662cebd011924d2303c7e62ee223 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2015a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'guile' +name = 'Guile' version = '1.8.8' homepage = 'http://www.gnu.org/software/guile' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015b.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2015b.eb similarity index 98% rename from easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015b.eb rename to easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2015b.eb index ecd844f29d41cf698f839d10eb9ab1232ddfb307..cd7c24301f88089bb13387fc148133d6cfca6d52 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015b.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2015b.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'guile' +name = 'Guile' version = '1.8.8' homepage = 'http://www.gnu.org/software/guile' diff --git a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2016a.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2016a.eb similarity index 98% rename from easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2016a.eb rename to easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2016a.eb index a7e7520df8fa003f7293267e94b661f649002ec6..a7b2c1f8edec0f0746651bee1c85156212b989c1 100644 --- a/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2016a.eb +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2016a.eb @@ -1,6 +1,6 @@ easyblock = 'ConfigureMake' -name = 'guile' +name = 'Guile' version = '1.8.8' homepage = 'http://www.gnu.org/software/guile' diff --git a/easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2016b.eb b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..1be1335f08ba4f6c9d72d889df136f98d6420401 --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-1.8.8-intel-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '1.8.8' + +homepage = 'http://www.gnu.org/software/guile' +description = """Guile is the GNU Ubiquitous Intelligent Language for Extensions, + the official extension language for the GNU operating system.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libtool', '2.4.6'), + ('GMP', '6.1.1'), + ('libunistring', '0.9.6'), + ('pkg-config', '0.29.1'), + ('libffi', '3.2.1'), + ('libreadline', '6.3'), +] + +configopts = " --enable-error-on-warning=no" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["guile", 'guile-config', 'guile-snarf', 'guile-tools']] + + ["lib/libguile.a", "include/libguile.h"], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/Guile/Guile-2.0.11-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/g/Guile/Guile-2.0.11-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..8c1960a3c8ffd7826305846e42a5b8f1d50d1acb --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-2.0.11-GCC-4.9.3-2.25.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '2.0.11' + +homepage = 'https://www.gnu.org/software/guile/' +description = """Guile is a programming language, designed to help programmers create flexible applications that + can be extended by users or other programmers with plug-ins, modules, or scripts.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('Autotools', '20150215')] +dependencies = [ + ('libunistring', '0.9.3'), + ('libffi', '3.2.1'), + ('gc', '7.4.4'), + ('GMP', '6.1.0'), +] + +sanity_check_paths = { + 'files': ['bin/guild', 'bin/guile', 'bin/guile-config', 'bin/guile-snarf', 'bin/guile-tools', + 'include/guile/%(version_major_minor)s/libguile.h', + 'lib/libguile-%(version_major_minor)s.a', 'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/guile/%(version_major_minor)s/libguile', 'lib/guile/%(version_major_minor)s/ccache'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/Guile/Guile-2.0.11-foss-2016a.eb b/easybuild/easyconfigs/g/Guile/Guile-2.0.11-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..94a0abd7af544a02bc574eb0dd7822573baf1684 --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-2.0.11-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '2.0.11' + +homepage = 'https://www.gnu.org/software/guile/' +description = """Guile is a programming language, designed to help programmers create flexible applications that + can be extended by users or other programmers with plug-ins, modules, or scripts.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('Autotools', '20150215')] +dependencies = [ + ('libunistring', '0.9.3'), + ('libffi', '3.2.1'), + ('gc', '7.4.4'), + ('GMP', '6.1.0'), +] + +sanity_check_paths = { + 'files': ['bin/guild', 'bin/guile', 'bin/guile-config', 'bin/guile-snarf', 'bin/guile-tools', + 'include/guile/%(version_major_minor)s/libguile.h', + 'lib/libguile-%(version_major_minor)s.a', 'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/guile/%(version_major_minor)s/libguile', 'lib/guile/%(version_major_minor)s/ccache'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..b39d4408171f96a0b2e86fcb9f229dc6c322c9f0 --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-6.5.1.eb @@ -0,0 +1,18 @@ +name = 'Gurobi' +version = '6.5.1' + +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/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/gc/gc-7.4.4-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/g/gc/gc-7.4.4-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..9c888969f86166b68366ff3d1327ad12f0b699d8 --- /dev/null +++ b/easybuild/easyconfigs/g/gc/gc-7.4.4-GCC-4.9.3-2.25.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'gc' +version = '7.4.4' + +homepage = 'http://hboehm.info/gc/' +description = """The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting + replacement for C malloc or C++ new.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +source_urls = [ + 'http://hboehm.info/gc/gc_source/', + 'https://github.com/ivmai/libatomic_ops/archive/', +] +sources = [ + SOURCE_TAR_GZ, + 'libatomic_ops-7_4_4.tar.gz', +] + +preconfigopts = "ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && " + +sanity_check_paths = { + 'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT, 'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT], + 'dirs': ['include/gc', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gc/gc-7.4.4-foss-2016a.eb b/easybuild/easyconfigs/g/gc/gc-7.4.4-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c12a61e57dee052e029b2371dc813333b13ad8c3 --- /dev/null +++ b/easybuild/easyconfigs/g/gc/gc-7.4.4-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'gc' +version = '7.4.4' + +homepage = 'http://hboehm.info/gc/' +description = """The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting + replacement for C malloc or C++ new.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [ + 'http://hboehm.info/gc/gc_source/', + 'https://github.com/ivmai/libatomic_ops/archive/', +] +sources = [ + SOURCE_TAR_GZ, + 'libatomic_ops-7_4_4.tar.gz', +] + +preconfigopts = "ln -s %(builddir)s/libatomic_ops*/ libatomic_ops && " + +sanity_check_paths = { + 'files': ['include/gc.h', 'lib/libcord.a', 'lib/libcord.%s' % SHLIB_EXT, 'lib/libgc.a', 'lib/libgc.%s' % SHLIB_EXT], + 'dirs': ['include/gc', 'share'], +} + +moduleclass = 'lib' 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/gdc-client/gdc-client-1.0.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.0.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..8bbf7589b7cdedb3bc6bf68999e63485bac2e150 --- /dev/null +++ b/easybuild/easyconfigs/g/gdc-client/gdc-client-1.0.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,57 @@ +easyblock = 'Bundle' + +name = 'gdc-client' +version = '1.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool' +description = """The gdc-client provides several convenience functions over the GDC API which provides general + download/upload via HTTPS.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.12'), + ('libxslt', '1.1.29'), + ('libyaml', '0.1.6'), +] + +exts_list = [ + ('setuptools', '19.2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('parcel', '20160602', { + 'source_urls': ['https://github.com/LabAdvComp/parcel/archive'], + 'source_tmpl': 'd3b619584606ed5d2f127f9ba12df7b764ebe975.tar.gz', + }), + ('lxml', '3.5.0b1', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lxml/'], + }), + ('PyYAML', '3.11', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PyYAML'], + 'modulename': 'yaml', + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + (name, version, { + 'source_urls': ['https://github.com/NCI-GDC/gdc-client/archive'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'modulename': 'gdc_client', + }), +] + +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': ['bin/gdc-client'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' 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-GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..8e1b03ad2a1a31dd1f68eecf691a1562e36b520e --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-GCCcore-4.9.3.eb @@ -0,0 +1,27 @@ +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': 'GCCcore', 'version': '4.9.3'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('binutils', '2.25'), +] + +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-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=$EBROOTLIBXML2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..91c8cacd60b8189ac10043664b35c5137601c5ac --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-foss-2016b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.8' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libxml2', '2.9.4'), + ('ncurses', '6.0'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.8-intel-2016b.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..6df1b22caa7b36e881f6f692bac1571f6f8b0c35 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.8-intel-2016b.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': 'intel', 'version': '2016b'} + +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/gflags/gflags-2.1.2-foss-2016a.eb b/easybuild/easyconfigs/g/gflags/gflags-2.1.2-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9a10acf8809ca45473cfe9b2224b29129ee36936 --- /dev/null +++ b/easybuild/easyconfigs/g/gflags/gflags-2.1.2-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'gflags' +version = '2.1.2' + +homepage = 'https://github.com/gflags/gflags' +description = """ +The gflags package contains a C++ library that implements commandline flags +processing. It includes built-in support for standard types such as string +and the ability to define flags in the source file in which they are used. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/gflags/gflags/archive/'] + +builddependencies = [ + ('CMake', '3.4.3'), +] + +configopts = '-DBUILD_SHARED_LIBS=on -DBUILD_STATIC_LIBS=on' + +sanity_check_paths = { + 'files': ['bin/gflags_completions.sh'] + + ['lib/%s' % x for x in ['libgflags.%s' % SHLIB_EXT, + 'libgflags_nothreads.%s' % SHLIB_EXT, 'libgflags.a', 'libgflags_nothreads.a']] + + ['include/gflags/gflags_completions.h'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glog/glog-0.3.4-foss-2016a.eb b/easybuild/easyconfigs/g/glog/glog-0.3.4-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..96493182e0f3f7e582b988f79d93bce2a74973fb --- /dev/null +++ b/easybuild/easyconfigs/g/glog/glog-0.3.4-foss-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'glog' +version = '0.3.4' + +homepage = 'https://github.com/google/glog' +description = """ +A C++ implementation of the Google logging module. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/google/glog/archive/'] + +sanity_check_paths = { + 'files': ['include/glog/logging.h', 'include/glog/raw_logging.h', 'lib/libglog.a', 'lib/libglog.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb index 850097aee1cedf775e7ba47d48f34a9ae066bbc2..44b64988419a4d275416c84d3b33936d60abdbe1 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-foss-2016a.eb @@ -7,11 +7,12 @@ homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = "X protocol and ancillary headers" toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] +builddependencies = [('xorg-macros', '1.19.0')] + sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], 'dirs': [], diff --git a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb index 5dd250fddb83cb74bdcd9c77717b510b4121f241..ce4d4d9aa43e17832c70aed8209192c46a8990d4 100644 --- a/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb +++ b/easybuild/easyconfigs/g/glproto/glproto-1.4.17-intel-2016a.eb @@ -7,11 +7,12 @@ homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = "X protocol and ancillary headers" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] +builddependencies = [('xorg-macros', '1.19.0')] + sanity_check_paths = { 'files': ['include/GL/%s.h' % x for x in ['glxint', 'glxmd', 'glxproto', 'glxtokens', 'internal/glcore']], 'dirs': [], 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-2016.06.eb b/easybuild/easyconfigs/g/gompi/gompi-2016.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..c1a2b47b81b261ce442a2cc87cf2c539a5c03d90 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2016.06.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2016.06' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '5.4.0-2.26' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver), # includes both GCC 5.4.0 and binutils 2.26 + ('OpenMPI', '1.10.3', '', ('GCC', gccver)), +] + +moduleclass = 'toolchain' 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/gompi/gompi-2016b.eb b/easybuild/easyconfigs/g/gompi/gompi-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..1a6033a5a733b9920a87d26a114f76d34f14aa3e --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2016b.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2016b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '5.4.0-2.26' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver), # includes both GCC 5.4.0 and binutils 2.26 + ('OpenMPI', '1.10.3', '', ('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-GCCcore-4.9.3.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..b01284c10608f12903a188ce89ca29e873b0a83b --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-GCCcore-4.9.3.eb @@ -0,0 +1,26 @@ +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': 'GCCcore', 'version': '4.9.3'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.25'), +] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' 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/gputools/gputools-0.28-ictce-5.3.0-e5cb024-R-3.0.2.eb b/easybuild/easyconfigs/g/gputools/gputools-0.28-ictce-5.3.0-e5cb024-R-3.0.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..d0c568100e5c022ba25a7f71444460ac5c7ccdf6 --- /dev/null +++ b/easybuild/easyconfigs/g/gputools/gputools-0.28-ictce-5.3.0-e5cb024-R-3.0.2.eb @@ -0,0 +1,28 @@ +easyblock = 'RPackage' + +name = 'gputools' +version = '0.28' +commit = 'e5cb024' +versionsuffix = '-%s-R-%%(rver)s' % commit + +homepage = 'https://github.com/nullsatz/gputools/wiki' +description = """This package provides R interfaces to a handful of common functions implemented + using the Nvidia CUDA toolkit. Some of the functions require at least GPU Compute Capability 1.3.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = ['https://github.com/nullsatz/gputools/archive'] +sources = ['%s.tar.gz' % commit] +checksums = ['daf006aa7892f641b22f545a1bb3cddb'] + +dependencies = [ + ('CUDA', '5.0.35', '-1', True), + ('R', '3.0.2'), +] + +sanity_check_paths = { + 'files': ["gputools/libs/gputools.so"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2016a.eb b/easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..674925f1b9997b83f0acef4e2c882b13fcd02e37 --- /dev/null +++ b/easybuild/easyconfigs/g/grace/grace-5.1.25-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'grace' +version = '5.1.25' + +homepage = 'http://freecode.com/projects/grace' +description = """Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif.""" + +source_urls = ['ftp://plasma-gate.weizmann.ac.il/pub/grace/src/stable'] +sources = [SOURCE_TAR_GZ] + +toolchain = {'name': 'foss', 'version': '2016a'} + +dependencies = [ + ('motif', '2.3.5'), + ('netCDF', '4.4.0'), +] + +runtest = 'tests' + +# we also need to run make links right before or after make install. +installopts = 'links' + +sanity_check_paths = { + 'files': ['bin/xmgrace'], + 'dirs': [], +} + +moduleclass = 'vis' 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/g/grib_api/grib_api-1.16.0-intel-2016a.eb b/easybuild/easyconfigs/g/grib_api/grib_api-1.16.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..24a8b1b236befafd0395db4172e05470846b1d44 --- /dev/null +++ b/easybuild/easyconfigs/g/grib_api/grib_api-1.16.0-intel-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'grib_api' +version = '1.16.0' + +homepage = 'https://software.ecmwf.int/wiki/display/GRIB/Home' +description = """The ECMWF GRIB API is an application program interface accessible from C, FORTRAN and Python + programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages. A useful set of + command line tools is also provided to give quick access to GRIB messages.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://software.ecmwf.int/wiki/download/attachments/3473437/'] +sources = ['grib_api-%(version)s-Source.tar.gz'] + +dependencies = [ + ('JasPer', '1.900.1'), +] + +configopts = '--with-jasper=$EBROOTJASPER' + +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..3ebc1003fc1fcd76ba7bd99add4536cac3b5e5c4 --- /dev/null +++ b/easybuild/easyconfigs/g/gtest/gtest-1.7.0-CrayGNU-2015.11.eb @@ -0,0 +1,19 @@ +easyblock = "Tarball" + +name = 'gtest' +version = '1.7.0' + +homepage = 'https://code.google.com/p/googletest/' +description = "Google's framework for writing C++ tests on a variety of platforms" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +sources = [SOURCE_ZIP] +source_urls = ['https://googletest.googlecode.com/files'] + +sanity_check_paths={ + 'files': ['CMakeLists.txt', ], + 'dirs': ['include', 'src'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/H5hut/H5hut-1.99.13-intel-2016b.eb b/easybuild/easyconfigs/h/H5hut/H5hut-1.99.13-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..1e6c268f5f543c3b9ade6b0534c179df82765a03 --- /dev/null +++ b/easybuild/easyconfigs/h/H5hut/H5hut-1.99.13-intel-2016b.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'H5hut' +version = '1.99.13' + +homepage = 'https://amas.psi.ch/H5hut/' +description = "HDF5 Utility Toolkit: High-Performance I/O Library for Particle-based Simulations" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://amas.psi.ch/H5hut/raw-attachment/wiki/DownloadSources/'] +sources = [SOURCE_TAR_GZ] +checksums = ['2a07a449afe50534de006ac6954a421a'] + +builddependencies = [ + ('Autotools', '20150215'), +] +dependencies = [ + # HDF5 v1.8.12 required because of API changes in v1.8.13 that this version of H5hut does not take into account + ('HDF5', '1.8.12'), +] + +configopts = "--enable-parallel --enable-fortran --with-hdf5=$EBROOTHDF5" + +# building in parallel tends to fail +parallel = 1 + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libH5hut.a', 'lib/libH5hutF.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/HAPGEN2/HAPGEN2-2.2.0.eb b/easybuild/easyconfigs/h/HAPGEN2/HAPGEN2-2.2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..9874a034c685570f1e8650de87afceab97e6ccf5 --- /dev/null +++ b/easybuild/easyconfigs/h/HAPGEN2/HAPGEN2-2.2.0.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 = 'HAPGEN2' +version = '2.2.0' + +homepage = 'https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html' +description = """'HAPGEN2' simulates case control datasets at SNP markers.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/download/builds/x86_64/v%(version)s/'] +sources = ['hapgen2_x86_64.tar.gz'] + +modextrapaths = {'PATH': ''} + +checksums = ['8d26727f37eabb09e45f702d4f3ed3cb'] + +sanity_check_paths = { + 'files': ["hapgen2", "LICENCE"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.11-foss-2015a.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4cc114e9725cde80d557d3c61fb3f98e32c6500c --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.11-foss-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.11' + +homepage = 'http://www.hdfgroup.org/products/hdf4/' +description = """HDF4 (also known as HDF) is a library and multi-object file +format for storing and managing data between machines.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'opt': True, 'pic': True} + +dependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), + ('Szip', '2.1'), + ('JasPer', '1.900.1'), +] + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src'] + + +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" + +sanity_check_paths = { + 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['bin', 'include/hdf'], +} + + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-foss-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..55975c97d5d6eb69d722f95fb9cba6909c8fb8b3 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-foss-2016b.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.10.0-patch1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9180ff0ef8dc2ef3f61bd37a7404f295'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..8eddf5504b701316f1ed1c0bc9e212c06bdf961f --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2016b.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.10.0-patch1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9180ff0ef8dc2ef3f61bd37a7404f295'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017.01.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017.01.eb new file mode 100644 index 0000000000000000000000000000000000000000..5cf3a3e7f5ab0fcc3442db85a32989eb24b38895 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.0-patch1-intel-2017.01.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.10.0-patch1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2017.01'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9180ff0ef8dc2ef3f61bd37a7404f295'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-intel-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..da7a64fcf9321ea2a758c27c1acf2e4df9190ae5 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.12-intel-2016b.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.12' + +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': True} + +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="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-gimkl-2.11.5-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-gimkl-2.11.5-serial.eb new file mode 100644 index 0000000000000000000000000000000000000000..3f80a99e7110b9291a808ba648c1bfdd381b435a --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-gimkl-2.11.5-serial.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.8.16' +versionsuffix = '-serial' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'gimkl', 'version': '2.11.5'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..d61bff1fffd789c7cdb00cb0c96015e70d27258f --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.16-iomkl-2016.07.eb @@ -0,0 +1,23 @@ +name = 'HDF5' +version = '1.8.16' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'iomkl', 'version': '2016.07'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +buildopts = 'CXXFLAGS="$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="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a-serial.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a-serial.eb new file mode 100644 index 0000000000000000000000000000000000000000..1cc3adf6f76998497e96e6998282bdea49ecd0e6 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a-serial.eb @@ -0,0 +1,22 @@ +name = 'HDF5' +version = '1.8.17' +versionsuffix = '-serial' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': False} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..359ef33d9bc499e99119cc08de9f4afc32bdfabd --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016a.eb @@ -0,0 +1,25 @@ +name = 'HDF5' +version = '1.8.17' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$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-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..5063dd3bc673ac638a76661fb9dd1ae72cab0eb1 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-foss-2016b.eb @@ -0,0 +1,25 @@ +name = 'HDF5' +version = '1.8.17' + +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': '2016b'} +toolchainopts = {'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="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7ab0f77fbacea4cbe12453b5d29c76f22451a586 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016a.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.17' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5-1.8.15_configure_intel.patch', + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/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="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..d67a77ebd21b4147bef1bcdede36e319fd20daea --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.17-intel-2016b.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.17' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5-1.8.15_configure_intel.patch', + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e6c0e7eab7c9710f7788bda951aa694fe9f6884f --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-foss-2016b.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.18' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [ + 'https://support.hdfgroup.org/ftp/HDF5/current18/src/', + 'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(versions)/src/' +] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd2148b740713ca0295442ec683d7b1c'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2016b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..d1efd2d906ef87afe0a3ad7393e5a1c98eab335b --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2016b.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.18' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [ + 'https://support.hdfgroup.org/ftp/HDF5/current18/src/', + 'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(versions)/src/' +] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd2148b740713ca0295442ec683d7b1c'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017.01.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017.01.eb new file mode 100644 index 0000000000000000000000000000000000000000..2b7452c39b768efdeb380bda5470256320125edc --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.18-intel-2017.01.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.18' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'intel', 'version': '2017.01'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [ + 'https://support.hdfgroup.org/ftp/HDF5/current18/src/', + 'https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(versions)/src/' +] + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd2148b740713ca0295442ec683d7b1c'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb b/easybuild/easyconfigs/h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..597c5e6d4283e72892c6e2e1b02365726b390ff2 --- /dev/null +++ b/easybuild/easyconfigs/h/HEALPix/HEALPix-2.20a-ictce-5.5.0.eb @@ -0,0 +1,15 @@ +name = 'HEALPix' +version = '2.20a' + +homepage = 'http://healpix.sourceforge.net/' +description = """Hierarchical Equal Area isoLatitude Pixelation of a sphere.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['Healpix_%(version)s_2011Feb09.tar.gz'] + +dependencies = [('CFITSIO', '3.350')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.4-foss-2016b.eb b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.4-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..83a592d05a588218c56f54e2d151527b802378d5 --- /dev/null +++ b/easybuild/easyconfigs/h/HISAT2/HISAT2-2.0.4-foss-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'MakeCp' + +name = 'HISAT2' +version = '2.0.4' + +homepage = 'https://ccb.jhu.edu/software/hisat2/index.shtml' +description = """HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads + (both DNA and RNA) against the general human population (as well as against a single reference genome).""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['%(namelower)s-%(version)s-source.zip'] +source_urls = ['ftp://ftp.ccb.jhu.edu/pub/infphilo/%(namelower)s/downloads/'] + +checksums = ['50119a693929e240b072d79e69dc211e'] + +dependencies = [ + ('NGS', '1.2.5'), + ('ncbi-vdb', '2.7.0'), +] + +buildopts = "USE_SRA=1 NCBI_NGS_DIR=$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/HMMER/HMMER-3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.0-goolf-1.4.10.eb index ac2ff916ef27a8d5fe2d372342bcccd7035baabc..ee8ba6219525463e65eaaac14e170c12c1d224e2 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.0-goolf-1.4.10.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'HMMER' version = '3.0' -homepage = 'http://hmmer.janelia.org/' +homepage = 'http://hmmer.org/' description = """HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other @@ -26,10 +26,8 @@ description = """HMMER is used for searching sequence databases for homologs of essentially as fast as BLAST.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -# eg. http://selab.janelia.org/software/hmmer3/3.0/hmmer-3.0-linux-intel-x86_64.tar.gz -versiondir = "hmmer%s" % ".".join(version.split('.')[:-1]) -sources = ['hmmer-%s-linux-intel-x86_64.tar.gz' % version] -source_urls = ['http://selab.janelia.org/software/%s/%s/' % (versiondir, version)] +source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] +sources = ['hmmer-%(version)s-linux-intel-x86_64.tar.gz'] sanity_check_paths = { 'files': ["bin/hmmemit", "bin/hmmsearch", "bin/hmmscan"], diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-5.3.0.eb index 52d15716803d368ab966c8e6b09891388fe31ef7..ee8eae3fa74e63e4a51bf096a4363f2cd2ece70f 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.0-ictce-5.3.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'HMMER' version = '3.0' -homepage = 'http://hmmer.janelia.org/' +homepage = 'http://hmmer.org/' description = """HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other @@ -28,10 +28,8 @@ description = """HMMER is used for searching sequence databases for homologs of toolchain = {'name': 'ictce', 'version': '5.3.0'} -# eg. http://selab.janelia.org/software/hmmer3/3.0/hmmer-3.0-linux-intel-x86_64.tar.gz -versiondir = "hmmer%s" % ".".join(version.split('.')[:-1]) -sources = ['hmmer-%s-linux-intel-x86_64.tar.gz' % version] -source_urls = ['http://selab.janelia.org/software/%s/%s/' % (versiondir, version)] +source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] +sources = ['hmmer-%(version)s-linux-intel-x86_64.tar.gz'] sanity_check_paths = { 'files': ["bin/hmmemit", "bin/hmmsearch", "bin/hmmscan"], diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-goolf-1.4.10.eb index 7b6ea628da41335a95395e8ce6f5349d6d4860b7..c4861d5fc598746c89329a2937505bb6ae0a134b 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-goolf-1.4.10.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'HMMER' version = '3.1b1' -homepage = 'http://hmmer.janelia.org/' +homepage = 'http://hmmer.org/' description = """HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other @@ -27,8 +27,8 @@ description = """HMMER is used for searching sequence databases for homologs of toolchain = {'name': 'goolf', 'version': '1.4.10'} +source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] sources = ['hmmer-%(version)s-linux-intel-x86_64.tar.gz'] -source_urls = ['http://selab.janelia.org/software/hmmer%(version_major)s/%(version)s/'] patches = ['hmmer-%(version)s_link-LIBS-utests.patch'] installopts = ' && cd easel && make install' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-5.3.0.eb index 65bc990310d9509ec8279b60ec1ede5e45b58278..de6a298e59614db1a83ceef298bfce564254906c 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-5.3.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'HMMER' version = '3.1b1' -homepage = 'http://hmmer.janelia.org/' +homepage = 'http://hmmer.org/' description = """HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other @@ -27,8 +27,8 @@ description = """HMMER is used for searching sequence databases for homologs of toolchain = {'name': 'ictce', 'version': '5.3.0'} +source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] sources = ['hmmer-%(version)s-linux-intel-x86_64.tar.gz'] -source_urls = ['http://selab.janelia.org/software/hmmer%(version_major)s/%(version)s/'] patches = ['hmmer-%(version)s_link-LIBS-utests.patch'] installopts = ' && cd easel && make install' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-6.2.5.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-6.2.5.eb index 9a8eaafde67a75860f1a7956ca1fdddc76d5867e..2a1f6d334f84885c75dde589aba27ed5a6a86868 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b1-ictce-6.2.5.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'HMMER' version = '3.1b1' -homepage = 'http://hmmer.janelia.org/' +homepage = 'http://hmmer.org/' description = """HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other @@ -27,8 +27,8 @@ description = """HMMER is used for searching sequence databases for homologs of toolchain = {'name': 'ictce', 'version': '6.2.5'} +source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] sources = ['hmmer-%(version)s-linux-intel-x86_64.tar.gz'] -source_urls = ['http://selab.janelia.org/software/hmmer%(version_major)s/%(version)s/'] patches = ['hmmer-%(version)s_link-LIBS-utests.patch'] installopts = ' && cd easel && make install' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb index 35be5919017ba96bc272791a9460d913f9a08a8b..0456b6d6ce73de3d5b8884605d4437d1ca9d8fe6 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-foss-2016a.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'HMMER' version = '3.1b2' -homepage = 'http://hmmer.janelia.org/' +homepage = 'http://hmmer.org/' description = """HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other @@ -27,8 +27,8 @@ description = """HMMER is used for searching sequence databases for homologs of toolchain = {'name': 'foss', 'version': '2016a'} +source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] sources = ['hmmer-%(version)s-linux-intel-x86_64.tar.gz'] -source_urls = ['http://selab.janelia.org/software/hmmer%(version_major)s/%(version)s/'] installopts = ' && cd easel && make install' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb index 36707aa8fe6a15212d908d36948a09704da18975..da1af277a57ae99f72e434ba381340650a9cfb5f 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'HMMER' version = '3.1b2' -homepage = 'http://hmmer.janelia.org/' +homepage = 'http://hmmer.org/' description = """HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other @@ -27,8 +27,8 @@ description = """HMMER is used for searching sequence databases for homologs of toolchain = {'name': 'intel', 'version': '2015a'} +source_urls = ['http://eddylab.org/software/hmmer%(version_major)s/%(version)s/'] sources = ['hmmer-%(version)s-linux-intel-x86_64.tar.gz'] -source_urls = ['http://selab.janelia.org/software/hmmer%(version_major)s/%(version)s/'] installopts = ' && cd easel && make install' 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-CrayGNU-2016.03.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..f64bec348b182077ae3001f5fb4b62469e7948e9 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.03.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': 'CrayGNU', 'version': '2016.03'} +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-2.1-CrayGNU-2016.04.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..57414cfc792fc92cea28fd419453ef5940ff7224 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.04.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': 'CrayGNU', 'version': '2016.04'} +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-2.1-CrayGNU-2016.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..b59f7317b17bb77c3fa73136961c83166c38abaa --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-2016.06.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': 'CrayGNU', 'version': '2016.06'} +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-2.1-CrayIntel-2016.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2016.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..9ab9de3734e6be345f482b6899caad7b8922ea02 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-2016.06.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': 'CrayIntel', 'version': '2016.06'} +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-2.1-foss-2016.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..e44a4ac54d1f94d5060c6251d9a82bd7f814b77f --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016.06.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': 'foss', 'version': '2016.06'} +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-2.1-foss-2016b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..5634e6bd4f5e7509ba9e568154071c1195c27ea4 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2016b.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': 'foss', 'version': '2016b'} +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-2.1-intel-2016.03-GCC-5.4.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..660c68898c6491851ec7de24000f66d3ebecb556 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016.03-GCC-5.4.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': 'intel', 'version': '2016.03-GCC-5.4'} +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-2.1-intel-2016b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..226f45477c78828844d9f938969a2395d1a7f362 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2016b.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': 'intel', 'version': '2016b'} +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-2.1-iomkl-2016.07.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..42249afb29b07367e46ba3664145aa64157146b4 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-iomkl-2016.07.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': 'iomkl', '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-2.1-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-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..40ff5797bac6c3ddecec02981d732eabb49524b7 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-foss-2016a-Python-2.7.11.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': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', 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-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/Hadoop/Hadoop-2.6.0-cdh5.8.0-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.8.0-native.eb new file mode 100644 index 0000000000000000000000000000000000000000..66a15912e54ab706f027dd29eec7d58ae5d45bb8 --- /dev/null +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.6.0-cdh5.8.0-native.eb @@ -0,0 +1,30 @@ +name = 'Hadoop' +version = '2.6.0-cdh5.8.0' +versionsuffix = '-native' + +homepage = 'http://archive.cloudera.com/cdh5/cdh/5/' +description = """Hadoop MapReduce by Cloudera""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.cloudera.com/cdh5/cdh/5/'] + +patches = ['Hadoop-TeraSort-on-local-filesystem.patch'] + +builddependencies = [ + ('Maven', '3.3.9'), + ('protobuf', '2.5.0'), # *must* be this version + ('CMake', '3.5.2'), + ('snappy', '1.1.3', '', ('GCC', '4.9.3-2.25')), +] + +dependencies = [('Java', '1.7.0_80')] + +build_native_libs = True + +extra_native_libs = [('snappy', 'lib/libsnappy.so*')] + +parallel = 1 + +moduleclass = 'tools' 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/Harminv/Harminv-1.4-foss-2016a.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..783b534519d5f33ac68f69b77528765c9a6354b8 --- /dev/null +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'Harminv' +version = '1.4' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/Harminv' +description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given + a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) + in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True, 'cstd': 'c99'} + +source_urls = ['http://ab-initio.mit.edu/harminv/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --with-blas=openblas --with-lapack=openblas --enable-shared" + +moduleclass = 'math' \ No newline at end of file diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.11.1-foss-2016a.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.11.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5f5821f26c1efd47e4c756ffa1d74681b911e31b --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.11.1-foss-2016a.eb @@ -0,0 +1,22 @@ +name = 'Hypre' +version = '2.11.1' + +homepage = "https://computation.llnl.gov/casc/linear_solvers/sls_hypre.html" +description = """Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. + The problems of interest arise in the simulation codes being developed at LLNL and elsewhere + to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://computation.llnl.gov/project/linear_solvers/download/'] +sources = [SOURCELOWER_TAR_GZ] + +start_dir = 'src' + +sanity_check_paths = { + 'files': ['lib/libHYPRE.a'], + 'dirs': ['include'] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.11.1-intel-2016a.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.11.1-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..2de6608fd997df47b43334fdc856d566899e984b --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.11.1-intel-2016a.eb @@ -0,0 +1,22 @@ +name = 'Hypre' +version = '2.11.1' + +homepage = "https://computation.llnl.gov/casc/linear_solvers/sls_hypre.html" +description = """Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. + The problems of interest arise in the simulation codes being developed at LLNL and elsewhere + to study physical phenomena in the defense, environmental, energy, and biological sciences.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://computation.llnl.gov/project/linear_solvers/download/'] +sources = [SOURCELOWER_TAR_GZ] + +start_dir = 'src' + +sanity_check_paths = { + 'files': ['lib/libHYPRE.a'], + 'dirs': ['include'] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-Python-2.7.11-parallel.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-Python-2.7.11-parallel.eb new file mode 100644 index 0000000000000000000000000000000000000000..f6c5608a09c2dcedfa351ad7ad62c907b0c98738 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-Python-2.7.11-parallel.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.5.0' +versionsuffix = '-Python-%(pyver)s-parallel' + +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': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('cray-hdf5-parallel/1.8.14', EXTERNAL_MODULE), +] + +prebuildopts = ' python setup.py configure --mpi && ' + +# sanity checks (import h5py) fails on login nodes (MPI not available) +options = {'modulename': 'os'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-Python-2.7.11-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-Python-2.7.11-serial.eb new file mode 100644 index 0000000000000000000000000000000000000000..59d61bd390919e2290cb34a07d72bd0b60af1a47 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-CrayGNU-2015.11-Python-2.7.11-serial.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '2.5.0' +versionsuffix = '-Python-%(pyver)s-serial' + +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': 'CrayGNU', 'version': '2015.11'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('cray-hdf5/1.8.13', EXTERNAL_MODULE), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s-linux-x86_64.egg'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb new file mode 100644 index 0000000000000000000000000000000000000000..5b6bd52a313b118ebdcee8008a404080568a7dee --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16-serial.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.5.0' + +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': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': False} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +hdf5ver = '1.8.16' +hdf5versuffix = '-serial' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s%s' % (hdf5ver, hdf5versuffix) + +prebuildopts = ' python setup.py configure --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.11'), + ('HDF5', hdf5ver, hdf5versuffix), +] + +builddependencies = [('pkgconfig', '1.1.0', '-Python-%(pyver)s')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16.eb new file mode 100644 index 0000000000000000000000000000000000000000..5f53eb490128ef4d60b63583332a1fa9ed4466d8 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-2.7.11-HDF5-1.8.16.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.5.0' + +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': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +hdf5ver = '1.8.16' +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=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.11'), + ('HDF5', hdf5ver), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-3.5.1-HDF5-1.8.16.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-3.5.1-HDF5-1.8.16.eb new file mode 100644 index 0000000000000000000000000000000000000000..21e131c882b137036c740102cbd74c140e5d10a0 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-3.5.1-HDF5-1.8.16.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.5.0' +hdf5ver = '1.8.16' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5ver + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['h5py-%%(version)s-foss-2016a-Python-%%(pyver)s-HDF5-%s.patch' % hdf5ver] + +dependencies = [ + ('Python', '3.5.1'), + ('HDF5', hdf5ver), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), +] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-3.5.1-HDF5-1.8.16.patch b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-3.5.1-HDF5-1.8.16.patch new file mode 100644 index 0000000000000000000000000000000000000000..4f52e53b79660c0f9a064640423c1654e56a7304 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-foss-2016a-Python-3.5.1-HDF5-1.8.16.patch @@ -0,0 +1,39 @@ +# Fix to get h5py built using Python 3.5.1 and mpi4py 2.0.0 +# Issue described at: https://github.com/h5py/h5py/issues/567 +# Patch taken from: +# https://github.com/rdhyee/h5py/commit/f2e3f132fdc1c2308b74e8428c063ac6a8118439.diff +# Fokke Dijkstra - June 21 2016 +diff --git a/h5py/h5p.pyx b/h5py/h5p.pyx +index da175dd..42fe4ed 100644 +--- a/h5py/h5p.pyx ++++ b/h5py/h5p.pyx +@@ -25,7 +25,8 @@ from h5py import _objects + from ._objects import phil, with_phil + + if MPI: +- from mpi4py.mpi_c cimport MPI_Comm, MPI_Info, MPI_Comm_dup, MPI_Info_dup, \ ++ # reverse https://github.com/h5py/h5py/commit/bdd573ff73711ccce339a91ac82a058cdd910498 ++ from mpi4py.libmpi cimport MPI_Comm, MPI_Info, MPI_Comm_dup, MPI_Info_dup, \ + MPI_Comm_free, MPI_Info_free + + # Initialization +diff --git a/setup_build.py b/setup_build.py +index bc3a8b0..6a360ec 100644 +--- a/setup_build.py ++++ b/setup_build.py +@@ -169,7 +169,16 @@ def run(self): + + # Run Cython + print("Executing cythonize()") ++ ++ # https://github.com/h5py/h5py/issues/532#issuecomment-73631137 ++ try: ++ import mpi4py ++ include_path = [mpi4py.get_include(),] ++ except: ++ include_path = [] ++ + self.extensions = cythonize(self._make_extensions(config), ++ include_path=include_path, + force=config.rebuild_required or self.force) + self.check_rerun_cythonize() diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.10.0-patch1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.10.0-patch1.eb new file mode 100644 index 0000000000000000000000000000000000000000..4c5a2d01152a6674150786e5c7b60ebeb17fda11 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.10.0-patch1.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': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +hdf5ver = '1.10.0-patch1' +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=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.12'), + ('HDF5', hdf5ver), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.8.17.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.8.17.eb new file mode 100644 index 0000000000000000000000000000000000000000..42eeacfdf55004c2c26d44da030ee3f3f77c3af1 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.8.17.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.6.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +hdf5ver = '1.8.17' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5ver + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.12'), + ('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/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.8.18.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.8.18.eb new file mode 100644 index 0000000000000000000000000000000000000000..433ac806520db8d7b8450d8d222868eecfae376d --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-2.7.12-HDF5-1.8.18.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': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +hdf5ver = '1.8.18' +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=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.12'), + ('HDF5', hdf5ver), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-3.5.2-HDF5-1.10.0-patch1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-3.5.2-HDF5-1.10.0-patch1.eb new file mode 100644 index 0000000000000000000000000000000000000000..07938a2cc233e965bc8832abfb3abb103defd3c4 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-3.5.2-HDF5-1.10.0-patch1.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.6.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +hdf5ver = '1.10.0-patch1' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5ver + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$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/h5py/h5py-2.6.0-foss-2016b-Python-3.5.2-HDF5-1.8.18.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-3.5.2-HDF5-1.8.18.eb new file mode 100644 index 0000000000000000000000000000000000000000..b9073d01d0863df6d9c5e4768cd456a88a4357b6 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-foss-2016b-Python-3.5.2-HDF5-1.8.18.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': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +hdf5ver = '1.8.18' +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=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '3.5.2'), + ('HDF5', hdf5ver), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..c1fd6e9c2f3521b73dd6b9a41f83dadcce12241a --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('HDF5', '1.8.17'), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), +] + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.10.0-patch1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.10.0-patch1.eb new file mode 100644 index 0000000000000000000000000000000000000000..ddafe208b0e7c1bf0e0f200752e844f00113808a --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.10.0-patch1.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 = '1.10.0-patch1' +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=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.12'), + ('HDF5', hdf5ver), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.8.17.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.8.17.eb new file mode 100644 index 0000000000000000000000000000000000000000..027c8b1e437015a3fc704af0deb5854e2f2ec990 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.8.17.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.6.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +hdf5ver = '1.8.17' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5ver + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.12'), + ('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/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.8.18.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.8.18.eb new file mode 100644 index 0000000000000000000000000000000000000000..1bb3147cb86e5716fafa7ec6a52e5557e5b2c65e --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-2.7.12-HDF5-1.8.18.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 = '1.8.18' +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=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '2.7.12'), + ('HDF5', hdf5ver), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.10.0-patch1.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.10.0-patch1.eb new file mode 100644 index 0000000000000000000000000000000000000000..3cae2c6786db31145a4c367169991f9706f3b7ec --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.10.0-patch1.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.6.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +hdf5ver = '1.10.0-patch1' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5ver + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$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/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=$EBROOTHDF5 && ' + +dependencies = [ + ('Python', '3.5.2'), + ('HDF5', hdf5ver), + ('pkgconfig', '1.1.0', '-Python-%(pyver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.8.18.eb b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.8.18.eb new file mode 100644 index 0000000000000000000000000000000000000000..e3874f47d4d0a67cb4265be15be6b958b05f948d --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.6.0-intel-2016b-Python-3.5.2-HDF5-1.8.18.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'h5py' +version = '2.6.0' + +homepage = 'http://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +hdf5ver = '1.8.18' +versionsuffix = '-Python-%%(pyver)s-HDF5-%s' % hdf5ver + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$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-3.1.1-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-cli.eb new file mode 100644 index 0000000000000000000000000000000000000000..3f8a48b472b4412387a3fa56efac409697f4bf4c --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-cli.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.1.1' +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-2016a-Python-2.7.11', + #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', + # specify location on shared 'scratch' filesystem for HOD working directories + #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', +} + +sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..613177ab49076d2d14c3579156d2cd37d948700f --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.1.1' +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': '2016a'} + +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', '2.7.11'), # provides netaddr, netifaces, mpi4py + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.5.1'), +] + +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-3.1.2-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-cli.eb new file mode 100644 index 0000000000000000000000000000000000000000..cb9ae643329bb3d7e33e78f1d20cded6ff461a32 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-cli.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.1.2' +versionsuffix = '-cli' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +# minimal version for interactive use: just uses system Python (netaddr/netifaces/mpi4py not required) +dependencies = [ + ('pbs_python', '4.6.0'), + ('vsc-base', '2.5.1'), +] + +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-2016a-Python-2.7.11', + #'HOD_CREATE_HOD_MODULE': 'hanythingondemand/%(version)s-intel-2016a-Python-2.7.11', + # specify location on shared 'scratch' filesystem for HOD working directories + #'HOD_BATCH_WORKDIR': '\$VSC_SCRATCH/hod', + #'HOD_CREATE_WORKDIR': '\$VSC_SCRATCH/hod', +} + +sanity_check_commands = [('hod', '--help'), ('hod', 'dists')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..d281a9b737f9325f794e9039e1ae69b9206e9b23 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/hpcugent/hanythingondemand' +description = """HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. +It uses the Torque resource manager to do node allocation.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +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', '2.7.11'), # provides netaddr, netifaces, mpi4py + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', versionsuffix + '-vsc-base-2.5.1'), +] + +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-3.1.3-cli.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-cli.eb new file mode 100644 index 0000000000000000000000000000000000000000..4846e39a8eb054ca2f45c2cc67e241b8aef40de1 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-cli.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.1.3' +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-3.1.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..1744dee95592f6461203c355c6e9006e221d0eeb --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-3.1.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'hanythingondemand' +version = '3.1.3' +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-3.1.4-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-5.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..ef0b1e1c2c957cd632fa8eea031435273fc089ba --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.2.0.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': '5.2.0'} + +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=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..0bf174a3ffce95efb791fea3cda8e82e943875f5 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-GCC-5.4.0-2.26.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-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-1.11.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..b656f492fea6a6c20aadca64a4e07040e396cf96 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-iccifort-2016.3.210-GCC-5.4.0-2.26.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-5.4.0-2.26'} + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016b.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..651e1648ba805bb3601f6a3684c363d010b73037 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.3-intel-2016b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.3' + +homepage = 'http://www.open-mpi.org/projects/hwloc/' +description = """The Portable Hardware Locality (hwloc) software package provides a portable abstraction + (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including + NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various + system attributes such as cache and memory information as well as the locality of I/O devices such as + network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering + information about modern computing hardware so as to exploit it accordingly and efficiently.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [('numactl', '2.0.11')] + +configopts = "--enable-libnuma=$EBROOTNUMACTL" + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.4-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/IGV/IGV-2.3.80-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb new file mode 100644 index 0000000000000000000000000000000000000000..444b68f2e7e024a0bc848f5d4a020a08b2e097a0 --- /dev/null +++ b/easybuild/easyconfigs/i/IGV/IGV-2.3.80-Java-1.7.0_80.eb @@ -0,0 +1,38 @@ +# 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 = 'IGV' +version = '2.3.80' + +homepage = 'http://www.broadinstitute.org/software/igv/' +description = """ The Integrative Genomics Viewer (IGV) is a high-performance visualization + tool for interactive exploration of large, integrated genomic datasets. It supports a wide + variety of data types, including array-based and next-generation sequence data, and genomic annotations. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/'] +sources = ['%(name)s_%(version)s.zip'] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +# add the installation dir to PATH +modextrapaths = { + 'PATH': '', +} + +modloadmsg = """ To execute IGV run igv.sh """ + +sanity_check_paths = { + 'files': ["igv.sh"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.75-Java-1.7.0_80.eb b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.75-Java-1.7.0_80.eb new file mode 100644 index 0000000000000000000000000000000000000000..d2575fc6ec14782d88e24ceae02f0d6f4588ffb6 --- /dev/null +++ b/easybuild/easyconfigs/i/IGVTools/IGVTools-2.3.75-Java-1.7.0_80.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 +# Modified by Adam Huffman +# The Francis Crick Institute + +easyblock = 'Tarball' + +name = 'IGVTools' +version = '2.3.75' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.broadinstitute.org/software/igv/' +description = """ This package contains command line utilities for preprocessing, + computing feature count density (coverage), sorting, and indexing data files. + See also http://www.broadinstitute.org/software/igv/igvtools_commandline. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/'] +sources = ['%(namelower)s_%(version)s.zip'] + +dependencies = [('Java', '1.7.0_80')] + +# add the installation dir to PATH +modextrapaths = { + 'PATH': '', +} + +sanity_check_paths = { + 'files': ["igvtools.jar", "igvtools"], + 'dirs': [], +} + +moduleclass = 'bio' 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 new file mode 100644 index 0000000000000000000000000000000000000000..2cca42e4db17e4f3fc75752f4d22c32041e161ea --- /dev/null +++ b/easybuild/easyconfigs/i/IMOD/IMOD-4.7.15_RHEL6-64_CUDA6.0.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# 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. 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 = [ + ('CUDA', '6.0.37'), + ('Java', '1.7.0_80'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-foss-2016a.eb b/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-foss-2016a.eb new file mode 100755 index 0000000000000000000000000000000000000000..0a6e6fc8c6b501876b9c40409c0cb0343731228a --- /dev/null +++ b/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'MakeCp' + +name = 'IMa2' +version = '8.27.12' + +homepage = 'https://bio.cst.temple.edu/~hey/software/software.htm#IMa2' +description = """IMa2 is a progam for population genetic analysis that can handle two or more populations.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://bio.cst.temple.edu/~hey/program_files/IMa2'] +sources = [SOURCELOWER_TAR_GZ] + +with_configure = True + +files_to_copy = [(['src/IMa2'], 'bin')] + +sanity_check_paths = { + 'files': ["bin/IMa2"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb b/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..54799f31a3cc27426b22acdc41f4df4c3aba0ece --- /dev/null +++ b/easybuild/easyconfigs/i/IMa2p/IMa2p-20151123-foss-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name ='IMa2p' +version = '20151123' +commit = '66e7ac7bc5e4c5bbadbd7de943465afeb4641770' + +homepage = 'https://github.com/arunsethuraman/ima2p' +description = """ +IMa2p is a parallel implementation of IMa2, using OpenMPI-C++ - a Bayesian MCMC +based method for inferring population demography under the IM (Isolation with +Migration) model. http://dx.doi.org/10.1111/1755-0998.12437 +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/arunsethuraman/ima2p/archive/'] +sources = ['%s.zip' % commit] + +# The configure script needs to be made executable +preconfigopts = 'chmod +x configure && ' +configopts = '--with-mpi=auto' + +sanity_check_paths = { + 'files': ['bin/IMa2p'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IMa2p/IMa2p-20160804-intel-2016b.eb b/easybuild/easyconfigs/i/IMa2p/IMa2p-20160804-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..28cdb8a360da0a5689161cfcdc12cdf25cc3c911 --- /dev/null +++ b/easybuild/easyconfigs/i/IMa2p/IMa2p-20160804-intel-2016b.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name ='IMa2p' +version = '20160804' +commit = '1ebe5777ed96b878cc81109bede84dc3f7bb5e3b' + +homepage = 'https://github.com/arunsethuraman/ima2p' +description = """ +IMa2p is a parallel implementation of IMa2, using OpenMPI-C++ - a Bayesian MCMC +based method for inferring population demography under the IM (Isolation with +Migration) model. http://dx.doi.org/10.1111/1755-0998.12437 +""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/arunsethuraman/ima2p/archive/'] +sources = ['%s.zip' % commit] + +# The configure script needs to be made executable +preconfigopts = 'chmod +x configure && ' +configopts = '--with-mpi=auto' + +sanity_check_paths = { + 'files': ['bin/IMa2p'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb b/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb new file mode 100644 index 0000000000000000000000000000000000000000..521eb6e805ea754a2aac71e9f2568a387f74cf46 --- /dev/null +++ b/easybuild/easyconfigs/i/IOR/IOR-3.0.1-foss-2016a-mpiio.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = "IOR" +version = "3.0.1" +versionsuffix = "-mpiio" + +homepage = 'https://github.com/chaos/ior' +description = """ The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, + or HDF5 interfaces. """ + +toolchain = {'name': 'foss', 'version': '2016a' } + +source_urls = [('https://github.com/chaos/ior/archive/')] +sources = ['%(version)s.tar.gz'] + +# configure opts listed below +# --with-PACKAGE[=ARG] use PACKAGE [ARG=yes] +# --without-PACKAGE do not use PACKAGE (same as --with-PACKAGE=no) +# --with-lustre support configurable Lustre striping values [default=check] +# --with-posix support IO with POSIX backend [default=yes] +# --with-mpiio support IO with MPI-IO backend [default=yes] +# --with-hdf5 support IO with HDF5 backend [default=no] +# --with-ncmpi support IO with NCMPI backend [default=no] +preconfigopts = "./bootstrap &&" + +sanity_check_paths = { + 'files': ["bin/ior"], + 'dirs': ["share"] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb b/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8bd48f9c2e06260dbcebefdf859096ddea916dee --- /dev/null +++ b/easybuild/easyconfigs/i/IOzone/IOzone-3.434-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'IOzone' +version = '3.434' + +homepage = 'http://www.iozone.org/' +description = """ +IOzone is a filesystem benchmark tool. The benchmark generates and measures a variety of file operations. Iozone has been ported + to many machines and runs under many operating systems. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(namelower)s%(version_major)s_%(version_minor)s.tar'] +source_urls = ['http://www.iozone.org/src/current/'] + +prebuildopts = 'cd src/current &&' +buildopts = 'linux-AMD64' + +files_to_copy = [ + (['src/current/iozone'], 'bin'), + (['src/current/%s' % docfile for docfile in ['gengnuplot.sh','report.pl','Changes.txt']],'share/doc'), + (['src/current/%s' % docfile for docfile in ['gengnuplot.sh','Generate_Graphs','gnu3d.dem']],'share'), + (['docs/iozone.1'], 'share/man/man1'), + (['docs/%s' % docfile for docfile in ['IOzone_msword_98.doc','IOzone_msword_98.pdf','Iozone_ps.gz','Run_rules.doc']], + 'share/doc'), +] + + +sanity_check_paths = { + 'files': ['bin/iozone'], + 'dirs': ['bin','share/doc','share/man'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.2.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-4.2.0-goolf-1.7.20-Python-2.7.11.eb index 4cb75395cca9617a8fbba4802f0eb38f0d1fc485..e5a53f115d6e67068aa85a5ff011e6976523f022 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.2.0-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.2.0-goolf-1.7.20-Python-2.7.11.eb @@ -60,7 +60,7 @@ exts_list = [ }), ('MarkupSafe', '0.23', { 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], - 'modulename': 'markupsafe', + 'modulename': 'markupsafe', }), ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb index 0626eb2c280f0dda6d8abf3ade6caa06fde5597a..ec8e81a4ce11f949736a5821796c8dcb8334d6c3 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-4.2.0-intel-2016a-Python-2.7.11.eb @@ -60,7 +60,7 @@ exts_list = [ }), ('MarkupSafe', '0.23', { 'source_urls': ['https://pypi.io/packages/source/M/MarkupSafe/'], - 'modulename': 'markupsafe', + 'modulename': 'markupsafe', }), ('Jinja2', '2.8', { 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.0.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/i/IPython/IPython-5.0.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..0789701c37512799d877275fb3f7ae8a9fd4a38a --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.0.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,143 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '5.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +dependencies = [ + ('Python', '2.7.11'), + ('PyZMQ', '15.3.0', '%s-zmq4' % versionsuffix), + ('testpath', '0.3', versionsuffix), + ('entrypoints', '0.2.2', versionsuffix), + ('path.py', '8.2.1', versionsuffix), + ('prompt-toolkit', '1.0.3', 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', '2.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('nbformat', '4.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + }), + ('Pygments', '2.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('certifi', '2016.2.28', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.4', { + '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/'], + }), + ('jupyter_client', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('setuptools', '24.0.3', { + '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', '0.7.3', { + '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', '4.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + }), + ('jupyter_core', '4.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + }), + ('ipykernel', '4.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + }), + ('pexpect', '4.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + }), + ('nbconvert', '4.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + }), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + }), + ('decorator', '4.0.10', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'patches': ['ipython-5.0.0_fix-test-paths-symlink.patch'], + 'modulename': 'IPython', + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), + ('iptest2', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-5.0.0-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/i/IPython/IPython-5.0.0-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..f78869f5b949647f8df5420688f60c0c69d03632 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.0.0-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,125 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '5.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +dependencies = [ + ('Python', '3.5.1'), + ('PyZMQ', '15.3.0', '%s-zmq4' % versionsuffix), + ('testpath', '0.3', versionsuffix), + ('entrypoints', '0.2.2', versionsuffix), + ('path.py', '8.2.1', versionsuffix), + ('prompt-toolkit', '1.0.3', 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', '2.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('nbformat', '4.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + }), + ('Pygments', '2.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + }), + ('tornado', '4.4', { + '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/'], + }), + ('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', '24.0.3', { + '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/'], + }), + ('pickleshare', '0.7.3', { + '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', '4.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + }), + ('jupyter_core', '4.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + }), + ('ipykernel', '4.3.1', { + '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', + }), +] + +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/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 new file mode 100644 index 0000000000000000000000000000000000000000..d3bbfe47b7c0bfcd1a26acaac76cee676caa0ccf --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-5.1.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,155 @@ +easyblock = 'Bundle' + +name = 'IPython' +version = '5.1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +dependencies = [ + ('Python', '2.7.12'), + ('PyZMQ', '15.4.0', '%s-zmq4' % versionsuffix), + ('testpath', '0.3', versionsuffix), + # required by 'nbconvert', but causes problems w.r.t. 'backports' module... + # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 + #('entrypoints', '0.2.2', versionsuffix), + ('path.py', '8.2.1', versionsuffix), + ('prompt-toolkit', '1.0.6', versionsuffix), +] + +# this is a bundle of Python packages +# XXX: the wheel packages (testpath, entrypoints, path.py, prompt-toolkit) have +# to be included as dependencies because bundling wheels does not work +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') + +exts_list = [ + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('requests', '2.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('nbformat', '4.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nbformat/'], + }), + ('Pygments', '2.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments/'], + 'modulename': 'pygments', + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + }), + ('certifi', '2016.8.8', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + }), + ('backports_abc', '0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + }), + ('tornado', '4.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe/'], + 'modulename': 'markupsafe', + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2/'], + 'modulename': 'jinja2', + }), + ('jupyter_client', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_client/'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32/'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema/'], + }), + ('mistune', '0.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune/'], + }), + ('ptyprocess', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ptyprocess/'], + }), + ('terminado', '0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/t/terminado/'], + }), + ('setuptools', '25.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('simplegeneric', '0.8.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplegeneric/'], + 'source_tmpl': 'simplegeneric-%(version)s.zip', + }), + ('ipython_genutils', '0.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython_genutils/'], + }), + ('pathlib2', '2.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'], + }), + ('pickleshare', '0.7.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pickleshare/'], + }), + ('traitlets', '4.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'], + }), + ('notebook', '4.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/n/notebook/'], + }), + ('jupyter_core', '4.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyter_core/'], + }), + ('ipykernel', '4.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipykernel/'], + }), + ('pexpect', '4.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pexpect/'], + }), + # disabled because entrypoints on which this depends pull in configparser, which causes problems + # see https://github.com/hpcugent/easybuild-easyconfigs/issues/3825 + #('nbconvert', '4.2.0', { + # 'source_urls': ['https://pypi.python.org/packages/source/n/nbconvert/'], + #}), + ('backports.shutil_get_terminal_size', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports.shutil_get_terminal_size/'], + }), + ('decorator', '4.0.10', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('ipython', version, { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'], + 'patches': ['ipython-5.0.0_fix-test-paths-symlink.patch'], + 'modulename': 'IPython', + }), + ('ipywidgets', '5.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/i/ipywidgets/'], + }), + ('widgetsnbextension', '1.2.6', { + 'source_urls': ['https://pypi.python.org/packages/source/w/widgetsnbextension/'], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + ('ipython -h', ''), + ('ipython notebook --help', ''), + ('iptest', ''), + ('iptest2', ''), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/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/IPython/ipython-5.0.0_fix-test-paths-symlink.patch b/easybuild/easyconfigs/i/IPython/ipython-5.0.0_fix-test-paths-symlink.patch new file mode 100644 index 0000000000000000000000000000000000000000..a2b0a97f5582abea35c43b1c9af4a82a51433ab5 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/ipython-5.0.0_fix-test-paths-symlink.patch @@ -0,0 +1,14 @@ +take into account that $TMPDIR may be a symlinked directory, this is required because path equality is checked +in some tests +author: Kenneth Hoste (HPC-UGent) +--- ipython-5.0.0/IPython/core/tests/test_paths.py.orig 2016-08-17 11:11:24.104380000 +0200 ++++ ipython-5.0.0/IPython/core/tests/test_paths.py 2016-08-17 11:11:24.153308000 +0200 +@@ -17,7 +17,7 @@ + from IPython.testing.decorators import skip_win32 + from IPython.utils.tempdir import TemporaryDirectory + +-TMP_TEST_DIR = tempfile.mkdtemp() ++TMP_TEST_DIR = os.path.realpath(tempfile.mkdtemp()) + HOME_TEST_DIR = os.path.join(TMP_TEST_DIR, "home_test_dir") + XDG_TEST_DIR = os.path.join(HOME_TEST_DIR, "xdg_test_dir") + XDG_CACHE_DIR = os.path.join(HOME_TEST_DIR, "xdg_cache_dir") diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.15-foss-2016a.eb b/easybuild/easyconfigs/i/ISL/ISL-0.15-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..bd7c2f7f2a1f70a91c4193c78c1e06b2a293c1ee --- /dev/null +++ b/easybuild/easyconfigs/i/ISL/ISL-0.15-foss-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'ISL' +version = '0.15' + +homepage = 'http://isl.gforge.inria.fr/' +description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://isl.gforge.inria.fr/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('GMP', '6.1.0')] + +sanity_check_paths = { + 'files': ['lib/libisl.%s' % SHLIB_EXT, 'lib/libisl.a'], + 'dirs': ['include/isl'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.17-foss-2016a.eb b/easybuild/easyconfigs/i/ISL/ISL-0.17-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a7b67d3ddff0859a3692e29edaa33969091b3618 --- /dev/null +++ b/easybuild/easyconfigs/i/ISL/ISL-0.17-foss-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'ISL' +version = '0.17' + +homepage = 'http://isl.gforge.inria.fr/' +description = """isl is a library for manipulating sets and relations of integer points bounded by linear constraints.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://isl.gforge.inria.fr/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('GMP', '6.1.0')] + +sanity_check_paths = { + 'files': ['lib/libisl.%s' % SHLIB_EXT, 'lib/libisl.a'], + 'dirs': ['include/isl'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.4-8-intel-2016a.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.4-8-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..bcbe21baac1e1abf56cfd3d58705c89a472999cb --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-6.9.4-8-intel-2016a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '6.9.4-8' + +homepage = 'http://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_XZ] +source_urls = ['http://www.imagemagick.org/download'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('freetype', '2.6.3'), + ('Ghostscript', '9.19'), + ('JasPer', '1.900.1'), + ('libjpeg-turbo', '1.4.2'), + ('LibTIFF', '4.0.6'), + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXt', '1.1.5'), + ('LittleCMS', '2.7'), +] + +builddependencies = [ + ('pkg-config', '0.29'), +] + +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/ImageMagick/ImageMagick-7.0.1-9-intel-2016a.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-9-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7765318123ddad977e8952e269cfde8122919a33 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.1-9-intel-2016a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.0.1-9' + +homepage = 'http://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_XZ] +source_urls = ['http://www.imagemagick.org/download'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('freetype', '2.6.3'), + ('Ghostscript', '9.19'), + ('JasPer', '1.900.1'), + ('libjpeg-turbo', '1.4.2'), + ('LibTIFF', '4.0.6'), + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXt', '1.1.5'), + ('LittleCMS', '2.7'), +] + +builddependencies = [ + ('pkg-config', '0.29'), +] + +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/ImageMagick/ImageMagick-7.0.2-9-intel-2016a.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.2-9-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d83125eb93ee3200df0fb25d34ffb690d8c3e89a --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.2-9-intel-2016a.eb @@ -0,0 +1,44 @@ +# 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 = '7.0.2-9' + +homepage = 'http://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_XZ] +source_urls = ['http://www.imagemagick.org/download'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('freetype', '2.6.3'), + ('Ghostscript', '9.19'), + ('JasPer', '1.900.1'), + ('libjpeg-turbo', '1.4.2'), + ('LibTIFF', '4.0.6'), + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXt', '1.1.5'), + ('LittleCMS', '2.7'), +] + +builddependencies = [ + ('pkg-config', '0.29'), +] + +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/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/Infernal/Infernal-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb index 33a89436184584e168a9d04a1af2c935853cce9a..033191a3d973369e24d665d435c6841281f4d523 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-goolf-1.4.10.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'Infernal' version = "1.1" -homepage = 'http://infernal.janelia.org/' +homepage = 'http://eddylab.org/infernal/' description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities.""" @@ -23,7 +23,9 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['ftp://selab.janelia.org/pub/software/%(namelower)s'] +source_urls = ['http://eddylab.org/%(namelower)s'] + +checksums = ['04bc8c9693cffba371b8559f023b6548'] sanity_check_paths = { 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb index 10d6e8c98637179d7556e086ff16afb45878880b..e7debfe98faa7978625074e5ad5c5154232e0400 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1-ictce-5.3.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'Infernal' version = "1.1" -homepage = 'http://infernal.janelia.org/' +homepage = 'http://eddylab.org/infernal/' description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities.""" @@ -23,7 +23,9 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['ftp://selab.janelia.org/pub/software/%(namelower)s'] +source_urls = ['http://eddylab.org/%(namelower)s'] + +checksums = ['04bc8c9693cffba371b8559f023b6548'] sanity_check_paths = { 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb index 9c4049ce58e9998e3929e18da57dd8adfc8fb4f1..5171c8b613137d5506d21a6a31bf908152b77e39 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-goolf-1.4.10.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'Infernal' version = '1.1rc1' -homepage = 'http://infernal.janelia.org/' +homepage = 'http://eddylab.org/infernal/' description = """Infernal ('INFERence of RNA ALignment') is for searching DNA sequence databases for RNA structure and sequence similarities.""" @@ -23,7 +23,9 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['ftp://selab.janelia.org/pub/software/%s' % name.lower()] +source_urls = ['http://eddylab.org/%(namelower)s'] + +checksums = ['300c208dd5550b422dd02d93c131958a'] sanity_check_paths = { 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb index ee33a329e8a21c174f556b90b892f29c9a35f60f..a1476edd290aeed8eb237426ae928150a6eb6ffa 100644 --- a/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1rc1-ictce-5.3.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'Infernal' version = '1.1rc1' -homepage = 'http://infernal.janelia.org/' +homepage = 'http://eddylab.org/infernal/' description = """Infernal ('INFERence of RNA ALignment') is for searching DNA sequence databases for RNA structure and sequence similarities.""" @@ -23,7 +23,9 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['ftp://selab.janelia.org/pub/software/%s' % name.lower()] +source_urls = ['http://eddylab.org/%(namelower)s'] + +checksums = ['300c208dd5550b422dd02d93c131958a'] sanity_check_paths = { 'files': ['bin/cm%s' % x for x in ['align', 'build', 'calibrate', 'convert', 'emit', 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 new file mode 100644 index 0000000000000000000000000000000000000000..efeb188af27eb851a0f7a33b1149ce3267a240f9 --- /dev/null +++ b/easybuild/easyconfigs/i/i-cisTarget/i-cisTarget-20160602-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,59 @@ +easyblock = 'Bundle' + +name = 'i-cisTarget' +version = '20160602' # corresponds to f8be714885560ddabdb1612cf9921a348ffac468 +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://gbiomed.kuleuven.be/apps/lcb/i-cisTarget' +description = """An integrative genomics method for the prediction of regulatory features and cis-regulatory modules + in Human, Mouse, and Fly""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +exts_list = [ + # airspeed requires this specific version of cachetools + ('cachetools', '0.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cachetools/'], + }), + ('airspeed', '0.5.4dev-20150515', { + 'source_urls': ['https://pypi.python.org/packages/source/a/airspeed/'], + }), + ('bx-python', '0.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bx-python/'], + 'modulename': 'bx', + }), + ('Wand', '0.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/W/Wand/'], + 'modulename': 'wand.image', + }), + # i-cisTarget sources are not freely available, contact lcbtools@ls.kuleuven.be + (name, version, { + 'source_tmpl': 'icisTarget-%(version)s.tar.gz', + 'modulename': 'cistargetx', + }), +] + +dependencies = [ + ('Python', '2.7.11'), + ('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', '1.3'), + ('Cluster-Buster', '20160106'), + ('Kent_tools', '20130806', '-linux.x86_64', True), +] + +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': ['bin/%s' % x for x in ['ctx-convert', 'ctx-db2r', 'ctx-gt', 'ctx-r2db', 'ctx-rcc']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/icc/icc-2016.3.210-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..9ce84e0f30037300a9c39401a24123eccba08fea --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2016.3.210-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 = '2016.3.210' + +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_update%(version_minor)s.tgz'] + +checksums = ['b256c5573d4bba3692c9c4a6ac994d1c'] + +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-2017.0.098-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-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..944d7a23b2fc72a2d39794af3a64e96db9b69648 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2016.3.210-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 = '2016.3.210' +versionsuffix = '-GCC-5.4.0-2.26' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version, versionsuffix), + ('ifort', version, versionsuffix), +] + +moduleclass = 'toolchain' 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/icmake/icmake-7.23.02-foss-2016a.eb b/easybuild/easyconfigs/i/icmake/icmake-7.23.02-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..ed01c4e7446195bd4845fce582e94f27d6e06bd1 --- /dev/null +++ b/easybuild/easyconfigs/i/icmake/icmake-7.23.02-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'PackedBinary' + +name = 'icmake' +version = '7.23.02' + +homepage = 'http://icmake.sourceforge.net/' +description = """Icmake is a hybrid between a 'make' utility and a 'shell script' language. Originally, it was written to + provide a useful tool for automatic program maintenance and system administrative tasks on old MS-DOS platforms.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fbb-git/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] + +install_cmd = 'cd %(name)s-%(version)s/%(name)s && sed -i \'s|usr/||g\' INSTALL.im && ' +install_cmd += './icm_bootstrap %(installdir)s && ./icm_install strip all /' + +sanity_check_paths = { + 'files': [ + 'bin/icmake', 'bin/icmbuild', 'bin/icmstart', 'bin/icmun', + 'lib/icmake/icm-comp', 'lib/icmake/icm-exec', 'lib/icmake/icm-pp' + ], + 'dirs': [] +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000000000000000000000000000000000..48e857188b4bdaab9adc156fcbc2e41010ca889d --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2016.3.210-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 = '2016.3.210' + +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_update%(version_minor)s.tgz'] + +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) + +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-2017.0.098-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-2016.03-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..8ee7c61e95bee2febd89f186b1413f2e598ee856 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016.03-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 = '2016.03' +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 = '2016.3.210' +dependencies = [ + ('icc', compver, versionsuffix), + ('ifort', compver, versionsuffix), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, versionsuffix))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2016b.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..0af3e3a3ab235793abce4ae2cd209383c6bf3314 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2016b.eb @@ -0,0 +1,20 @@ +# This is an easyconfig file for EasyBuild, see http://hpcugent.github.io/easybuild +easyblock = "Toolchain" + +name = 'iimpi' +version = '2016b' + +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' +dependencies = [ + ('icc', compver, suff), + ('ifort', compver, suff), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, suff))), +] + +moduleclass = 'toolchain' 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-iimpi-2016.03-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..490c4fbf4200decba44a6a2a48bc8d55710f15c7 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016.03-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 = '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': 'iimpi', 'version': '2016.03-GCC-5.4.0-2.26'} + +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['f72546df27f5ebb0941b5d21fd804e34'] + +dontcreateinstalldir = 'True' + +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-iimpi-2016b.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..cce72ce10ae171c391fd9ef0f21aa0fe498ec027 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iimpi-2016b.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': 'iimpi', 'version': '2016b'} + +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-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-2016.07.eb b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..425ca0043d7dc40220caa45310c79f3a1b4090c9 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.3.3.210-iompi-2016.07.eb @@ -0,0 +1,35 @@ +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': '2016.07'} + +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-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-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..565380f44c465ac127ade7010c2e84ee92ab0c2d --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.3.181-iccifort-2016.3.210-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 = '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': 'iccifort', 'version': '2016.3.210-GCC-5.4.0-2.26'} + +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/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/inputproto/inputproto-2.3.2-intel-2016a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.2-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5bb475eb735dd16939c45bd4c0346eefee0d9674 --- /dev/null +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3.2-intel-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'inputproto' +version = '2.3.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org InputProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +builddependencies = [('xorg-macros', '1.19.0')] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XI2.h', 'XI.h', 'XIproto.h', 'XI2proto.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..1de4297cceeadc693a73588b680f4c47234c198f --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2016.03-GCC-5.4.eb @@ -0,0 +1,26 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2016.03' +gcc_maj_min = '5.4' +versionsuffix = '-GCC-%s' % gcc_maj_min + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210' +gccver = '%s.0' % gcc_maj_min +binutilsver = '2.26' +gccsuff = '-GCC-%s-%s' % (gccver, binutilsver) +dependencies = [ + ('GCCcore', gccver), + ('binutils', binutilsver, '-GCCcore-%s' % gccver), + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.3.210', '', ('iimpi', '%s%s' % (version, gccsuff))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/intel/intel-2016b.eb b/easybuild/easyconfigs/i/intel/intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..92aacd886cb8392383012810ad3933f00d6f5747 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2016b' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2016.3.210' +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', '5.1.3.181', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.3.3.210', '', ('iimpi', version)), +] + +moduleclass = 'toolchain' 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-GCCcore-4.9.3-Perl-5.24.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..0acb163cda03df350f6cf8ddf755ede403528e2e --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-4.9.3-Perl-5.24.0.eb @@ -0,0 +1,29 @@ +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': 'GCCcore', 'version': '4.9.3'} + +source_urls = ['http://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('binutils', '2.25'), +] + +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/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/io_lib/io_lib-1.14.8-foss-2016a.eb b/easybuild/easyconfigs/i/io_lib/io_lib-1.14.8-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9d67e520661f177d3acbb9427b4175809ea46dab --- /dev/null +++ b/easybuild/easyconfigs/i/io_lib/io_lib-1.14.8-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'io_lib' +version = '1.14.8' + +homepage = 'http://sourceforge.net/projects/staden/files/io_lib/' +description = """Io_lib is a library of file reading and writing code to provide a general purpose trace file (and Experiment + File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" C structure with the data loaded + into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [('http://sourceforge.net/projects/staden/files/%(namelower)s/%(version)s', 'download')] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ["bin/scramble", "bin/append_sff", "bin/ztr_dump"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb b/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..54ed73649a82ac957b0c23edce844f606f677b99 --- /dev/null +++ b/easybuild/easyconfigs/i/iomkl/iomkl-2016.07.eb @@ -0,0 +1,20 @@ +easyblock = "Toolchain" + +name = 'iomkl' +version = '2016.07' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI.""" + +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-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-2016.07.eb b/easybuild/easyconfigs/i/iompi/iompi-2016.07.eb new file mode 100644 index 0000000000000000000000000000000000000000..6cfe2ee8254f50fe5787da149c0d25ed6817e077 --- /dev/null +++ b/easybuild/easyconfigs/i/iompi/iompi-2016.07.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'iompi' +version = '2016.07' + +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 = [ + ('icc', compver), + ('ifort', compver), + ('OpenMPI', '1.10.3', '', ('iccifort', compver)), +] + +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/JAGS/JAGS-4.2.0-foss-2016a.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b168dd347edbce51532b5cb6a85b19ba9cf7b50e --- /dev/null +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.2.0-foss-2016a.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'JAGS' +version = '4.2.0' + +homepage = 'http://mcmc-jags.sourceforge.net/' +description = """JAGS is Just Another Gibbs Sampler. It is a program for analysis + of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [('http://sourceforge.net/projects/mcmc-jags/files/JAGS/%(version_major)s.x/Source/', 'download')] +sources = [SOURCE_TAR_GZ] + +configopts = ' --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' + +sanity_check_paths = { + 'files': ["bin/jags", "libexec/jags-terminal", "lib/libjags.%s" % SHLIB_EXT], + 'dirs': [] +} + +modextrapaths = { + 'JAGS_INCLUDE': 'include/JAGS', + 'JAGS_LIB': 'lib', +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_72.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_72.eb new file mode 100644 index 0000000000000000000000000000000000000000..e078225e6a9116d0ac173525d9ecc185962a3a5a --- /dev/null +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_72.eb @@ -0,0 +1,22 @@ +easyblock = 'JAR' + +name = 'JUnit' +version = '4.12' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://sourceforge.net/projects/junit' +description = """A programmer-oriented testing framework for Java.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s.jar'] +source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] + +dependencies = [('Java', '1.8.0_72')] + +sanity_check_paths = { + 'files': sources, + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_77.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_77.eb new file mode 100644 index 0000000000000000000000000000000000000000..1879fb86c091836855facb2102b9e752e54a20d6 --- /dev/null +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_77.eb @@ -0,0 +1,22 @@ +easyblock = 'JAR' + +name = 'JUnit' +version = '4.12' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://sourceforge.net/projects/junit' +description = """A programmer-oriented testing framework for Java.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s.jar'] +source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] + +dependencies = [('Java', '1.8.0_77')] + +sanity_check_paths = { + 'files': sources, + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_92.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_92.eb new file mode 100644 index 0000000000000000000000000000000000000000..f9eed98346b24b96a7291da0eaea0e72510be7ae --- /dev/null +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.12-Java-1.8.0_92.eb @@ -0,0 +1,22 @@ +easyblock = 'JAR' + +name = 'JUnit' +version = '4.12' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://sourceforge.net/projects/junit' +description = """A programmer-oriented testing framework for Java.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s.jar'] +source_urls = ['http://search.maven.org/remotecontent?filepath=junit/junit/%(version)s/'] + +dependencies = [('Java', '1.8.0_92')] + +sanity_check_paths = { + 'files': sources, + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2016a.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..77a86b683148862d19aff1ecbf6434438e0de64d --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2016b.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..4da54a15727bdf0d278935ee4c698782d18a67e7 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2016b.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'JasPer' +version = '1.900.1' + +homepage = 'http://www.ece.uvic.ca/~frodo/jasper/' +description = """The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_ZIP] +source_urls = ['http://www.ece.uvic.ca/~frodo/jasper/software/'] + +sanity_check_paths = { + 'files': ["bin/jasper", "lib/libjasper.a"], + 'dirs': ["include"], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/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/Java/Java-1.8.0_92.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_92.eb new file mode 100644 index 0000000000000000000000000000000000000000..72fb7c3057a255d72355e188bd6dd6997770eb97 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_92.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8.0_92' + +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/Jellyfish/Jellyfish-2.2.6-goolf-1.7.20.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..09aa380fc622d13b62213af965a1353c81f26310 --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.2.6-goolf-1.7.20.eb @@ -0,0 +1,33 @@ +# 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 = 'Jellyfish' +version = '2.2.6' + +homepage = 'http://www.genome.umd.edu/jellyfish.html' +description = """ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/gmarcais/Jellyfish/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +# The tests for the Bloom filter are statistical tests and can randomly fail, they actually don't make a lot of sense +runtest = "check GTEST_FILTER=-'*Bloom*'" + +postinstallcmds = ["cp config.h %(installdir)s/include/%(namelower)s-%(version)s/%(namelower)s/"] + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +modextrapaths = {'CPATH': 'include/%(namelower)s-%(version)s'} + +moduleclass = 'bio' 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-4.2.0-foss-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.2.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0fe7cf019d2938ad8132c41643eebdea96758177 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.2.0-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '4.2.0' + +homepage = 'http://www.canonware.com/jemalloc' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +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/j/jemalloc/jemalloc-4.2.0-intel-2016a.eb b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.2.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..dccd9491cd5f755bb20cddb0bc35a468caaa7f67 --- /dev/null +++ b/easybuild/easyconfigs/j/jemalloc/jemalloc-4.2.0-intel-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'jemalloc' +version = '4.2.0' + +homepage = 'http://www.canonware.com/jemalloc' +description = """jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and + scalable concurrency support.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +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/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/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..b2f1cf65eb7bd22f80852cc42e83e0f97cbc94f6 --- /dev/null +++ b/easybuild/easyconfigs/j/jhbuild/jhbuild-3.15.92-GCCcore-4.9.3.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'jhbuild' +version = '3.15.92' + +homepage = 'https://wiki.gnome.org/action/show/Projects/Jhbuild' +description = """JHBuild allows you to automatically download and compile “modules” (i.e. source code packages). +Modules are listed in “module set” files, which also include dependency information so that JHBuild can discover +what modules need to be built and in what order.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +sources = ['%(version)s.tar.gz'] +source_urls = [('https://github.com/GNOME/jhbuild/archive/')] + +# jhbuild is python so it has a python dependency, but we want to give people freedom to use whatever python they +# chose during a build process +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +builddependencies = [ + ('binutils', '2.25'), +] + +dependencies = [ + ('Autotools', '20150215'), + ('pkg-config', '0.29.1'), + ('gettext', '0.19.8'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('M4', '1.4.17'), + ('CVS', '1.11.23'), +] + +# We use the simple install method as per: +# https://developer.gnome.org/jhbuild/stable/getting-started.html.en +# to avoid unnecessary dependencies. This requires us to build in the install dir so that all libs are found. +buildininstalldir = True +skipsteps = ['configure'] +prebuildopts = './autogen.sh --prefix=%(installdir)s &&' + +# Make sure there are no "not found" in the sanitycheck output +sanity_check_commands = [('! jhbuild', 'sanitycheck| grep not\ found')] + +sanity_check_paths = { + 'files': ['bin/jhbuild'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyterhub/jupyterhub-0.6.1-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/j/jupyterhub/jupyterhub-0.6.1-foss-2016a-Python-3.5.1.eb new file mode 100755 index 0000000000000000000000000000000000000000..3484e3c6a6d7476637dcb7a91251b8815d3a41c0 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyterhub/jupyterhub-0.6.1-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,46 @@ +easyblock = 'Bundle' + +name = 'jupyterhub' +version = '0.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://jupyter.org' +description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed for + centralized deployments in companies, university classrooms and research labs.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +dependencies = [ + ('Python', '3.5.1'), + ('IPython', '5.0.0', versionsuffix), + ('configurable-http-proxy', '1.3.0', '-nodejs-4.4.7'), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('SQLAlchemy', '1.0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('requests', '2.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + ('pamela', '0.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pamela/'], + }), + ('jupyterhub', version, { + 'source_urls': ['https://pypi.python.org/packages/source/j/jupyterhub/'], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/jupyterhub'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/jupyterhub'], +} + +sanity_check_commands = ['jupyterhub --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20130806-linux.x86_64.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20130806-linux.x86_64.eb new file mode 100644 index 0000000000000000000000000000000000000000..d103de7895830adcb2c10f2ff62080148725a281 --- /dev/null +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-20130806-linux.x86_64.eb @@ -0,0 +1,28 @@ +easyblock = 'BinariesTarball' + +name = 'Kent_tools' +version = '20130806' +versionsuffix = '-linux.x86_64' + +homepage = 'http://genome.cse.ucsc.edu/' +description = """Kent tools: collection of tools used by the UCSC genome browser.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download from http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/, and pack into tarball with: +# mkdir Kent_tools +# rsync -aP rsync://hgdownload.cse.ucsc.edu/genome/admin/exe/linux.x86_64/ Kent_tools +# tar cfvz Kent_tools-20130806.tar.gz Kent_tools +sources = [SOURCE_TAR_GZ] + +postinstallcmds = [ + "cp -a %(builddir)s/Kent_tools/blat/{blat,gfClient,gfServer} %(installdir)s/bin", + "cp -a %(builddir)s/Kent_tools/blat/FOOTER.txt %(installdir)s/bin/FOOTER_blat.txt", +] + +sanity_check_paths = { + 'files': ['bin/FOOTER', 'bin/blat', 'bin/getRna', 'bin/liftOver', 'bin/mafGene', 'bin/splitFile', 'bin/twoBitToFa'], + 'dirs': [], +} + +moduleclass = 'bio' 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/kallisto/kallisto-0.43.0-intel-2016b.eb b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..24e6fb2d59ae0bd49d42357d02ec405be1cce9b5 --- /dev/null +++ b/easybuild/easyconfigs/k/kallisto/kallisto-0.43.0-intel-2016b.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'kallisto' +version = '0.43.0' + +homepage = 'http://pachterlab.github.io/kallisto/' +description = """kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally + of target sequences using high-throughput sequencing reads.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/pachterlab/kallisto/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.5.2')] +dependencies = [('HDF5', '1.8.17')] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/kallisto'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb index 86f8eb23deab5d8ecf18f05b9112073eb106751a..645a67a71bbcb125bc118e41d71a170553bfdb81 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-foss-2016a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] +builddependencies = [('xorg-macros', '1.19.0')] + sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], 'dirs': [], diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb index e5d229774cb855a940a5dfddae98e54b8fa30cb7..2c6fbcd6f5390fab961f71e5562404fe833ef230 100644 --- a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2016a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] +builddependencies = [('xorg-macros', '1.19.0')] + sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], 'dirs': [], diff --git a/easybuild/easyconfigs/k/khmer/khmer-1.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/k/khmer/khmer-1.1-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..a821aa77f2956ea7ee6facad0f12a37e92bf4290 --- /dev/null +++ b/easybuild/easyconfigs/k/khmer/khmer-1.1-goolf-1.4.10-Python-2.7.5.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'khmer' +version = '1.1' +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': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/ged-lab/khmer/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.5'), +] + +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/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-3.8.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..fe4a09d2cd410520940832a4879a22068ea22013 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-GCCcore-4.9.3.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.8.1' + +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': 'GCCcore', 'version': '4.9.3'} + +source_urls = ["http://llvm.org/releases/%(version)s"] +sources = ["llvm-%(version)s.src.tar.xz"] + +builddependencies = [ + ('binutils', '2.25'), + ('CMake', '3.6.1'), + # We use the minimal Python in GCCcore + ('Python', '2.7.12', '-bare'), +] + +dependencies = [ + ('ncurses', '6.0'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +# required to install extra tools in bin/ +configopts += "-DLLVM_INSTALL_UTILS=ON" + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-foss-2016b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..959113598997d12dc9db166f08179dda1d747eba --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-foss-2016b.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.8.1' + +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" + +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-3.8.1-intel-2016b.eb b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..243e52187d062fd16de946f82743168db236c9d7 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-3.8.1-intel-2016b.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'LLVM' +version = '3.8.1' + +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"] + +builddependencies = [ + ('CMake', '3.5.2'), + ('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" + +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-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/LMDB/LMDB-0.9.18-foss-2016a.eb b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.18-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..2961d2e3756c46b97c72d55a9be1cddfb9b9f883 --- /dev/null +++ b/easybuild/easyconfigs/l/LMDB/LMDB-0.9.18-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'LMDB' +version = '0.9.18' + +homepage = 'https://github.com/LMDB/lmdb' +description = """ +OpenLDAP's Lightning Memory-Mapped Database (LMDB) library. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(name)s_%(version)s.tar.gz'] +source_urls = ['https://github.com/LMDB/lmdb/archive/'] + +files_to_copy = [ + (['liblmdb.a', 'liblmdb.%s' % SHLIB_EXT], 'lib'), + (['lmdb.h'], 'include') +] + +sanity_check_paths = { + 'files': ['include/lmdb.h', 'lib/liblmdb.a', 'lib/liblmdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' 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/LevelDB/LevelDB-1.18-foss-2016a.eb b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f3fb0f0115443177d356af4c05f8b351649df7ac --- /dev/null +++ b/easybuild/easyconfigs/l/LevelDB/LevelDB-1.18-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'LevelDB' +version = '1.18' + +homepage = 'https://github.com/google/leveldb' +description = """ +LevelDB is a fast key-value storage library written at Google that provides an +ordered mapping from string keys to string values. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/google/leveldb/archive/'] + +files_to_copy = [ + (['libleveldb.%s.%%(version)s' % SHLIB_EXT, 'libleveldb.a'], 'lib'), + (['include/leveldb/*.h'], 'include/leveldb') +] + +postinstallcmds=[ + 'cd %(installdir)s/lib; ln -s libleveldb.so.%(version)s libleveldb.so.%(version_major)s', + 'cd %%(installdir)s/lib; ln -s libleveldb.so.%%(version)s libleveldb.%s' % SHLIB_EXT, +] + + +sanity_check_paths = { + 'files': ['include/leveldb/cache.h','include/leveldb/table.h', + 'lib/libleveldb.a', 'lib/libleveldb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..07fa7682edf77f542e46a009b0bf33d41f846393 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Alan O'Cais (JSC) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.6' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..d8f291e4e8f30afe990e7b24afbc22407475aac7 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Alan O'Cais (JSC) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.6' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-foss-2016a.eb b/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8da640da4e6b6eb7e4cd932626a428f6a0c5eb03 --- /dev/null +++ b/easybuild/easyconfigs/l/LibUUID/LibUUID-1.0.3-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'LibUUID' +version = '1.0.3' + +homepage = 'http://sourceforge.net/projects/libuuid/' +description = """Portable uuid C library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/uuid/uuid.h', 'lib/libuuid.a', 'lib/libuuid.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..56cf148c48df8b112d85d0dbe91aaca049655e72 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-intel-2016a.eb @@ -0,0 +1,23 @@ +name = 'Libint' +version = '1.1.4' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ('http://sourceforge.net/projects/libint/files/v1-releases/', 'download') + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.%s' % (x,y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..accf89b9e8944ce9c93960b8f490434c441896db --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.6-intel-2016b.eb @@ -0,0 +1,27 @@ +name = 'Libint' +version = '1.1.6' + +homepage = 'https://sourceforge.net/p/libint/' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = ['release-%s.tar.gz' % '-'.join(version.split('.'))] +source_urls = ['https://github.com/evaleev/libint/archive/'] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "aclocal -I lib/autoconf && libtoolize && autoconf && " + +configopts = "--enable-deriv --enable-r12" + +sanity_check_paths = { + 'files': ['include/lib%(x)s/lib%(x)s.h' % {'x': x} for x in ['deriv', 'int', 'r12']] + + ['include/libint/hrr_header.h', 'include/libint/vrr_header.h'] + + ['lib/lib%s.%s' % (x,y) for x in ['deriv', 'int', 'r12'] for y in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-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/Lmod/Lmod-6.4.2.eb b/easybuild/easyconfigs/l/Lmod/Lmod-6.4.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..8be10c542cf7be5acf2893c798cd3a5df6cdbfd8 --- /dev/null +++ b/easybuild/easyconfigs/l/Lmod/Lmod-6.4.2.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = "Lmod" +version = "6.4.2" + +homepage = "http://sourceforge.net/projects/lmod/" +description = """Lmod is a Lua based module system. Modules allow for dynamic modification + of a user's environment under Unix systems. See www.tacc.utexas.edu/tacc-projects/lmod + for a complete description. Lmod is a new implementation that easily handles the MODULEPATH + Hierarchical problem. It is drop-in replacement for TCL/C modules and reads TCL modulefiles directly.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(version)s.tar.gz'] +source_urls = [ + 'https://github.com/TACC/Lmod/archive', + 'http://sourceforge.net/projects/lmod/files/', + 'http://sourceforge.net/projects/lmod/files/Testing' +] + +dependencies = [("Lua", "5.1.4-8")] + +sanity_check_paths = { + 'files': ["lmod/%(version)s/libexec/lmod", "lmod/%(version)s/init/profile"], + 'dirs': [] +} + +moduleclass = "tools" diff --git a/easybuild/easyconfigs/l/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/Loki/Loki-0.1.7-intel-2016b.eb b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..a25e47aac4fbfaae99f635c077a2c19fb096b4b4 --- /dev/null +++ b/easybuild/easyconfigs/l/Loki/Loki-0.1.7-intel-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'Loki' +version = '0.1.7' + +homepage = 'http://loki-lib.sourceforge.net/' +description = """ Loki is a C++ library of designs, containing flexible implementations of common design patterns and + idioms. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://sourceforge.net/projects/loki-lib/files/Loki/Loki %(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +skipsteps = ['configure'] + +installopts = "prefix=%(installdir)s" + +sanity_check_paths={ + 'files': ['lib/libloki.a', 'lib/libloki.%s' % SHLIB_EXT, 'lib/libloki.%s.%%(version)s' % SHLIB_EXT], + 'dirs': ['include/loki'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb new file mode 100644 index 0000000000000000000000000000000000000000..08d864aaf628672e6e666a6ae398fcc2944abb49 --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.1.4-8.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = "Lua" +version = "5.1.4-8" + +homepage = "http://www.lua.org/" +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['lua-%s.tar.gz' % version.replace('-', '.')] +source_urls = ['http://sourceforge.net/projects/lmod/files/'] + +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"], + 'dirs': [] +} + +moduleclass = "lang" 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/lftp/lftp-4.4.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goolf-1.4.10.eb index e96735ec2cf1d29cb7687c0356336456731fab88..d1eb5179b8511d6649ba1a59e8a7a2acd54a92dd 100644 --- a/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/lftp/lftp-4.4.1-goolf-1.4.10.eb @@ -29,7 +29,7 @@ source_urls = [ 'http://ftp.yar.ru/pub/source/lftp/old/', ] -dependencies = [('gnutls', '3.1.8')] +dependencies = [('GnuTLS', '3.1.8')] sanity_check_paths = { 'files': ['bin/lftp'], diff --git a/easybuild/easyconfigs/l/lftp/lftp-4.6.4-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/lftp/lftp-4.6.4-GNU-4.9.3-2.25.eb index a70f4084e336f1d6476b1dface08574c3dba61c2..f9975e31e2983291b5753b4308132d42608cc57c 100644 --- a/easybuild/easyconfigs/l/lftp/lftp-4.6.4-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/lftp/lftp-4.6.4-GNU-4.9.3-2.25.eb @@ -30,7 +30,7 @@ source_urls = [ ] dependencies = [ - ('gnutls', '3.4.7'), + ('GnuTLS', '3.4.7'), ('gettext', '0.19.6'), ('zlib', '1.2.8'), ] 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/libICE/libICE-1.0.9-foss-2016a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb index 78420c88a590034de06fce4417ca4bad9af04eba..dc0eb73d0742db45da000d72e6fc90facb513c26 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-foss-2016a.eb @@ -17,6 +17,7 @@ dependencies = [ builddependencies = [ ('xproto', '7.0.28'), + ('xorg-macros', '1.19.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb index bd5ecc8bcd8f1d04a11ffc308d7a8573d32fe62d..e723c9c6e8c83a29f6f377a34d60bbb0df3ebd10 100644 --- a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2016a.eb @@ -17,6 +17,7 @@ dependencies = [ builddependencies = [ ('xproto', '7.0.28'), + ('xorg-macros', '1.19.0'), ] sanity_check_paths = { 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/libSM/libSM-1.2.2-foss-2016a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb index 289966eec9e12f3ff0c65cbc9c1c96f9d35878e0..5aaa76c22f2ed25bc6a33e0e7382331ed267a684 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-foss-2016a.eb @@ -18,6 +18,7 @@ dependencies = [ builddependencies = [ ('xproto', '7.0.28'), ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb index 1bab5701feb9f0dd86b8630edad1b63106a22873..f63a385fdd69f221a2dc6488d162c8c994ee9cbd 100644 --- a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2016a.eb @@ -18,6 +18,7 @@ dependencies = [ builddependencies = [ ('xproto', '7.0.28'), ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb index 7bbdcf2dc4fb174924175df615f4b5c21a6f131f..29c369131f246b6d87e797ac5b1fd373f7990390 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-foss-2016a.eb @@ -19,6 +19,7 @@ builddependencies = [ ('libpthread-stubs', '0.3'), ('kbproto', '1.0.7'), ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb index 5df5e13e4384191b805c2779f3afd5e1e101b8e1..5d0e481e2b0ebc02f527c7bc86e3450c913fc025 100644 --- a/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libX11/libX11-1.6.3-intel-2016a.eb @@ -19,6 +19,7 @@ builddependencies = [ ('libpthread-stubs', '0.3'), ('kbproto', '1.0.7'), ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb index 9f49697147bae9290a9a921ea3c702f77639b874..6f68f2e8c7c85a71f48a5556c234822299bd70a0 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-foss-2016a.eb @@ -8,7 +8,6 @@ description = """The libXau package contains a library implementing the X11 Auth This is useful for restricting client access to the display.""" toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] @@ -16,6 +15,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('pkg-config', '0.29'), ('xproto', '7.0.28'), + ('xorg-macros', '1.19.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb index 8003dc09d5d3cd0b349f966978efd6969b40fcfe..6c2ae5abd8663f0ba44815398a273514ff323944 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-intel-2016a.eb @@ -8,13 +8,14 @@ description = """The libXau package contains a library implementing the X11 Auth This is useful for restricting client access to the display.""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('pkg-config', '0.29'), ('xproto', '7.0.28'), + ('xorg-macros', '1.19.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb index 1fc949ad4e5cd2e60767ee593359b56e2cb6de9d..ecc5385774088401f734a076f16c94f5f788706f 100644 --- a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-foss-2016a.eb @@ -13,6 +13,15 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('fixesproto', '5.0'), + ('xorg-macros', '1.19.0'), + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('xtrans', '1.3.5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb index e7e9608bd8a46029604e707f99994f39dc8bea0d..8068f14ea72a07a27dd4adead1db4f27207dbcb9 100644 --- a/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXcursor/libXcursor-1.1.14-intel-2016a.eb @@ -13,6 +13,15 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('fixesproto', '5.0'), + ('xorg-macros', '1.19.0'), + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('xtrans', '1.3.5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb index 19c75463d3f65c4878f29968c1535732cd8292ca..b9a8c3b204c32e0964abe7537b7bb67692e4e7e5 100644 --- a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-foss-2016a.eb @@ -11,10 +11,24 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] +builddependencies = [ + ('xorg-macros', '1.19.0'), + ('fixesproto', '5.0'), + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('kbproto', '1.0.7'), + ('xtrans', '1.3.5'), + ('damageproto', '1.2.1'), +] + dependencies = [ ('libX11', '1.6.3'), ('libxcb', '1.11.1'), ('libXau', '1.0.8'), + ('libXfixes', '5.0.1'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb index bc72561b6e0a46282df0e90e2d59abd0eb44deea..bbe2ea95f7ee7bbf4e56237ccdca997e93a58628 100644 --- a/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXdamage/libXdamage-1.1.4-intel-2016a.eb @@ -11,10 +11,24 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] +builddependencies = [ + ('xorg-macros', '1.19.0'), + ('fixesproto', '5.0'), + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('kbproto', '1.0.7'), + ('xtrans', '1.3.5'), + ('damageproto', '1.2.1'), +] + dependencies = [ ('libX11', '1.6.3'), ('libxcb', '1.11.1'), ('libXau', '1.0.8'), + ('libXfixes', '5.0.1'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb index 09bc32a4bba3ae5d7f9bea473fc2c4be2f39f331..f64b25d2063e1e17c97511c378813de27e026a7c 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-foss-2016a.eb @@ -9,7 +9,6 @@ useful for allowing clients to interact with the X Display Manager. """ toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] @@ -17,6 +16,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('pkg-config', '0.29'), ('xproto', '7.0.28'), + ('xorg-macros', '1.19.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb index 6ec7ecf45d88d64d24fa159f1350cf2a3c7f0cef..0f3fd57765052c29708f44c18b5f7ff0e25014c2 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-intel-2016a.eb @@ -9,14 +9,16 @@ useful for allowing clients to interact with the X Display Manager. """ toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('pkg-config', '0.29'), ('xproto', '7.0.28'), + ('xorg-macros', '1.19.0'), ] + sanity_check_paths = { 'files': ['lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], 'dirs': [], diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb index 0a0acbe42bf70074256a9de37d354bb918784788..dcc203e11e33dbbcd6c22746d6320e11a3e6fc75 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-foss-2016a.eb @@ -7,7 +7,6 @@ homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """Common X Extensions library""" toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] @@ -16,6 +15,11 @@ builddependencies = [ ('xproto', '7.0.28'), ('xextproto', '7.3.0'), ('libpthread-stubs', '0.3'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('kbproto', '1.0.7'), + ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb index 2d93058e5e8b822d4af7a1fb10549da9bd12706b..ba7aa8aa456109612b1d347c77cc86714ceb9f5f 100644 --- a/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXext/libXext-1.3.3-intel-2016a.eb @@ -7,7 +7,6 @@ homepage = "http://www.freedesktop.org/wiki/Software/xlibs" description = """Common X Extensions library""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] @@ -16,6 +15,11 @@ builddependencies = [ ('xproto', '7.0.28'), ('xextproto', '7.3.0'), ('libpthread-stubs', '0.3'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('kbproto', '1.0.7'), + ('xtrans', '1.3.5'), + ('xorg-macros', '1.19.0'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb index aa11951f76a4627bd897f4b8978f517b9a556a97..76dc5940533315442d1d5e9466aef4517062ac59 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-foss-2016a.eb @@ -14,6 +14,17 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('fixesproto', '5.0'), ('xextproto', '7.3.0'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28'), + ('kbproto', '1.0.7'), + ('xcb-proto', '1.11', '', True), + ('libpthread-stubs', '0.3'), + ('inputproto', '2.3.1'), + ('xtrans', '1.3.5'), +] + +dependencies = [ + ('libX11', '1.6.3') ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb index 3dd084da608f66d69538186f7f973b7c6a84e14b..d0b72a86ea21335893b7296c1a36e6ec7884324f 100644 --- a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2016a.eb @@ -14,6 +14,17 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('fixesproto', '5.0'), ('xextproto', '7.3.0'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28'), + ('kbproto', '1.0.7'), + ('xcb-proto', '1.11', '', True), + ('libpthread-stubs', '0.3'), + ('inputproto', '2.3.1'), + ('xtrans', '1.3.5'), +] + +dependencies = [ + ('libX11', '1.6.3') ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5af14da529b4240466d26a1bbf2b82bff1786a31 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.2-intel-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'libXfixes' +version = '5.0.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Fixes extension library""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('fixesproto', '5.0'), + ('xextproto', '7.3.0'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28'), + ('kbproto', '1.0.7'), + ('xcb-proto', '1.11', '', True), + ('libpthread-stubs', '0.3'), + ('inputproto', '2.3.1'), + ('xtrans', '1.3.5'), +] + +dependencies = [ + ('libX11', '1.6.3') +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..d6e94f632323290c1d678227570998272dd0c0e9 --- /dev/null +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a-freetype-2.6.3.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'libXft' +version = '2.3.2' +freetypever = '2.6.3' + +versionsuffix = '-freetype-%s' % freetypever + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('inputproto', '2.3.1'), + ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), + ('renderproto', '0.11'), + ('xcb-proto', '1.11', '', True), + ('xextproto', '7.3.0'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), +] + + +dependencies = [ + ('libX11', '1.6.3'), + ('libXrender', '0.9.9'), + ('freetype', '2.6.3'), + ('fontconfig', '2.11.95'), +] + +sanity_check_paths = { + 'files': ['lib/libXft.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb index 1a968a5adaeef52cd3170d1f441505b873c67ae9..b95d581275b0e4e873620c348080475c85877db2 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-foss-2016a.eb @@ -12,10 +12,18 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('inputproto', '2.3.1'), ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), ('renderproto', '0.11'), + ('xcb-proto', '1.11', '', True), + ('xextproto', '7.3.0'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), ] + dependencies = [ ('libX11', '1.6.3'), ('libXrender', '0.9.9'), diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb index 3c4a37832119f5d6995418c9db25f52736f50007..1cc411ee297e31ae42ee6f2d1c654e9e1fd1ea50 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a-fontconfig-2.11.95.eb @@ -13,8 +13,15 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('inputproto', '2.3.1'), ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), ('renderproto', '0.11'), + ('xcb-proto', '1.11', '', True), + ('xextproto', '7.3.0'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb index 17ddfd09d93227633ebd4817091fa53002d6330a..6589aeeb49211187e7e94433407d6d9adc9a5cf7 100644 --- a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2016a.eb @@ -12,10 +12,18 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('inputproto', '2.3.1'), ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), ('renderproto', '0.11'), + ('xcb-proto', '1.11', '', True), + ('xextproto', '7.3.0'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), ] + dependencies = [ ('libX11', '1.6.3'), ('libXrender', '0.9.9'), diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb index c94df236e015e156d9b1a069c959cf1e4eb42496..2f7d28f58a9286cab00b2757211dcc21cfdfe7aa 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-foss-2016a.eb @@ -16,6 +16,11 @@ builddependencies = [ ('xextproto', '7.3.0'), ('inputproto', '2.3.1'), ('xorg-macros', '1.19.0'), + ('fixesproto', '5.0'), + ('kbproto', '1.0.7'), + ('xcb-proto', '1.11', '', True), + ('libpthread-stubs', '0.3'), + ('xtrans', '1.3.5'), ] dependencies = [ @@ -24,7 +29,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', + 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb index 5e9d4cb87a9181d5ba3d50c5a01659c2484d6181..028286d16106e70b0c7e1583db76cecd4a824bae 100644 --- a/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.6-intel-2016a.eb @@ -16,6 +16,11 @@ builddependencies = [ ('xextproto', '7.3.0'), ('inputproto', '2.3.1'), ('xorg-macros', '1.19.0'), + ('fixesproto', '5.0'), + ('kbproto', '1.0.7'), + ('xcb-proto', '1.11', '', True), + ('libpthread-stubs', '0.3'), + ('xtrans', '1.3.5'), ] dependencies = [ @@ -24,7 +29,8 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], + 'files': ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', + 'lib/libXi.%s' % SHLIB_EXT, 'lib/libXi.a'], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb index e0a2e3d206ef13162384e489b00dbf8340a2fdf6..7f990b2124d3bb600678f32720e039b66f80d8d6 100644 --- a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-foss-2016a.eb @@ -16,6 +16,12 @@ builddependencies = [ ('xineramaproto', '1.2.1'), ('xextproto', '7.3.0'), ('xproto', '7.0.28'), + ('xorg-macros', '1.19.0'), + ('renderproto', '0.11'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('libpthread-stubs', '0.3'), + ('xtrans', '1.3.5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb index 59633745894cf15d8d270872106bacbd247724e6..7e2411fa015702b7cca4f6f18e6793e551c00412 100644 --- a/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXinerama/libXinerama-1.1.3-intel-2016a.eb @@ -16,6 +16,12 @@ builddependencies = [ ('xineramaproto', '1.2.1'), ('xextproto', '7.3.0'), ('xproto', '7.0.28'), + ('xorg-macros', '1.19.0'), + ('renderproto', '0.11'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('libpthread-stubs', '0.3'), + ('xtrans', '1.3.5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb index b6614e79e7fc4785f278a783d5d1771dcdf785a2..62c6216169214283720fc84d30928d5476c96bb8 100644 --- a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-foss-2016a.eb @@ -12,9 +12,16 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('inputproto', '2.3.1'), + ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), ('randrproto', '1.5.0'), ('renderproto', '0.11'), + ('xcb-proto', '1.11', '', True), ('xextproto', '7.3.0'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb index d7c99042a39ce2e1b271f3274d45aecd7dc59829..d6e4b7406dd0d243923f4fac9f32ec0438d37237 100644 --- a/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXrandr/libXrandr-1.5.0-intel-2016a.eb @@ -12,9 +12,16 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('inputproto', '2.3.1'), + ('kbproto', '1.0.7'), + ('libpthread-stubs', '0.3'), ('randrproto', '1.5.0'), ('renderproto', '0.11'), + ('xcb-proto', '1.11', '', True), ('xextproto', '7.3.0'), + ('xorg-macros', '1.19.0'), + ('xproto', '7.0.28'), + ('xtrans', '1.3.5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb index 1e63340752407e5ab7b4abfa4fe7878a4c47fa69..b4c2ef6a53d9be61463351401f4a540f84f006a7 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-foss-2016a.eb @@ -12,11 +12,15 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('xorg-macros', '1.19.0'), ('kbproto', '1.0.7'), ('renderproto', '0.11'), + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), - ('xorg-macros', '1.19.0'), - ('xproto', '7.0.28') + ('xtrans', '1.3.5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb index fefc99f4eb0a28753443a0b2e9d580846b0f7439..2c473580acb50d43f37ed664b7e47ac4c7e39b6d 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2016a.eb @@ -12,8 +12,15 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('xorg-macros', '1.19.0'), ('kbproto', '1.0.7'), ('renderproto', '0.11'), + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('xtrans', '1.3.5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb index e37e36b1f5b4cfc120c6b3f86aa181a8d4cbef97..c7e832fe55b48198971de7dec48cafb1634c14cb 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-foss-2016a.eb @@ -8,7 +8,6 @@ description = """libXt provides the X Toolkit Intrinsics, an abstract widget lib based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).""" toolchain = {'name': 'foss', 'version': '2016a'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] @@ -16,6 +15,12 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), ('kbproto', '1.0.7'), + ('xorg-macros', '1.19.0'), + ('xcb-proto', '1.11', '', True), + ('libpthread-stubs', '0.3'), + ('xextproto', '7.3.0'), + ('inputproto', '2.3.1'), + ('xtrans', '1.3.5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb index 66391ee4ad35f010f7de8221ad303f5a73d9b9dd..e12535727a9bc6a76361c58b90577f257193c2f1 100644 --- a/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.5-intel-2016a.eb @@ -8,7 +8,6 @@ description = """libXt provides the X Toolkit Intrinsics, an abstract widget lib based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).""" toolchain = {'name': 'intel', 'version': '2016a'} -toolchainopts = {'optarch': True} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] @@ -16,6 +15,12 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), ('kbproto', '1.0.7'), + ('xorg-macros', '1.19.0'), + ('xcb-proto', '1.11', '', True), + ('libpthread-stubs', '0.3'), + ('xextproto', '7.3.0'), + ('inputproto', '2.3.1'), + ('xtrans', '1.3.5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-foss-2016a.eb b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..ea33d4f1808c86ff591f1961ff50843358527358 --- /dev/null +++ b/easybuild/easyconfigs/l/libXxf86vm/libXxf86vm-1.1.4-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libXxf86vm' +version = '1.1.4' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 XFree86 video mode extension library""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +builddependencies = [ + ('xf86vidmodeproto', '2.3.1'), + ('xorg-macros', '1.19.0'), +] + +dependencies = [ + ('libX11', '1.6.3'), +] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xf86vmode.h']+ + ['lib/libXxf86vm.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libbitmask/libbitmask-2.0.eb b/easybuild/easyconfigs/l/libbitmask/libbitmask-2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..5a0206f95032209215fec0ab760ccb524bb73c83 --- /dev/null +++ b/easybuild/easyconfigs/l/libbitmask/libbitmask-2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libbitmask' +version = '2.0' + +homepage = 'http://oss.sgi.com/projects/cpusets/' +description = "libbitmask provides a convenient, powerful bitmask data type" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['ftp://oss.sgi.com/projects/cpusets/download/'] +sources = [SOURCE_TAR_BZ2] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = "aclocal && libtoolize && autoconf && automake --add-missing && " + +sanity_check_paths = { + 'files': ['include/bitmask.h', 'lib/libbitmask.a', 'lib/libbitmask.so'], + 'dirs': ['share'], +} + +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/libcmaes/libcmaes-0.9.5-foss-2016a.eb b/easybuild/easyconfigs/l/libcmaes/libcmaes-0.9.5-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..33991cf99da11bcaba30d7f89780f4d0bb926987 --- /dev/null +++ b/easybuild/easyconfigs/l/libcmaes/libcmaes-0.9.5-foss-2016a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libcmaes' +version = '0.9.5' + +homepage = 'http://beniz.github.io/libcmaes/' +description = """libcmaes is a multithreaded C++11 library for high performance +blackbox stochastic optimization using the CMA-ES algorithm +for Covariance Matrix Adaptation Evolution Strategy.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/beniz/%(namelower)s/archive'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Eigen', '3.2.8'), +] + +sanity_check_paths = { + 'files': ['lib/libcmaes.a', 'lib/libcmaes.%s' % SHLIB_EXT, 'lib/pkgconfig/libcmaes.pc'], + 'dirs': ['bin', 'include/libcmaes'], +} + +preconfigopts = "./autogen.sh && " + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libcpuset/libcpuset-1.0.eb b/easybuild/easyconfigs/l/libcpuset/libcpuset-1.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..51fb71266e59fa4bfd6c55ac35600a4bcba31c34 --- /dev/null +++ b/easybuild/easyconfigs/l/libcpuset/libcpuset-1.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libcpuset' +version = '1.0' + +homepage = 'http://oss.sgi.com/projects/cpusets/' +description = "libcpuset provides full access to cpuset capabilities" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['ftp://oss.sgi.com/projects/cpusets/download/'] +sources = [SOURCE_TAR_BZ2] + +builddependencies = [('Autotools', '20150215')] +dependencies = [('libbitmask', '2.0')] + +preconfigopts = "mv configure.in configure.ac && aclocal && libtoolize && autoconf && automake --add-missing && " + +sanity_check_paths = { + 'files': ['include/cpuset.h', 'lib/libcpuset.a', 'lib/libcpuset.so'], + 'dirs': ['share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goolf-1.4.10.eb index e765208e8d31bbf53fbccb161fc7747da2f3cfd9..d1965504ac23730d66fbe94f4a213caa135a2d28 100644 --- a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-goolf-1.4.10.eb @@ -11,7 +11,7 @@ toolchainopts = {'optarch': True} source_urls = ['http://ab-initio.mit.edu/libctl/'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('guile', '1.8.8')] +dependencies = [('Guile', '1.8.8')] # fix for guile-config being broken because shebang line contains full path to bin/guile configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' diff --git a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-5.3.0.eb index d73a51293468555a9e2bae5c79ad4e1f56fba2ad..e2eae48a9cc16c38c04aecbc1397d92a4f419116 100644 --- a/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libctl/libctl-3.2.1-ictce-5.3.0.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True} source_urls = ['http://ab-initio.mit.edu/libctl/'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('guile', '1.8.8')] +dependencies = [('Guile', '1.8.8')] # fix for guile-config being broken because shebang line contains full path to bin/guile configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' diff --git a/easybuild/easyconfigs/l/libctl/libctl-3.2.2-foss-2016a.eb b/easybuild/easyconfigs/l/libctl/libctl-3.2.2-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c0df76a350a9ebf78b48f7ad9b4fccf2ee867af3 --- /dev/null +++ b/easybuild/easyconfigs/l/libctl/libctl-3.2.2-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libctl' +version = '3.2.2' + +homepage = 'http://ab-initio.mit.edu/libctl' +description = """libctl is a free Guile-based library implementing flexible control files for scientific simulations.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True} + +source_urls = ['http://ab-initio.mit.edu/libctl/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Guile', '2.0.11')] + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libctl/libctl-3.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libctl/libctl-3.2.2-intel-2015a.eb index 0de2f0bd938d65de14493ce42034937df366cd65..86ba253737cf9997f183843783f6512144cc5aea 100644 --- a/easybuild/easyconfigs/l/libctl/libctl-3.2.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libctl/libctl-3.2.2-intel-2015a.eb @@ -12,7 +12,7 @@ toolchainopts = {'optarch': True} source_urls = ['http://ab-initio.mit.edu/libctl/'] sources = [SOURCELOWER_TAR_GZ] -dependencies = [('guile', '1.8.8')] +dependencies = [('Guile', '1.8.8')] # fix for guile-config being broken because shebang line contains full path to bin/guile configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.18.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libdap/libdap-3.18.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..dc2d40a9157369e7e89af9ba94b2c3eca9e9aee4 --- /dev/null +++ b/easybuild/easyconfigs/l/libdap/libdap-3.18.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libdap' +version = '3.18.1' +versionsuffix = "-Python-2.7.11" + +homepage = 'http://opendap.org/download/libdap' +description = """A C++ SDK which contains an implementation of DAP 2.0 + and the development versions of DAP3, up to 3.4. + This includes both Client- and Server-side support classes.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.opendap.org/pub/source/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.5.39'), +] + +dependencies = [ + ('cURL', '7.47.0'), + ('libxml2', '2.9.3', versionsuffix), + ('LibUUID', '1.0.3'), +] + +sanity_check_paths = { + 'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' 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/libdwarf/libdwarf-20150310-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libdwarf/libdwarf-20150310-GCC-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..7d27b9549934ec63b9678ab135fa332eca2363ab --- /dev/null +++ b/easybuild/easyconfigs/l/libdwarf/libdwarf-20150310-GCC-4.9.2.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'libdwarf' +version = '20150310' + +homepage = 'http://www.prevanders.net/dwarf.html' +description = """The DWARF Debugging Information Format is of interest to programmers working on compilers +and debuggers (and anyone interested in reading or writing DWARF information))""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.prevanders.net'] + +dependencies = [('libelf', '0.8.13')] + +with_configure = True +preconfigopts = 'env CFLAGS="-fPIC $CFLAGS" ' +configopts = "--enable-shared " + +# This is dirty but libdwarf cannot find it's own library in the build process... +prebuildopts = ' LD_LIBRARY_PATH="../libdwarf:$LD_LIBRARY_PATH" ' + +files_to_copy = [ + (["dwarfdump/dwarfdump"], "bin"), + (["libdwarf/libdwarf.a", "libdwarf/libdwarf.%s" % SHLIB_EXT], "lib"), + (["libdwarf/libdwarf.h", "libdwarf/dwarf.h"], "include"), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["bin", "lib", "include"] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.8.3.eb b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.8.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..370d7d47bc7608ef05f4d296439ea52ec39a713c --- /dev/null +++ b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.8.3.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'libelf' +version = '0.8.13' + +homepage = 'http://www.mr511.de/software/english.html' +description = """libelf is a free ELF object file access library""" + +toolchain = {'name': 'GCC', 'version': '4.8.3'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.mr511.de/software/'] + +modextrapaths = {'CPATH': 'include/libelf'} + +sanity_check_paths = { + 'files': ['lib/libelf.a', 'lib/libelf.%s' % SHLIB_EXT, 'lib/libelf.so.0', 'include/libelf/libelf.h'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.9.2.eb index 9babe1877c9ef230910b0577610b4573492a5ad7..2157a2a132af00833a075d759ef780405060d206 100644 --- a/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libelf/libelf-0.8.13-GCC-4.9.2.eb @@ -11,8 +11,10 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCE_TAR_GZ] source_urls = ['http://www.mr511.de/software/'] +modextrapaths = {'CPATH': 'include/libelf'} + sanity_check_paths = { - 'files': ['lib/libelf.a', 'lib/libelf.%s' % SHLIB_EXT, 'lib/libelf.so.0', 'include/libelf.h'], + 'files': ['lib/libelf.a', 'lib/libelf.%s' % SHLIB_EXT, 'lib/libelf.so.0', 'include/libelf/libelf.h'], 'dirs': ['lib/pkgconfig'] } diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..7a3944e39b3e9278e33a0ae98f87997d341e9f58 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCC-4.9.3-2.25.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': 'GCC', 'version': '4.9.3-2.25'} + +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/libffi/libffi-3.2.1-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..54836f268142e76549cf500628d173edfe85589e --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-GCC-5.4.0-2.26.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': 'GCC', 'version': '5.4.0-2.26'} + +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/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/libffi/libffi-3.2.1-foss-2016b.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..14329b386711b005ecc1d5a385542e0d4ef56071 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2016b.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': '2016b'} + +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/libffi/libffi-3.2.1-intel-2016b.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..fc2b624589d4b9f1a47b8afebad86c61db7dab65 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-intel-2016b.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': 'intel', 'version': '2016b'} + +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/libfontenc/libfontenc-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-foss-2016a.eb index b21fd6654ef5273b817c42258a2d78b40bbf78a6..0d11f8dc5f403b6281c7b9e3aebaf380c0b21ff0 100644 --- a/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-foss-2016a.eb @@ -13,6 +13,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), + ('xorg-macros', '1.19.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-intel-2016a.eb b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-intel-2016a.eb index 458d0fa78b28b783fe667bfb6acca1f91fb4d89a..089bcb63fe7c732e42628bc694322162a14f99a9 100644 --- a/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libfontenc/libfontenc-1.1.3-intel-2016a.eb @@ -13,6 +13,7 @@ source_urls = [XORG_LIB_SOURCE] builddependencies = [ ('xproto', '7.0.28'), + ('xorg-macros', '1.19.0'), ] sanity_check_paths = { 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/libharu/libharu-2.3.0-foss-2016a.eb b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f150abd20cc8e5ebf00b17ffde62418c88de1f2b --- /dev/null +++ b/easybuild/easyconfigs/l/libharu/libharu-2.3.0-foss-2016a.eb @@ -0,0 +1,37 @@ +## +# 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 +## + +easyblock = 'CMakeMake' + +name = 'libharu' +version = '2.3.0' + +homepage = 'http://libharu.org/' +description = """libHaru is a free, cross platform, open source library for generating PDF files.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [' https://github.com/libharu/libharu/archive/'] +sources = ['RELEASE_%s.tar.gz' % '_'.join(version.split('.'))] + +dependencies = [('libpng', '1.6.23')] + +builddependencies = [('CMake', '3.6.1')] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libhpdf.%s' % SHLIB_EXT], + 'dirs': ['if', 'include', 'lib'] +} + +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-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5ff48e3ecbbbbfe64fa1ae7d6eff0c77193c58a9 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.0-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.5.0' + +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] + +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/libjpeg-turbo/libjpeg-turbo-1.5.0-foss-2016b.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.0-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..375efca54b38ae95391f52117f05d5ed2696633c --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.0-foss-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.5.0' + +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', '2.12.02'), +] + +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/libjpeg-turbo/libjpeg-turbo-1.5.0-intel-2016b.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..192e5f589733e265231fb5783d7851510e2f63cb --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.5.0-intel-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.5.0' + +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/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/libmatheval/libmatheval-1.1.11-foss-2015b.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2015b.eb index 2fd935d0b5e5b5100d7893e711c282d54c805e23..e1b1e8de360914306a697eadf9804345c047e38e 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-foss-2015b.eb @@ -17,7 +17,7 @@ dependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), ('byacc', '20150711'), - ('guile', '1.8.8'), + ('Guile', '1.8.8'), ] configopts = '--with-pic ' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2015b.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2015b.eb index 5c07ab422c00b5f43f6641ccebbd687d59137667..61dae0d3d6a1dc4a92617148a4dbc5a5caab654a 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2015b.eb @@ -17,7 +17,7 @@ dependencies = [ ('flex', '2.5.39'), ('Bison', '3.0.4'), ('byacc', '20150711'), - ('guile', '1.8.8'), + ('Guile', '1.8.8'), ] configopts = '--with-pic ' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016a.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e8c49e497ec884bcf9dbbe639e39271adb489485 --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libmatheval' +version = '1.1.11' + +homepage = 'http://www.gnu.org/software/libmatheval/' +description = """GNU libmatheval is a library (callable from C and Fortran) to parse + and evaluate symbolic expressions input as text.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('byacc', '20160324'), + ('Guile', '1.8.8'), +] + +configopts = '--with-pic ' + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016b.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..1e97665ea81cac89541c4f5daed0fe495d5052b4 --- /dev/null +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.11-intel-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libmatheval' +version = '1.1.11' + +homepage = 'http://www.gnu.org/software/libmatheval/' +description = """GNU libmatheval is a library (callable from C and Fortran) to parse + and evaluate symbolic expressions input as text.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('byacc', '20160606'), + ('Guile', '1.8.8'), +] + +configopts = '--with-pic ' + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +sanity_check_paths = { + 'files': ['lib/libmatheval.a', 'include/matheval.h'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb index f514350317d8a3396e0a98ab0739848978f39ad9..5c4d14cc828662b693c8a158021412fd5109c9aa 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-goolf-1.4.10.eb @@ -17,7 +17,7 @@ dependencies = [ ('flex', '2.5.35'), ('Bison', '2.5'), ('byacc', '20120526'), - ('guile', '1.8.8'), + ('Guile', '1.8.8'), ] configopts = '--with-pic ' diff --git a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb index 9c911d9a3d98b8f8b0518c2dd0550aca8cc9d609..69e1e6bcedf93b9529f1bfcc3226700299c84c18 100644 --- a/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libmatheval/libmatheval-1.1.8-ictce-5.3.0.eb @@ -17,7 +17,7 @@ dependencies = [ ('flex', '2.5.35'), ('Bison', '2.5'), ('byacc', '20120526'), - ('guile', '1.8.8'), + ('Guile', '1.8.8'), ] configopts = '--with-pic ' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..1b97f391040ef77b162ca16a3b6a8e6af6460dfc --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.21-CrayGNU-2015.11.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.21' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +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-1.6.23-foss-2016a.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.23-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..af1401e11b5368f7ce51eec51ac6a1452e5696b5 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.23-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.23' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'foss', 'version': '2016a'} +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-1.6.23-foss-2016b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.23-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..edfa6b1a1932dfbd5ae85fb29cce144bf9157eb1 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.23-foss-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.23' + +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-1.6.23-intel-2016b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.23-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..22d3511f9d8f4672893e0aa22179ad5041b7a024 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.23-intel-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.23' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.24-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.24-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..a2901e08909e0d2c01b2f2b4aa4b9efa99a3f1dd --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.24-GCCcore-4.9.3.eb @@ -0,0 +1,32 @@ +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': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.25'), +] + +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-1.6.24-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-1.6.24-intel-2016b.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.24-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..712306e890560fca6f5ec9c06c847b371980470e --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.24-intel-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': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +majminver = ''.join(version.split('.')[:2]) +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', 'lib/libpng.a', + 'lib/libpng.%s' % SHLIB_EXT, 'lib/libpng%s.a' % majminver, 'lib/libpng%s.%s' % (majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.26-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/libpsortb/libpsortb-1.0-foss-2016a.eb b/easybuild/easyconfigs/l/libpsortb/libpsortb-1.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..41eb85171a98b7488d3da4b5a1ef4cb59bd0270e --- /dev/null +++ b/easybuild/easyconfigs/l/libpsortb/libpsortb-1.0-foss-2016a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libpsortb' +version = '1.0' + +homepage = "http://psort.org/" +description = """PSORT family of programs for subcellular localization prediction as well as other datasets and + resources relevant to localization prediction.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.psort.org/download/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib64/libhmmer.so','lib64/libsvmloc.so'], + 'dirs': [], +} + +moduleclass = 'bio' \ No newline at end of file diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2016.03.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..c434630db4d4707fa07e9a6982c63946512afdff --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-2016.03.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': 'CrayGNU', 'version': '2016.03'} +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-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-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..0c4b37fadc3908d427e672bbd287f88474ffbf34 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-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': 'GCC', 'version': '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-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..645b3114fd3bcbea8a8c24663410b9da5b577b99 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-GCC-5.4.0-2.26.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': '5.4.0-2.26'} +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-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-foss-2016b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..7cdfb75d7adebf1437204c622cf20878dc0de234 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2016b.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': '2016b'} +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-intel-2016b.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e527eb31ce2b0a38da552abfc4beaf9db7c7d0c3 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2016b.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': 'intel', 'version': '2016b'} +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/libsodium/libsodium-1.0.11-foss-2016b.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..9f0f8fead0fb89fd35a62a1ed4b14d7535ed9805 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-foss-2016b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.11' + +homepage = 'http://doc.libsodium.org/' +description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, + password hashing and more.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://download.libsodium.org/libsodium/releases/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['b58928d035064b2a46fb564937b83540'] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.%s' % SHLIB_EXT, 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-intel-2016b.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..84ddd92f67cf0c547dc618aad7cb99630bc3c1c8 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.11-intel-2016b.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.11' + +homepage = 'http://doc.libsodium.org/' +description = """Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, + password hashing and more.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://download.libsodium.org/libsodium/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..ba5556d8b58c436d3c6963f04275aab0e2180431 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCC-5.4.0-2.26.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': 'GCC', 'version': '5.4.0-2.26'} + +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-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..ae9366cdfd6f30e337176402093840ef7781c7b4 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-4.9.3.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'http://www.gnu.org/software/libtool' +description = """GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries + behind a consistent, portable interface.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + ('binutils', '2.25') +] + +dependencies = [ + ('M4', '1.4.17'), +] + +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-foss-2016b.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ea26f7eae745717f4fe3957f4da39eef8121e9a5 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-foss-2016b.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': '2016b'} + +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-intel-2016b.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..c877e8af5c37794954131c3cc774c34950c66a29 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-intel-2016b.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': '2016b'} + +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/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..6d7bea7d3d375e9962e77f668d4a3ac104470d8d --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-GCC-4.9.3-2.25.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.3' + +homepage = 'http://www.gnu.org/software/libunistring/' +description = """This library provides functions for manipulating Unicode strings and for manipulating C strings + according to the Unicode standard.""" + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +parallel = 1 + +sanity_check_paths = { + 'files' : ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs' : ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-intel-2016b.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..a1958c52c67032d5e96425f06b3e1224daf2398b --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.6-intel-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libunistring' +version = '0.9.6' + +homepage = 'http://www.gnu.org/software/libunistring/' +description = """This library provides functions for manipulating Unicode strings and for manipulating C strings + according to the Unicode standard.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = [GNU_SOURCE] + +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libunistring.a', 'lib/libunistring.%s' % SHLIB_EXT] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs': ['include/unistring'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..6bc89f03e758c89c71eb1d8fd7b6cd8ae5096000 --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb @@ -0,0 +1,23 @@ +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': 'GCC', 'version': '4.9.2'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SAVANNAH_SOURCE] + +sanity_check_paths = { + 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], + 'dirs': [] +} + +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/libxc/libxc-2.2.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4f8d72a6348448066ad51e5093f386222e0a0904 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.3' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..a8378f30876e07fe358031c9e97886218e07434e --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.3-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.3' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fd83352b3068984fde6c1590772f4d38bec2a18c --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '3.0.0' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..951b7f060524ccb3711edb6bd9b6bf5ae92a9d79 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-3.0.0-intel-2016b.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '3.0.0' + +homepage = 'http://www.tddft.org/programs/octopus/wiki/index.php/Libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared --enable-fortran' + +# From the libxc mailing list +# To summarize: expect less tests to fail in libxc 2.0.2, but don't expect +# a fully working testsuite soon (unless someone wants to volunteer to do +# it, of course ) In the meantime, unless the majority of the tests +# fail, your build should be fine. +#runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libxc%s.%s' % (x,y) for x in ['', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb index fa27444b38602619c535a125c015a34a5f30e451..7a2944d9e46a7130a6fdb62591efc11df63f94fc 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-foss-2016a.eb @@ -17,6 +17,7 @@ builddependencies = [ ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), ] dependencies = [ ('libXau', '1.0.8'), diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb index 098e8569bb68c496a81ab6224dd11b7d4e2fd6b5..c69ddcedb6e6f44db032a47bcc2ef5bb1cdf5843 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.11.1-intel-2016a.eb @@ -13,9 +13,11 @@ source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] builddependencies = [ + ('pkg-config', '0.29'), ('xcb-proto', '1.11', '', True), ('xproto', '7.0.28'), ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), ] dependencies = [ ('libXau', '1.0.8'), diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb index 5f450a09888a55b8da1306ac37a3d9bfffec94a6..54ae81472226e4269eaa839529452486711d2c8a 100644 --- a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-foss-2016a.eb @@ -22,6 +22,10 @@ dependencies = [ builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb index 8611f0332bd3f25d136cb0b0941c0bccfb71e6be..b3bcbc8fa66888609ac068d37861a0b62ce847a2 100644 --- a/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxkbcommon/libxkbcommon-0.6.1-intel-2016a.eb @@ -22,6 +22,10 @@ dependencies = [ builddependencies = [ ('flex', '2.6.0'), ('Bison', '3.0.4'), + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb index e1868be130ff398cabf41c2b25011dc0b7649851..b18cebf5edfe15fafef037c8c98a3bc8eb5feb71 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10-Python-2.7.3.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.8.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -13,20 +14,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.7'), - ('Python', pythonver), + ('Python', '2.7.3'), ] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb index 00021cddc927def653589c79778a6281c6125a56..8dce8ccf026a985e59443dadc034a5467ad1f248 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goolf-1.4.10.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.8.0' @@ -15,13 +13,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb index 5a92ef8bcb6c45abb4b30d473c350bbe58df8c0e..ecc03cc89879e7574a2d6dda45c7195f77c1bc8d 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0-Python-2.7.3.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.8.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,20 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.7'), - ('Python', pythonver), + ('Python', '2.7.3'), ] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb index 98b15d6f97412023622f8b60ec1e4026c2e5f2bc..e6c885e909be27f3c699a6491ab49c6394202da5 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-5.3.0.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.8.0' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb index 3f185c7e6d12585f91d9a7e745b987de5b7a23d9..b3162eb734e7b86a0bcef72a0f8138162a9a135e 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-intel-2015a-Python-2.7.3.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.8.0' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,20 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.3' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.8'), - ('Python', pythonver), + ('Python', '2.7.3'), ] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb index ee43d716e22326706f520952b966791780ce6699..437c090f565f41f0227f03c999a96bb5a3e205c1 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goolf-1.4.10.eb @@ -1,11 +1,10 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.0' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} @@ -15,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb index f0aa6dee9cb24a65f7885798ea62e7ae936da42e..de12c4768fc8a485c3adb888d0d9d585753be7ec 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-5.3.0.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.0' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-foss-2015b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-foss-2015b.eb index 03c075bd1ad120d75cf42b76c40171a8fbadd5f4..4a999c8acc9c85094e6d81c5942ca320e3c14178 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-foss-2015b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -17,13 +15,5 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] - -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb index ae7f22f7a4879db23c81cc74d16da7ac406148c4..758bb9dd8441658b60b063f021d3953c2db438c6 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10-Python-2.7.5.eb @@ -7,6 +7,7 @@ description = """Libxml2 is the XML C parser and toolchain developed for the Gno outside of the Gnome platform).""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} source_urls = [ 'http://xmlsoft.org/sources/', @@ -14,8 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - dependencies = [ ('zlib', '1.2.8'), ('Python', '2.7.5'), diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb index 544880545882f3f6c20049a7865e12751323e67b..4e5a1b7c92866540212495f3f5cd8936d7ea6acf 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.4.10.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb index b09000568f8db517f296a5991790e8657ed87348..ef65dcb9acc3a5ca1e9644f781f661a8951eb572 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb index aa7e4b1f778e00617c3d95c2057846db16512f20..c4fbddee119f9f128fb3c1cd80b1c6e75e59de9d 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb index e50f08d5e37560069cdf6158b737748924811bab..345f7339bbbd37920163a46d5a2b33fc49f26a00 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.3.0.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.7')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb index 9d4e84392a22f9d5a177706e700433ffbc5069c9..0cdd2e03c2cbc0a3c1ac84b1fe01d32b77b11a34 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0-Python-2.7.6.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.9.1' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,20 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.6' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.7'), - ('Python', pythonver), + ('Python', '2.7.6'), ] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb index 0cdacffa3af6fd2ec1e7825282e6488f47af531b..35cce5f83232858d2fec4bc624a7abdec05b235f 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.5.0.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb index ca67a911c12c9b5c5244a06bb8a459740ceb6bcd..9322eb079f38c76ff91b1a02d82687be4c0d6bb8 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-7.1.2.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb index c6335dd8b2f74a716215ae7f98f6becd3cae7cdb..7322bbf1cfcaec2585222fdce9fa19fb1ab5c328 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-intel-2014b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.1' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..47732da727b21a4eeabf404bbfa1b02f1b651c0f --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.8.3.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': '4.8.3'} +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/libxml2-2.9.2-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/libxml2-2.9.2-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb index 841eddc11e74280cdfe8eeebfe8c230067635006..84f6203208c0d900800053d9e93973166fb2f02a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.2.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.3-2.25.eb index 8d892b499fd15242aee8ba21b4c92f8a434cf7df..80b60e88bec9a3c33027537187dccdf9d60772c2 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GCC-4.9.3-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb index 3c33fb41dada3f6026c6e84977b08a46bda80cb2..8fb7cc97f084af04b80afd04124e6a63dc9c9467 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-GNU-4.9.3-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb index ae39cc8c24a233b63d52b459e44d9d655fcce23c..0d7eb11ba26209348356964703c2f93eb2c0f612 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015a.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb index ad02e51c2e0b8cc8fde45590554164500bb40d2c..933fed03d3849081a4eb88ffbf7e11db4e7ae826 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-foss-2015b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb index f232e382c068930ef87c3117dfc1502063d04f79..935739296d91df4d6c8e30aa1c53936866a6e7e5 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb index 54c5dad803dc36681877716fb5eed01f228cc478..22db63d4d819a1e1dbd653d6220b5b3bee595ea7 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.16.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb index 22d8c149d6182236593bddd12650e24ac05c118c..42669ee57de4d05ba61fbbd7c5f20599ce5ef2a7 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb index acdd85b6e6aace5c28f4aebde20699524ac346f3..947a255ee98d9c0bf53dcb38fa7afeecbc7a314b 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb index 22aefe7d0cda545af8245c0aa775c2cfe7e636d8..d0e28b417879628ed190db3f6f2a1977e781c4cb 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb index 37724f23f1b4a7ba85174a824f4ffa561c475639..b4846f1d26a11fdf51871f84e70f9eeb2ad07715 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.10.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.9.2' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,15 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.10' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.8'), - ('Python', pythonver), + ('Python', '2.7.10'), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb index 307b1793d4b0e1a6358aa8a2629b6df694701eee..af7eb40b20cf055c503e181c25e118e3487cf1ab 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a-Python-2.7.9.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.9.2' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,15 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.9' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.8'), - ('Python', pythonver), + ('Python', '2.7.9'), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb index 1a4f4c99c405566e2a75e7207a9e9cae081db8f7..28e034ab2caf64623deb5d6df860dca27b562bb5 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015a.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb index b95f92dfd972c2ab5f1dc8c34d76ca2032849a8a..a9be90146562af4f948d84eb5ad9001da5864495 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2015b.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.2' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-CrayGNU-2016.03.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-CrayGNU-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..135641e29dfac96075b40ceeccaf0b06a976766f --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-CrayGNU-2016.03.eb @@ -0,0 +1,21 @@ +# contributed by Luca Marsella (CSCS) +name = 'libxml2' +version = "2.9.3" + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'CrayGNU', 'version': '2016.03'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb index ba6d0a4c3f26989449ef72ed359a4fb73933c8a8..4447186030ad7baa52166e810271a66f8a1c5abe 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-GCC-4.9.3-2.25.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.3' @@ -16,13 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb index 6cafc86e4f1dfbfc33ad5c06b6c66069a96293bc..38a9a0dfbcd8e59d5d4be4f1dffb4889be9de3b1 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a-Python-2.7.11.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.9.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,15 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.11' -pythonshortver = '.'.join(pythonver.split('.')[:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.8'), - ('Python', pythonver), + ('Python', '2.7.11'), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb index 59e0331739e491981981c5cba731ee5ee494be69..3f244ca27186be38a8c247a06f64f348d8f9b8c3 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2015a.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.3' @@ -16,8 +14,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [ ('zlib', '1.2.8'), ] diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb index 0df5cbd9574ae3f33a2dfe201fbf9d97571fbeb2..5c76876c0d7dc35140cded0f61d42a8f70730338 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a-Python-2.7.11.eb @@ -15,8 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - dependencies = [ ('zlib', '1.2.8'), ('Python', '2.7.11'), diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a.eb index 9f21eb1b663320556b4e5a4ce63eb3cd42a74085..45737f40c5f3de6fa5cc69229b80c4a32e9f45ad 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-foss-2016a.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.3' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb index 1f39ac3f7d499c91a45b4cba2d5e7ed9b663af26..b5f12f37c260039129046dcf2e74cba810255c04 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-gimkl-2.11.5.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.3' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-goolf-1.7.20.eb index 66513c188bb1828608c819f54afe2890174c8cbb..116952d9c812f84337f07d876165a9fa20a1619a 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-goolf-1.7.20.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.3' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.10.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.10.eb index 34777c9cc6854fe24010d28e50f4775ff509cd8b..f919243b0f910a3e6650c2aa96cc2c01fe1c06e5 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.10.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.10.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.9.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,15 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.10' -pythonshortver = '.'.join(pythonver.split('.')[0:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.8'), - ('Python', pythonver), + ('Python', '2.7.10'), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.11.eb index b28071061aede91e38954f4b53595cce896a95b2..95fbcbd2d44c99e91af66736044879a65d20c7a6 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2015b-Python-2.7.11.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.9.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,15 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pythonver = '2.7.11' -pythonshortver = '.'.join(pythonver.split('.')[:2]) -versionsuffix = '-%s-%s' % ('Python', pythonver) - dependencies = [ ('zlib', '1.2.8'), - ('Python', pythonver), + ('Python', '2.7.11'), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11.eb index 41e2af0e98c1c7b46d1cfb791bef67d5eb1eacd6..b50b2e930b8987ff725ed42a0b8311f992c65b5b 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a-Python-2.7.11.eb @@ -1,5 +1,6 @@ name = 'libxml2' version = '2.9.3' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://xmlsoft.org/' description = """Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable @@ -14,15 +15,9 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --with-zlib=$EBROOTZLIB' - -pyver = '2.7.11' -pyshortver = '.'.join(pyver.split('.')[:2]) -versionsuffix = '-Python-%s' % pyver - dependencies = [ ('zlib', '1.2.8'), - ('Python', pyver), + ('Python', '2.7.11'), ] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb index b762d969015cee07367d5f5be54962ad7912cfe8..483a54f92aae8eaf516059af2fa45bdb20d2c943 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.3-intel-2016a.eb @@ -1,5 +1,3 @@ -easyblock = 'ConfigureMake' - name = 'libxml2' version = '2.9.3' @@ -17,13 +15,6 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python --with-zlib=$EBROOTZLIB' - dependencies = [('zlib', '1.2.8')] -sanity_check_paths = { - 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.%s' % SHLIB_EXT, 'lib64/libxml2.%s' % SHLIB_EXT)], - 'dirs': ['bin', 'include/libxml2/libxml'], -} - 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 new file mode 100644 index 0000000000000000000000000000000000000000..798eea2998235307d5d00aea8af3c0fb879a244b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCC-5.4.0-2.26.eb @@ -0,0 +1,22 @@ +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': 'GCC', 'version': '5.4.0-2.26'} +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-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..4873fafcda4f4fe7a885b55a2163ad7a73e521c1 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-GCCcore-4.9.3.eb @@ -0,0 +1,27 @@ +name = 'libxml2' +version = '2.9.4' + +homepage = 'http://xmlsoft.org/' +description = """Libxml2 is the XML C parser and +toolchain developed for the Gnome project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.25'), +] + +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 new file mode 100644 index 0000000000000000000000000000000000000000..59cbe77a84c29e822094e4106f30403a5a38f533 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016a.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': '2016a'} +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-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 new file mode 100644 index 0000000000000000000000000000000000000000..abee889e32e45347aeb79b9ea097e43f8db010fd --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-foss-2016b.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': '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'), +] + +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 new file mode 100644 index 0000000000000000000000000000000000000000..ab1c0ecd3e4e06b1de1d0d901c284ae53423efa1 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.4-intel-2016b.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': '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'), +] + +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/libxslt/libxslt-1.1.29-intel-2016b.eb b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.29-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..be5d33a181fd8f55bd8fc55aecb8121618417729 --- /dev/null +++ b/easybuild/easyconfigs/l/libxslt/libxslt-1.1.29-intel-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libxslt' +version = '1.1.29' + +homepage = 'http://xmlsoft.org/' +description = """Libxslt is the XSLT C library developed for the GNOME project + (but usable outside of the Gnome platform).""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] + +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('libxml2', '2.9.4'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4-intel-2016a.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e6719ce26146c6b9818377a365d0f9981d9f10be --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4-intel-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.4' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/hfp/libxsmm/archive/'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4.4-intel-2016b.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4.4-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..d0e021010344e7a80b6befb1a144f4dd87b258fa --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.4.4-intel-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.4.4' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/hfp/libxsmm/archive/'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2016b.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e7ae73819e10f919c4caf95037ce7959735c73cb --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2016b.eb @@ -0,0 +1,28 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.1.6' + +homepage = 'http://pyyaml.org/wiki/LibYAML' +description = """LibYAML is a YAML 1.1 parser and emitter written in C.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['yaml-%(version)s.tar.gz'] +source_urls = ['http://pyyaml.org/download/libyaml/'] + +sanity_check_paths = { + 'files': ["include/yaml.h", "lib/libyaml.a", "lib/libyaml.%s" % SHLIB_EXT], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCcore-4.9.3.eb index cda484e29cbf51c2939315442e9482a9ce287f97..a97266b7553266b7864d679c568a10772271cee0 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-4.1.0-GCCcore-4.9.3.eb @@ -15,7 +15,7 @@ source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] patches = ['likwid-%(version)s-config-mk.patch'] -builddependencies = [('binutils', '2.25', '', ('GCCcore', '4.9.3'))] +builddependencies = [('binutils', '2.25')] skipsteps = ['configure'] buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s' 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/l/lxml/lxml-3.6.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/l/lxml/lxml-3.6.4-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..2329541fb323ef2ca6b4b3271e19a2091a81d380 --- /dev/null +++ b/easybuild/easyconfigs/l/lxml/lxml-3.6.4-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'lxml' +version = '3.6.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://lxml.de/' +description = """The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://lxml.de/files/'] +sources = [SOURCE_TGZ] + +dependencies = [ + ('Python', '2.7.12'), + ('libxml2', '2.9.4'), + ('libxslt', '1.1.29'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' 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 new file mode 100644 index 0000000000000000000000000000000000000000..ab6365038384b116ad80f0d641dd1fda0c4ab45d --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCC-5.4.0-2.26.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': 'GCC', 'version': '5.4.0-2.26'} + +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-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 new file mode 100644 index 0000000000000000000000000000000000000000..83effb6682bc6daab9c4a5d934fc9d58748617a2 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-4.9.4.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': '4.9.4'} + +sources = [SOURCELOWER_TAR_GZ] +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 = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000000000000000000000000000000000..702e8595184d52126dd9f26b583214f6a082cd6e --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-5.4.0.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': '5.4.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.26', '', True)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-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 new file mode 100644 index 0000000000000000000000000000000000000000..9a89ad1fbdf638acdb27a35a66649bcbde50dd13 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GCCcore-6.2.0.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': '6.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +# use same binutils version that was used when building GCC toolchain +builddependencies = [('binutils', '2.27', '', True)] + +# '-fgnu89-inline' is required to avoid linking errors with older glibc's, +# see https://github.com/hpcugent/easybuild-easyconfigs/issues/529 +configopts = "--enable-cxx CPPFLAGS=-fgnu89-inline" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-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 new file mode 100644 index 0000000000000000000000000000000000000000..3d6737ba0844df35224d64b4791b3038305d375c --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2016b.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': '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 = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000000000000000000000000000000000..d339ed79b83a37832f155aa63944b49b636e753e --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-intel-2016b.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': '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 = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' 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/MACH/MACH-1.0.18.eb b/easybuild/easyconfigs/m/MACH/MACH-1.0.18.eb new file mode 100644 index 0000000000000000000000000000000000000000..b2fe855c565215f0e3c172f776504c98c1456224 --- /dev/null +++ b/easybuild/easyconfigs/m/MACH/MACH-1.0.18.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 = 'MACH' +version = '1.0.18' + +homepage = 'http://csg.sph.umich.edu/abecasis/MACH/' +description = """MACH 1.0 is a Markov Chain based haplotyper +that can resolve long haplotypes or infer missing genotypes +in samples of unrelated individuals.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://csg.sph.umich.edu/abecasis/MACH/download/'] +sources = ['mach.%(version)s.Linux.tgz'] + +modextrapaths = {'PATH': 'executables'} + +sanity_check_paths = { + 'files': ["executables/mach1", "executables/thunder", "README"], + 'dirs': ["examples"] +} + +moduleclass = 'bio' 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/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb b/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb new file mode 100644 index 0000000000000000000000000000000000000000..35b0a5d11b4ae3da09ef4b5a688b5966e77871f3 --- /dev/null +++ b/easybuild/easyconfigs/m/MATSim/MATSim-0.8.1-intel-2016b-Java-1.8.0_112.eb @@ -0,0 +1,31 @@ +easyblock = 'PackedBinary' + +name = 'MATSim' +version = '0.8.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.matsim.org/' +description = """MATSim is an open-source framework to implement large-scale agent-based transport simulations.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/matsim-org/matsim/releases/download/%(namelower)s-%(version)s/'] +sources = ['%(namelower)s-%(version)s.zip'] + +dependencies = [ + ('Java', '1.8.0_112', '', True), + ('X11', '20160819'), +] + +sanity_check_paths = { + 'files': ['%(namelower)s-%(version)s.jar'], + 'dirs': ['libs'], +} + +modextrapaths = {'CLASSPATH': 'libs/*'} + +modloadmsg = """To execute MATSim GUI: java -jar \\${EBROOTMATSIM}/%(namelower)s-%(version)s.jar +To execute MATSim in batch mode: java org.matsim.run.Controller +You might have to adjust the requested memory""" + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/m/MCL/MCL-14.137-foss-2016a.eb b/easybuild/easyconfigs/m/MCL/MCL-14.137-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..cade8a0bf76776a209c7104aeb86849b4bd7e112 --- /dev/null +++ b/easybuild/easyconfigs/m/MCL/MCL-14.137-foss-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'MCL' +version = '14.137' + +homepage = 'http://micans.org/mcl/' +description = """The MCL algorithm is short for the Markov Cluster Algorithm, a fast +and scalable unsupervised cluster algorithm for graphs (also known as networks) based +on simulation of (stochastic) flow in graphs. """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://micans.org/%(namelower)s/src/'] +sources = ['%(namelower)s-%(version_major)s-%(version_minor)s.tar.gz'] + +sanity_check_paths = { + 'files': ['bin/mcl'], + 'dirs': ['share'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb new file mode 100644 index 0000000000000000000000000000000000000000..caffaedaa3164f9c4e05705552abf415db0bfbfc --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2013a.eb @@ -0,0 +1,18 @@ +name = 'MCR' +version = 'R2013a' + +homepage = 'http://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [ + 'http://www.mathworks.com/supportfiles/MCR_Runtime/%(version)s/', +] +sources = ['%(name)s_%(version)s_glnxa64_installer.zip'] + +dependencies = [('Java', '1.8.0_31')] + +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/MEGACC/MEGACC-7.0.18-1.eb b/easybuild/easyconfigs/m/MEGACC/MEGACC-7.0.18-1.eb new file mode 100644 index 0000000000000000000000000000000000000000..a3ab3c425714ee1778c6d3233548f51c4e9d413a --- /dev/null +++ b/easybuild/easyconfigs/m/MEGACC/MEGACC-7.0.18-1.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2016, UNIGE +# Authors:: Yann Sagon +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'Tarball' + +name = 'MEGACC' +version = '7.0.18-1' + +homepage = 'http://www.megasoftware.net' +description = """MEGA-Computing Core - Sophisticated and user-friendly software suite for analyzing DNA and + protein sequence data from species and populations.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(namelower)s-%(version)s.x86_64.tar.gz'] +source_urls = ['http://www.megasoftware.net/releases/'] + +sanity_check_paths = { + 'files': ["megacc", "megaproto"], + 'dirs': [], +} + +modextrapaths = { + 'PATH': '', +} + +moduleclass = 'bio' 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/MIGRATE-N/MIGRATE-N-4.2.8-foss-2016a.eb b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-4.2.8-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b6f05aeb5d714d8b9f28bd3bff2a2a08590704c8 --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-4.2.8-foss-2016a.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'MIGRATE-N' +version = '4.2.8' + +homepage = 'http://popgen.sc.fsu.edu/Migrate/Migrate-n.html' +description = """ +Migrate estimates population parameters, effective population sizes +and migration rates of n populations, using genetic data. It +uses a coalescent theory approach taking into account history of +mutations and uncertainty of the genealogy. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['migrate-%(version)s.src.tar.gz'] +source_urls = [ + 'http://popgen.sc.fsu.edu/currentversions/', + 'http://popgen.sc.fsu.edu/oldversions/%(version_major)s.x/%(version_major_minor)s', + 'http://popgen.sc.fsu.edu/oldversions/', + 'http://popgen.sc.fsu.edu/newversions/', +] + +patches = [ + 'migrate-%(version)s_install.patch', +] + +dependencies = [ + ('zlib', '1.2.8'), +] + +configopts = '--enable-A4 "CC=$CC" STDCPLUS=-lstdc++ ' +prebuildopts = 'make mpis && make clean && ' + +start_dir = 'src' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['migrate-n','migrate-n-mpi']], + 'dirs': ['man'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MIGRATE-N/migrate-4.2.8_install.patch b/easybuild/easyconfigs/m/MIGRATE-N/migrate-4.2.8_install.patch new file mode 100644 index 0000000000000000000000000000000000000000..97957ab44e0d8b4679fd3bbbbbef722071947ff5 --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/migrate-4.2.8_install.patch @@ -0,0 +1,13 @@ +#Create parent directories during install +#B. Hajgato January 18th, 2016 +--- src/configure.orig 2014-12-28 03:46:09.000000000 +0100 ++++ src/configure 2016-01-18 14:57:26.331047715 +0100 +@@ -3411,7 +3411,7 @@ + test -s conftest.dir/conftest.one && + test -s conftest.dir/conftest.two + then +- ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c" ++ ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c -D" + break 3 + fi + fi diff --git a/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..c98b95b63b9ec0dde123247e475e4b4cbd2f94a0 --- /dev/null +++ b/easybuild/easyconfigs/m/MIRA/MIRA-4.0.2-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'MIRA' +version = '4.0.2' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://sourceforge.net/p/mira-assembler/wiki/Home/' +description = """MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), + IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads).""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(namelower)s-%(version)s.tar.bz2'] +source_urls = [('http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/', 'download')] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = '--with-boost-libdir=$EBROOTBOOST/lib --with-expat=$EBROOTEXPAT' + +patches = ['MIRA-%(version)s-quirks.patch'] + +builddependencies = [('flex', '2.5.39')] +dependencies = [ + ('Boost', '1.61.0', versionsuffix), + ('expat', '2.1.1'), + ('zlib', '1.2.8'), + ('gperftools', '2.5'), +] + +sanity_check_paths = { + 'files': ["bin/mira"], + 'dirs': ["bin", "share"], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MM-align/MM-align-20130815-goolf-1.4.10.eb b/easybuild/easyconfigs/m/MM-align/MM-align-20130815-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..6c78bbddafbee7052f01c57e9a95343e47c6aaea --- /dev/null +++ b/easybuild/easyconfigs/m/MM-align/MM-align-20130815-goolf-1.4.10.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CmdCp' + +name = 'MM-align' +version = '20130815' + +homepage = 'http://zhanglab.ccmb.med.umich.edu/MM-align/' +description = """ MM-align is an algorithm for structurally aligning + multiple-chain protein-protein complexes. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://zhanglab.ccmb.med.umich.edu/MM-align/'] +sources = ['MMalign.f'] + +checksums = [('md5', '1456e12b1697ea3758d2ac361ae1a7d8')] + +skipsteps = ['source'] + +cmds_map = [('MMalign.f', '$F77 -static -O3 -ffast-math -lm -o MMalign %(source)s')] + +files_to_copy = [(['MMalign'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/MMalign'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb new file mode 100644 index 0000000000000000000000000000000000000000..5b23296323609c153956821f81aff57083cd5946 --- /dev/null +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-goolf-1.4.10-20140425-24cf06.eb @@ -0,0 +1,37 @@ +# 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 = 'MOSAIK' +version = '2.2.28' +git_commit_id = '24cf06' #first six digits of the commit id we will download from github +versionsuffix = '-20140425-%s' % git_commit_id + +homepage = 'https://code.google.com/p/mosaik-aligner/' +description = """ MOSAIK is a reference-guided aligner for next-generation + sequencing technologies """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/wanpinglee/MOSAIK/archive/'] +sources = ['%s.tar.gz' % (git_commit_id)] + +dependencies = [('zlib', '1.2.8')] + +parallel = 1 + +start_dir = "src" + +buildopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' + +files_to_copy = ["bin", "../README", "demo"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["MosaikAligner", "MosaikBuild", "MosaikJump", "MosaikText"]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb new file mode 100644 index 0000000000000000000000000000000000000000..77047640bff14a422b775c5a282966e3c32103a4 --- /dev/null +++ b/easybuild/easyconfigs/m/MOSAIK/MOSAIK-2.2.28-ictce-6.2.5-20140425-24cf06.eb @@ -0,0 +1,37 @@ +# 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 = 'MOSAIK' +version = '2.2.28' +git_commit_id = '24cf06' #first six digits of the commit id we will download from github +versionsuffix = '-20140425-%s' % git_commit_id + +homepage = 'https://code.google.com/p/mosaik-aligner/' +description = """ MOSAIK is a reference-guided aligner for next-generation + sequencing technologies """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +source_urls = ['https://github.com/wanpinglee/MOSAIK/archive/'] +sources = ['%s.tar.gz' % (git_commit_id)] + +dependencies = [('zlib', '1.2.8')] + +parallel = 1 + +start_dir = "src" + +buildopts = ' BIN_DIR="./bin" OBJ_DIR="./obj"' + +files_to_copy = ["bin", "../README", "demo"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["MosaikAligner", "MosaikBuild", "MosaikJump", "MosaikText"]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016b.eb b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..1d9a8972b99841fe9b97a613de351926dc1c7651 --- /dev/null +++ b/easybuild/easyconfigs/m/MPFR/MPFR-3.1.4-intel-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'MPFR' +version = '3.1.4' + +homepage = 'http://www.mpfr.org' +description = """The MPFR library is a C library for multiple-precision + floating-point computations with correct rounding.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://www.mpfr.org/mpfr-%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +patches = ['MPFR_ictce_remove-deprecated-mp.patch'] + +dependencies = [('GMP', '6.1.1')] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libmpfr.%s' % SHLIB_EXT, 'include/mpfr.h'], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/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..c8deee658d0e7a205e20769344c3c5ed5b670328 --- /dev/null +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-foss-2016a-Java-1.8.0_92.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +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/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb index 25c03b4120b295fbdac1c9082800e66e3d9c72b5..273c10ebdec0227e91ee0d895ea0bcd1fdb283da 100644 --- a/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb +++ b/easybuild/easyconfigs/m/MPJ-Express/MPJ-Express-0.44-goolf-1.4.10-Java-1.7.0_75.eb @@ -29,8 +29,10 @@ dependencies = [ # 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",] +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', 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=${EBROOTGTI}' + +sanity_check_paths = { + 'files': ['bin/mustrun', 'include/mustConfig.h'], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..44efa704efcce91063ab660dac48bb3382122748 --- /dev/null +++ b/easybuild/easyconfigs/m/MView/MView-1.57-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "Tarball" + +name = 'MView' +version = "1.57" +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://sourceforge.net/projects/bio-mview/' +description = """ MView reformats the results of a sequence database search or a + multiple alignment, optionally adding HTML markup.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [('http://sourceforge.net/projects/bio-mview/files/bio-mview/mview-%(version)s/', 'download')] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('Perl', '5.16.3')] + +sanity_check_paths = { + 'files': ["bin/mview"], + 'dirs': ["lib"], +} + +modextravars = { + 'PERL5LIB': '$root/lib' +} + +moduleclass = 'bio' 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/Maq/Maq-0.7.0.eb b/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..b78da99d835e73dde489c08ffbf4aeefd4667406 --- /dev/null +++ b/easybuild/easyconfigs/m/Maq/Maq-0.7.0.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'Maq' +version = '0.7.0' + +homepage = 'http://maq.sourceforge.net/maq-man.shtml' +description = """ Maq is a software that builds mapping +assemblies from short reads generated by the +next-generation sequencing machines. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://sourceforge.net/projects/maq/files/maq/%(version)s/'] +sources = ['maq-%(version)s_x86_64-linux.tar.bz2'] + +checksums= ["65edff1529c84783d0a4b9208a91efa9"] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ["asub", "maq", "maq.pdf", "maq.1", "solid2fastq.pl"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb index ae90e1a3edf9664fc1f1c343bec1e1d96ea1e74e..65b18122ab7997ddda6aa25d5eaef65eedf24b35 100644 --- a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.13-intel-2016a.eb @@ -30,10 +30,12 @@ builddependencies = [('CMake', '3.4.3')] separate_build_dir = True -configopts = "-DWITH_PCRE=system -DWITH_JEMALLOC=yes -DWITH_ZLIB=system -DMYSQL_MAINTAINER_MODE=ON" +configopts = "-DWITH_PCRE=system -DWITH_JEMALLOC=yes -DWITH_ZLIB=system -DMYSQL_MAINTAINER_MODE=ON " +configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co sanity_check_paths = { - 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'scripts/mysql_install_db'], + 'files': ['bin/mysql', 'bin/mysqld_safe', 'lib/libmysqlclient.%s' % SHLIB_EXT, 'lib/libmysqld.%s' % SHLIB_EXT, + 'scripts/mysql_install_db'], 'dirs': ['include', 'share'], } diff --git a/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.14-foss-2016a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.14-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f3af0400620569685e3b9a294beb1393e5ae9287 --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.14-foss-2016a.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '10.1.14' + +homepage = 'https://mariadb.org/' +description = """MariaDB An enhanced, drop-in replacement for MySQL.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +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', '4.2.0'), + ('PCRE', '8.38'), + ('XZ', '5.2.2', '-gettext-0.19.7'), + ('Boost', '1.61.0', '-Python-2.7.11'), + ('libxml2', '2.9.3'), +] + +builddependencies = [('CMake', '3.4.3')] + +separate_build_dir = True + +configopts = "-DWITH_PCRE=system -DWITH_JEMALLOC=yes -DWITH_ZLIB=system -DMYSQL_MAINTAINER_MODE=ON " +configopts = "-DDISABLE_LIBMYSQLCLIENT_SYMBOL_VERSIONING=TRUE " # required because of ld.gold +configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co + +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/MariaDB/MariaDB-10.1.14-intel-2016a.eb b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.14-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9fd709497a2a0a8a9c4801ff50d3db93bf428a0d --- /dev/null +++ b/easybuild/easyconfigs/m/MariaDB/MariaDB-10.1.14-intel-2016a.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'MariaDB' +version = '10.1.14' + +homepage = 'https://mariadb.org/' +description = """MariaDB An enhanced, drop-in replacement for MySQL.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +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', '4.2.0'), + ('PCRE', '8.38'), + ('XZ', '5.2.2', '-gettext-0.19.7'), + ('Boost', '1.61.0', '-Python-2.7.11'), + ('libxml2', '2.9.3'), +] + +builddependencies = [('CMake', '3.4.3')] + +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 + +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/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/Meep/Meep-1.2-goolf-1.4.10.eb b/easybuild/easyconfigs/m/Meep/Meep-1.2-goolf-1.4.10.eb index 9c0e3d28b0fe66fbdca84721e64096d5bf7f5339..4c276a60f7abffa3f655e376adfa615ce416735f 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.2-goolf-1.4.10.eb @@ -21,6 +21,7 @@ dependencies = [ ('HDF5', '1.8.7'), ('libctl', '3.2.1'), ('GSL', '1.15'), + ('Guile', '1.8.8'), ] configopts = '--with-pic --with-mpi --without-gcc-arch --with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared ' diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb b/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb index 475c5f321c7a187e89e19bf1bb2594257723e056..a044e520c41cf9e84e194272cf312bf38a3671d0 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-5.3.0.eb @@ -23,7 +23,8 @@ dependencies = [ ('HDF5', '1.8.7'), ('libctl', '3.2.1'), ('GSL', '1.15'), - ('FFTW', '3.3.1') + ('FFTW', '3.3.1'), + ('Guile', '1.8.8'), ] configopts = "--with-pic --with-mpi --with-blas=mkl_em64t --with-lapack=mkl_em64t --without-gcc-arch " diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.3-foss-2016a.eb b/easybuild/easyconfigs/m/Meep/Meep-1.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..de57379a00bef82b8060edba5d108f35b87033cc --- /dev/null +++ b/easybuild/easyconfigs/m/Meep/Meep-1.3-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Meep' +version = '1.3' + +homepage = 'http://ab-initio.mit.edu/wiki/index.php/Meep' +description = """Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package + developed at MIT to model electromagnetic systems.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True, 'opt': True, 'optarch': True, 'unroll': True, 'pic': True} + +source_urls = [ + 'http://ab-initio.mit.edu/meep/', + 'http://ab-initio.mit.edu/meep/old/', +] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['Meep-%(version)s_version-string-without-spaces.patch'] + +dependencies = [ + ('Harminv', '1.4'), + ('HDF5', '1.8.17'), + ('libctl', '3.2.2'), + ('GSL', '2.1'), + ('Guile', '2.0.11'), +] + +configopts = "--with-pic --with-mpi --with-blas=mkl_em64t --with-lapack=mkl_em64t --without-gcc-arch " +configopts += "--with-libctl=$EBROOTLIBCTL/share/libctl --enable-shared " + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts += 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb index baee3155cfdb2c7e519d33b9cc6bccc97c15aa35..942d69d506ce704e27fde356d49894e91db75b09 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb @@ -23,7 +23,8 @@ dependencies = [ ('HDF5', '1.8.14'), ('libctl', '3.2.2'), ('GSL', '1.16'), - ('FFTW', '3.3.4') + ('FFTW', '3.3.4'), + ('Guile', '1.8.8'), ] configopts = "--with-pic --with-mpi --with-blas=mkl_em64t --with-lapack=mkl_em64t --without-gcc-arch " diff --git a/easybuild/easyconfigs/m/Mercurial/Mercurial-3.8.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/Mercurial/Mercurial-3.8.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..be41158956de4863d99e75bb5923b0c09c434dd5 --- /dev/null +++ b/easybuild/easyconfigs/m/Mercurial/Mercurial-3.8.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +easyblock = "PythonPackage" + +name = 'Mercurial' +version = '3.8.3' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'http://mercurial.selenic.com/' +description = """Mercurial is a free, distributed source control management tool. It efficiently handles projects +of any size and offers an easy and intuitive interface. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://www.mercurial-scm.org/release/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11') +] + +sanity_check_paths = { + 'files': ['bin/hg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/mercurial'], +} + +moduleclass = 'tools' 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/MetaGeneAnnotator/MetaGeneAnnotator-20080819-x86-64.eb b/easybuild/easyconfigs/m/MetaGeneAnnotator/MetaGeneAnnotator-20080819-x86-64.eb new file mode 100644 index 0000000000000000000000000000000000000000..c2a182a4a912452cc7a2e7a907d70e8f52410e1b --- /dev/null +++ b/easybuild/easyconfigs/m/MetaGeneAnnotator/MetaGeneAnnotator-20080819-x86-64.eb @@ -0,0 +1,21 @@ +easyblock = 'PackedBinary' + +name = 'MetaGeneAnnotator' +version = '20080819' +versionsuffix = '-x86-64' + +homepage = 'http://metagene.nig.ac.jp/' +description = """MetaGeneAnnotator is a gene-finding program for prokaryote and phage.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://metagene.nig.ac.jp/metagene/'] +sources = ['mga_x86_64.tar.gz'] +checksums = ['bd95616ad676393397e2d8ae0609da97'] + +sanity_check_paths = { + 'files': ['mga_linux_ia64'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb b/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6f7d234353db884cacfa4c3086a177c88957bb4d --- /dev/null +++ b/easybuild/easyconfigs/m/Metal/Metal-2011-03-25-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Metal' +version = '2011-03-25' + +homepage = 'http://csg.sph.umich.edu/abecasis/Metal/' +description = """ +Metal - Meta Analysis Helper +The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a + convenient, rapid and memory efficient manner. +""" + +sources = ['generic-%(namelower)s-%(version)s.tar.gz'] +source_urls = ['http://csg.sph.umich.edu/abecasis/Metal/download/'] + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +patches=['Metal-%(version)s_Makefile.patch'] + +skipsteps=['configure'] + +buildopts='all' + +installopts = 'INSTALLDIR=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ['bin/metal'], + 'dirs': [''], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/Metal/Metal-2011-03-25_Makefile.patch b/easybuild/easyconfigs/m/Metal/Metal-2011-03-25_Makefile.patch new file mode 100644 index 0000000000000000000000000000000000000000..bda2c78a0563d7fb6ecc6468696604e6575b3a46 --- /dev/null +++ b/easybuild/easyconfigs/m/Metal/Metal-2011-03-25_Makefile.patch @@ -0,0 +1,14 @@ +# Remove static flag. +# Author: Fokke Dijkstra - University of Groningen +--- Makefile 2011-03-25 12:16:03.000000000 +0100 ++++ Makefile 2015-03-12 13:57:32.814999663 +0100 +@@ -27,7 +27,7 @@ + # on systems where gcc supports the long + # long data type and on Windows. + # +-CFLAGS=-O2 -I./libsrc -I./pdf -D_FILE_OFFSET_BITS=64 -static ++CFLAGS=-O2 -I./libsrc -I./pdf -D_FILE_OFFSET_BITS=64 + + # executable file names and locations + BINDIR = executables + 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/Molden/Molden-5.6-foss-2016a.eb b/easybuild/easyconfigs/m/Molden/Molden-5.6-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8709166ea01c41bd7cc18fb3e105966ff8fdb30c --- /dev/null +++ b/easybuild/easyconfigs/m/Molden/Molden-5.6-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = "MakeCp" + +name = 'Molden' +version = '5.6' + +homepage = 'http://www.cmbi.ru.nl/molden/' +description = """Molden is a package for displaying Molecular Density from the + Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical + packages Mopac/Ampac""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(namelower)s%(version)s.tar.gz'] +source_urls = ['ftp://ftp.cmbi.ru.nl/pub/molgraph/molden'] + +buildopts = 'CC="$CC" FC="$F90" molden' + +files_to_copy = [(['molden'], 'bin'), 'CopyRight', 'README', 'REGISTER'] + +sanity_check_paths = { + 'files': ['bin/molden', 'README', 'REGISTER'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-2012.1.27-intel-2015a.eb b/easybuild/easyconfigs/m/Molpro/Molpro-2012.1.27-intel-2015a.eb index 519d0887cc6bcde316957c81c2ad13afebd29555..de8bfef38e7145f0b8f39b6039a39377e8bcd7a7 100644 --- a/easybuild/easyconfigs/m/Molpro/Molpro-2012.1.27-intel-2015a.eb +++ b/easybuild/easyconfigs/m/Molpro/Molpro-2012.1.27-intel-2015a.eb @@ -11,7 +11,6 @@ toolchainopts = {'usempi': True} sources = ['%(namelower)s.%(version)s.tar.gz'] # license file -import os -license_file = os.path.join(os.getenv('HOME'), 'licenses', name, 'license.lic') +license_file = HOME + '/licenses/%(name)s/license.lic' moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb index 25842fde1cbdab04660df875ce9b9ebaefc805d7..c80d4d1ee107df67c5dd30b1362f790aa0531355 100644 --- a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2010.1.23.Linux_x86_64.eb @@ -15,7 +15,6 @@ precompiled_binaries = True # license file - uncomment if a licence file is supplied by your site and # is valid for all users - the value of license_file may have to be changed -#import os -#license_file = os.path.join(os.getenv('HOME'), 'licenses', name, 'license.lic') +#license_file = HOME + '/licenses/%(name)s/license.lic' moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb index 3d1681fc2e6200a3d33c6255254a2f99a1efb8f0..251958da52a5a8a82c26fc0480764e38117a9e01 100644 --- a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.0.linux_x86_64_intel.eb @@ -15,7 +15,6 @@ precompiled_binaries = True # license file - uncomment if a licence file is supplied by your site and # is valid for all users - the value of license_file may have to be changed -#import os -#license_file = os.path.join(os.getenv('HOME'), 'licenses', name, 'license.lic') +#license_file = HOME + '/licenses/%(name)s/license.lic' moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb new file mode 100644 index 0000000000000000000000000000000000000000..22912ecf4ac22e7ef4cd50e038e766db8c832752 --- /dev/null +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.10.linux_x86_64_openmp.eb @@ -0,0 +1,20 @@ +name = 'Molpro' +versionprefix = 'mpp-' +version = '2015.1.10' +versionsuffix = '.linux_x86_64_openmp' + +homepage = 'https://www.molpro.net' +description = """Molpro is a complete system of ab initio programs for molecular electronic structure calculations.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# no source URL available, requires registration to download +sources = ['%(namelower)s-%(versionprefix)s%(version)s%(versionsuffix)s.sh'] + +precompiled_binaries = True + +# license file - uncomment if a licence file is supplied by your site and +# is valid for all users - the value of license_file may have to be changed +#license_file = HOME + '/licenses/%(name)s/license.lic' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb new file mode 100644 index 0000000000000000000000000000000000000000..47852f7b9afccf29b6606fd517d2c722c117b81f --- /dev/null +++ b/easybuild/easyconfigs/m/Molpro/Molpro-mpp-2015.1.3.linux_x86_64_openmp.eb @@ -0,0 +1,20 @@ +name = 'Molpro' +versionprefix = 'mpp-' +version = '2015.1.3' +versionsuffix = '.linux_x86_64_openmp' + +homepage = 'https://www.molpro.net' +description = """Molpro is a complete system of ab initio programs for molecular electronic structure calculations.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# no source URL available, requires registration to download +sources = ['%(namelower)s-%(versionprefix)s%(version)s%(versionsuffix)s.sh'] + +precompiled_binaries = True + +# license file - uncomment if a licence file is supplied by your site and +# is valid for all users - the value of license_file may have to be changed +#license_file = HOME + '/licenses/%(name)s/license.lic' + +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/Mono/Mono-4.6.2.7-intel-2016b.eb b/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..4b58a5cd7107097e5a08ff4a5a29a97e8a66acde --- /dev/null +++ b/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7-intel-2016b.eb @@ -0,0 +1,21 @@ +name = 'Mono' +version = '4.6.2.7' + +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'} + +source_urls = ['http://download.mono-project.com/sources/mono/'] +sources = [SOURCELOWER_TAR_BZ2] + +builddependencies = [ + ('Autotools', '20150215'), + ('Bison', '3.0.4'), + ('gettext', '0.19.8'), +] + +configopts = "--with-large-heap=yes" + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7.eb b/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7.eb new file mode 100644 index 0000000000000000000000000000000000000000..ea1fdc28134c61ebb33ae50a7e1e6d66b9737d91 --- /dev/null +++ b/easybuild/easyconfigs/m/Mono/Mono-4.6.2.7.eb @@ -0,0 +1,21 @@ +name = 'Mono' +version = '4.6.2.7' + +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': 'dummy', 'version': 'dummy'} + +source_urls = ['http://download.mono-project.com/sources/mono/'] +sources = [SOURCELOWER_TAR_BZ2] + +builddependencies = [ + ('Autotools', '20150215'), + ('Bison', '3.0.4'), + ('gettext', '0.19.8'), +] + +configopts = "--with-large-heap=yes" + +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/MyMediaLite/MyMediaLite-3.11-intel-2016b.eb b/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.11-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ece632eb0f506a54ca730bff865a2bdc4e931e6b --- /dev/null +++ b/easybuild/easyconfigs/m/MyMediaLite/MyMediaLite-3.11-intel-2016b.eb @@ -0,0 +1,14 @@ +name = 'MyMediaLite' +version = '3.11' + +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', '4.6.2.7')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MySQL-python/MySQL-python-1.2.5-intel-2016a-Python-2.7.11-MariaDB-10.1.14.eb b/easybuild/easyconfigs/m/MySQL-python/MySQL-python-1.2.5-intel-2016a-Python-2.7.11-MariaDB-10.1.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..aa22bf318ab9120533dd00c54ee608f43888928a --- /dev/null +++ b/easybuild/easyconfigs/m/MySQL-python/MySQL-python-1.2.5-intel-2016a-Python-2.7.11-MariaDB-10.1.14.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'MySQL-python' +version = '1.2.5' + +homepage = 'https://github.com/farcepest/MySQLdb1' +description = """MySQL database connector for Python""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] + +mariadb_ver = '10.1.14' +versionsuffix = '-Python-%%(pyver)s-MariaDB-%s' % mariadb_ver + +dependencies = [ + ('Python', '2.7.11'), + ('MariaDB', mariadb_ver), +] + +# enable static linking to fix problem with unresolved symbols in mysql.so +prebuildopts = "sed -i 's/static = False/static = True/g' site.cfg && " + +options = {'modulename': 'MySQLdb'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MySQL-python/MySQL-python-1.2.5-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/MySQL-python/MySQL-python-1.2.5-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..69281bf60758fa912e023cfac3b214ed2d88b16e --- /dev/null +++ b/easybuild/easyconfigs/m/MySQL-python/MySQL-python-1.2.5-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'MySQL-python' +version = '1.2.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/farcepest/MySQLdb1' +description = """MySQL database connector for Python""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_ZIP] + +dependencies = [ + ('Python', '2.7.11'), + ('MariaDB', '10.1.13'), +] + +# enable static linking to fix problem with unresolved symbols in mysql.so +prebuildopts = "sed -i 's/static = False/static = True/g' site.cfg && " + +options = {'modulename': 'MySQLdb'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb b/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..fdd34a04e13eb6ae2d398cbc50d03b66b93e63d8 --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.0.0-CrayGNU-2015.11.eb @@ -0,0 +1,29 @@ +easyblock = "ConfigureMake" + +name = 'magma' +version = '2.0.0' + +homepage = 'http://icl.cs.utk.edu/magma/' +description = """The MAGMA project aims to develop a dense linear algebra library similar to +LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://icl.cs.utk.edu/projectsfiles/magma/downloads/'] + +patches = [('magma-2.0.0.patch')] + +builddependencies = [ ('cudatoolkit/7.0.28-1.0502.10742.5.1', EXTERNAL_MODULE) ] + +skipsteps = ['configure'] + +preinstallopts = "export EBINSTALLPREFIX=%(installdir)s && " + +sanity_check_paths={ + 'files': ['lib/libmagma.so', 'lib/libmagma.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/magma/magma-2.0.0.patch b/easybuild/easyconfigs/m/magma/magma-2.0.0.patch new file mode 100644 index 0000000000000000000000000000000000000000..ab1d3a79dbef186815db685bee53f558fb4df61c --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.0.0.patch @@ -0,0 +1,112 @@ +Patch for correctly using variables by EasyBuild for + - the Cray wrappers and + - the CUDA path + +Author: Guilherme Peretti-Pezzi (CSCS) + +diff -ru magma-2.0.0.orig//Makefile magma-2.0.0/Makefile +--- magma-2.0.0.orig//Makefile 2016-02-09 22:06:38.000000000 +0100 ++++ magma-2.0.0/Makefile 2016-03-25 17:35:34.000000000 +0100 +@@ -4,7 +4,7 @@ + # Users should make all changes in make.inc + # It should not be necesary to change anything in here. + +-include make.inc ++include make.inc.openblas + + # defaults if nothing else is given in make.inc + CC ?= gcc +diff -ru magma-2.0.0.orig//make.inc.openblas magma-2.0.0/make.inc.openblas +--- magma-2.0.0.orig//make.inc.openblas 2016-02-09 22:04:46.000000000 +0100 ++++ magma-2.0.0/make.inc.openblas 2016-03-25 17:29:35.000000000 +0100 +@@ -1,72 +1,49 @@ + #////////////////////////////////////////////////////////////////////////////// +-# -- MAGMA (version 2.0.0) -- ++# -- MAGMA (version 1.6.1) -- + # Univ. of Tennessee, Knoxville + # Univ. of California, Berkeley + # Univ. of Colorado, Denver +-# @date February 2016 ++# @date January 2015 + #////////////////////////////////////////////////////////////////////////////// + +-# GPU_TARGET contains one or more of Fermi, Kepler, or Maxwell, ++# GPU_TARGET contains one or more of Tesla, Fermi, or Kepler, + # to specify for which GPUs you want to compile MAGMA: +-# Fermi - NVIDIA compute capability 2.x cards +-# Kepler - NVIDIA compute capability 3.x cards +-# Maxwell - NVIDIA compute capability 5.x cards ++# Tesla - NVIDIA compute capability 1.x cards (no longer supported in CUDA 6.5) ++# Fermi - NVIDIA compute capability 2.x cards ++# Kepler - NVIDIA compute capability 3.x cards + # The default is "Fermi Kepler". +-# Note that NVIDIA no longer supports 1.x cards, as of CUDA 6.5. + # See http://developer.nvidia.com/cuda-gpus + # + #GPU_TARGET ?= Fermi Kepler ++GPU_TARGET = Kepler + +-# -------------------- +-# programs +- +-CC = gcc +-CXX = g++ ++#CXX = CC # Variable already defined by EasyBuild ++#CC = cc # Variable already defined by EasyBuild + NVCC = nvcc +-FORT = gfortran ++FORT = $(F90) + + ARCH = ar + ARCHFLAGS = cr + RANLIB = ranlib + +- +-# -------------------- +-# flags +- + # Use -fPIC to make shared (.so) and static (.a) library; + # can be commented out if making only static library. + FPIC = -fPIC + +-CFLAGS = -O3 $(FPIC) -DADD_ -Wall -fopenmp +-FFLAGS = -O3 $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument +-F90FLAGS = -O3 $(FPIC) -DADD_ -Wall -Wno-unused-dummy-argument -x f95-cpp-input +-NVCCFLAGS = -O3 -DADD_ -Xcompiler "$(FPIC)" ++CFLAGS += -DADD_ -DMAGMA_SETAFFINITY ++CXXFLAGS += -DADD_ -DMAGMA_SETAFFINITY ++FFLAGS += -DADD_ -Wall -Wno-unused-dummy-argument ++F90FLAGS += -DADD_ -Wall -Wno-unused-dummy-argument -x f95-cpp-input ++NVCCFLAGS = -O3 -DADD_ -Xcompiler "-fno-strict-aliasing $(FPIC)" + LDFLAGS = $(FPIC) -fopenmp + +-# C++11 (gcc >= 4.7) is not required, but has benefits like atomic operations +-CXXFLAGS := $(CFLAGS) -std=c++11 +-CFLAGS += -std=c99 +- +- +-# -------------------- +-# libraries +- + # gcc with OpenBLAS (includes LAPACK) +-LIB = -lopenblas +- +-LIB += -lcublas -lcusparse -lcudart +- +- +-# -------------------- +-# directories ++LIB = -lcublas -lcusparse + + # define library directories preferably in your environment, or here. +-#OPENBLASDIR ?= /usr/local/openblas +-#CUDADIR ?= /usr/local/cuda +--include make.check-openblas +--include make.check-cuda ++CUDADIR=$(EBROOTCUDA) + + LIBDIR = -L$(CUDADIR)/lib64 \ +- -L$(OPENBLASDIR)/lib + + INC = -I$(CUDADIR)/include ++prefix = $(EBINSTALLPREFIX) diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb index c4a3658b9ff28289fb6c0e1eaa744ea8069e6c75..f342cd436f639f006e21fee8938c9565ba613d2e 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-foss-2016a.eb @@ -14,6 +14,7 @@ source_urls = [XORG_UTIL_SOURCE] builddependencies = [ ('xproto', '7.0.28'), + ('xorg-macros', '1.19.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb index 943da96f822de922217509d7658695c91eedd7df..c9d36fd77f8a40ccf3a01b0fc27aca798bf63300 100644 --- a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.5-intel-2016a.eb @@ -14,6 +14,7 @@ source_urls = [XORG_UTIL_SOURCE] builddependencies = [ ('xproto', '7.0.28'), + ('xorg-macros', '1.19.0'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-Python-2.7.11.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..28d0aa443eb5182514dab6913af50daad3c6dcbd --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-CrayGNU-2015.11-Python-2.7.11.eb @@ -0,0 +1,45 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'CrayGNU', 'version': '2015.11'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..fe357bb5d5d7407c89c928b2cd6c33cfe39a4619 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-foss-2016a-Python-3.5.1.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': 'foss', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '3.5.1'), + ('freetype', '2.6.2'), + ('libpng', '1.6.21'), +] + +exts_list = [ + ('Cycler', '0.9.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'patches': ['matplotlib-1.5.1_fix-Tcl-Tk-libdir.patch'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..633cf0c29a062199cadbc7bd7dee64d1b8f45fb8 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.1-intel-2016b-Python-2.7.12.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', '2.7.12'), + ('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-1.5.1-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-2.7.12.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..b85eaba8bb72e0cae3f2e94ada54fdec7a576345 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,44 @@ +easyblock = 'Bundle' + +name = 'matplotlib' +version = '1.5.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.12'), + ('freetype', '2.6.5'), + ('libpng', '1.6.24'), +] + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'source_tmpl': 'cycler-%(version)s.tar.gz', + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.5.2-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/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..ee0afa54ae67902c3a251384703e149bcc58e6dd --- /dev/null +++ b/easybuild/easyconfigs/m/minieigen/minieigen-0.5.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'minieigen' +version = '0.5.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://launchpad.net/minieigen/' +description = """A small wrapper for core parts of EIgen, c++ library for linear algebra.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +dependencies = [ + ('Boost', '1.61.0', versionsuffix), + ('Eigen', '3.2.9'), + ('Python', '2.7.12'), +] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/minieigen.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.5-foss-2016a.eb b/easybuild/easyconfigs/m/motif/motif-2.3.5-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3a9a7c7e64cf16fdee51014d6584821f3d548fd9 --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.5-foss-2016a.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.5' + +homepage = 'http://motif.ics.com/' +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building + applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. + It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +# use -O1 to dance around icc segfaulting +toolchainopts = {'lowopt': True} + +sources = ['%(name)s-%(version)s.tar.gz'] +source_urls = [SOURCEFORGE_SOURCE] + +dependencies = [ + ('libXt', '1.1.5'), + ('libXau', '1.0.8'), + ('libX11', '1.6.3'), + ('libXext', '1.3.3'), + ('libXdmcp', '1.1.2'), + ('libpng', '1.6.21'), + ('xbitmaps', '1.1.1'), + ('freetype', '2.6.3'), + ('libjpeg-turbo', '1.4.2'), + ('bzip2', '1.0.6'), +] +builddependencies = [ + ('Autotools', '20150215'), + ('flex', '2.6.0'), + ('Bison', '3.0.4'), + ('util-linux', '2.28'), +] + +# makefile is not parallel safe +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], + 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], +} + +moduleclass = 'vis' \ No newline at end of file diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016b-Python-2.7.12-timed-pingpong.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016b-Python-2.7.12-timed-pingpong.eb new file mode 100644 index 0000000000000000000000000000000000000000..e2e1da4cf2fed21ddae3580171add02847b0c4c7 --- /dev/null +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3.1-intel-2016b-Python-2.7.12-timed-pingpong.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'mpi4py' +version = '1.3.1' +label = 'timed-pingpong' +versionsuffix = '-Python-%%(pyver)s-%s' % label + +homepage = 'https://bitbucket.org/mpi4py/mpi4py' +description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for + the Python programming language, allowing any Python program to exploit multiple processors.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [BITBUCKET_DOWNLOADS] +sources = [SOURCE_TAR_GZ] + +patches = ['mpi4py-%%(version)s_%s.patch' % label] + +dependencies = [('Python', '2.7.12')] + +# force rebuilding everything, including patched files +buildopts = '--force' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/mpi4py'], +} + +# check that timed pingpong routines that are added via the patch are available +sanity_check_commands = [ + ('python', '-c "from mpi4py.MPI import Comm; import sys; sys.exit((1, 0)[\'PingpongRS\' in dir(Comm)])"'), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..eade0fd4f9c129a5587fbbda53d42a3f4e4383de --- /dev/null +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-2.0.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'mpi4py' +version = '2.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/mpi4py/mpi4py' +description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for + the Python programming language, allowing any Python program to exploit multiple processors.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [BITBUCKET_DOWNLOADS] +sources = [SOURCE_TAR_GZ] + +dependencies = [('Python', '2.7.12')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/mpi4py'], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..56a88f540cebb4d5ab9cb7362a1223386572d2bf --- /dev/null +++ b/easybuild/easyconfigs/m/mpmath/mpmath-0.19-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Author: Adam Huffman +# adam.huffman@crick.ac.uk +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'mpmath' +version = '0.19' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://mpmath.org/' +description = """mpmath can be used as an arbitrary-precision substitute for Python's float/complex + types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation + can be performed just as well at 10-digit or 1000-digit precision, with either real or complex + numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely + high precision work.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/fredrik-johansson/mpmath/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [('Python', '2.7.11')] + +runtest = 'python -c "import mpmath; mpmath.runtests();"' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/mpmath'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..2b7c9b71bd4f3547314375c81cadca7581eb8a6a --- /dev/null +++ b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-goolf-1.4.10.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'mrFAST' +version = '2.6.0.1' + +homepage = 'http://mrfast.sourceforge.net/' +description = """ mrFAST & mrsFAST are designed to map short reads generated with the + Illumina platform to reference genome assemblies; in a fast and memory-efficient manner. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +buildopts = ' CC="$CC"' + +files_to_copy = [ (['mrfast'], 'bin'), "LICENSE" ] + +sanity_check_paths = { + 'files': ["bin/mrfast"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..086efed6cd9cd8a0485a31db3a0ca34cbbc8b035 --- /dev/null +++ b/easybuild/easyconfigs/m/mrFAST/mrFAST-2.6.0.1-ictce-6.2.5.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'mrFAST' +version = '2.6.0.1' + +homepage = 'http://mrfast.sourceforge.net/' +description = """ mrFAST & mrsFAST are designed to map short reads generated with the + Illumina platform to reference genome assemblies; in a fast and memory-efficient manner. """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +parallel = 1 + +buildopts = ' CC="$CC"' + +files_to_copy = [ (['mrfast'], 'bin'), "LICENSE" ] + +sanity_check_paths = { + 'files': ["bin/mrfast"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..7da0c48dde771f7d63121a9f6ff7b082a5c3737f --- /dev/null +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-goolf-1.4.10.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'mrsFAST' +version = '2.6.0.4' + +homepage = 'http://mrsfast.sourceforge.net' +description = """ mrsFAST is designed to map short reads to reference genome assemblies + in a fast and memory-efficient manner. mrsFAST is a cache-oblivous short read mapper that + optimizes cache usage to get higher performance. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/sfu-compbio/mrsfast/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('zlib', '1.2.8')] + +patches = ['mrsFAST-%(version)s-intel-compiler.patch'] + +parallel = 1 + +files_to_copy = [ (['mrsfast'], 'bin'), "Changelog" ] + +sanity_check_paths = { + 'files': ["bin/mrsfast"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..fda1eaa51f751f599eda43a41d7bbb3280411913 --- /dev/null +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-ictce-6.2.5.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'mrsFAST' +version = '2.6.0.4' + +homepage = 'http://mrsfast.sourceforge.net' +description = """ mrsFAST is designed to map short reads to reference genome assemblies + in a fast and memory-efficient manner. mrsFAST is a cache-oblivous short read mapper that + optimizes cache usage to get higher performance. """ + +toolchain = {'name': 'ictce', 'version': '6.2.5'} + +source_urls = ['https://github.com/sfu-compbio/mrsfast/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('zlib', '1.2.8')] + +patches = ['mrsFAST-%(version)s-intel-compiler.patch'] + +parallel = 1 + +files_to_copy = [ (['mrsfast'], 'bin'), "Changelog" ] + +sanity_check_paths = { + 'files': ["bin/mrsfast"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-intel-compiler.patch b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-intel-compiler.patch new file mode 100644 index 0000000000000000000000000000000000000000..b7cc2ac14d62d0cf494d72df8e80df30e0aa2107 --- /dev/null +++ b/easybuild/easyconfigs/m/mrsFAST/mrsFAST-2.6.0.4-intel-compiler.patch @@ -0,0 +1,20 @@ +replace hardcoded gcc by $CC so it can be built with intel toolchains +Pablo Escobar - sciCORE + +diff -ru mrsfast-2.6.0.4.orig/Makefile mrsfast-2.6.0.4/Makefile +--- mrsfast-2.6.0.4.orig/Makefile 2013-07-24 00:53:41.000000000 +0200 ++++ mrsfast-2.6.0.4/Makefile 2014-05-07 11:35:36.394689000 +0200 +@@ -1,3 +1,5 @@ ++CC?=gcc ++ + ALL: mrsfast + + LDFLAGS=-s -static +@@ -5,5 +7,5 @@ + CFLAGS= -O2 -s + + mrsfast: baseFAST.o MrsFAST.o Common.o CommandLineParser.o RefGenome.o HashTable.o Reads.o Output.o +- gcc $^ -o $@ ${LDFLAGS} ${LIBS} ++ $(CC) $^ -o $@ ${LDFLAGS} ${LIBS} + rm *.o +Only in mrsfast-2.6.0.4: mrsfast diff --git a/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb b/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb index d474edee9b07e13b9eb4080dc4a5fa438a105c12..b4d2d3ae9302b6b2d64b94ef2843676fb54aac9a 100644 --- a/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb +++ b/easybuild/easyconfigs/m/mutil/mutil-1.822.3-intel-2016a.eb @@ -21,7 +21,7 @@ source_urls = [ ] dependencies = [ - ('gnutls', '3.3.21'), + ('GnuTLS', '3.3.21'), ('libgpg-error', '1.21'), ('libgcrypt', '1.6.5'), ] diff --git a/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..6be49aff6f1294e636355778a15a63eea61f3321 --- /dev/null +++ b/easybuild/easyconfigs/m/mympingpong/mympingpong-0.7.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'mympingpong' +version = '0.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/hpcugent/mympingpong' +description = """A mpi4py based random pair pingpong network stress test.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +vsc_base_ver = '2.5.1' +dependencies = [ + ('Python', '2.7.12'), + ('vsc-base', vsc_base_ver, versionsuffix), + ('vsc-mympirun', '3.4.3', versionsuffix), + ('matplotlib', '1.5.1', versionsuffix), + ('h5py', '2.6.0', versionsuffix + '-HDF5-1.8.17'), + ('mpi4py', '1.3.1', versionsuffix + '-timed-pingpong'), + ('lxml', '3.6.4', versionsuffix), + ('hwloc', '1.11.3'), +] + +options = {'modulename': 'vsc.mympingpong'} + +sanity_check_paths = { + 'files': ['bin/mympingpong', 'bin/mympingponganalysis'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'perf' 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/m/mysqlclient/mysqlclient-1.3.7-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/mysqlclient/mysqlclient-1.3.7-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..292d557dbaf9243e20a167d9e8ee553a3c90c512 --- /dev/null +++ b/easybuild/easyconfigs/m/mysqlclient/mysqlclient-1.3.7-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'mysqlclient' +version = '1.3.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/PyMySQL/mysqlclient-python' +description = """Python interface to MySQL""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('MariaDB', '10.1.14'), +] + +# enable static linking to fix problem with unresolved symbols in mysql.so +prebuildopts = "sed -i 's/static = False/static = True/g' site.cfg && " + +options = {'modulename': 'MySQLdb'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mysqlclient/mysqlclient-1.3.7-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/m/mysqlclient/mysqlclient-1.3.7-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..3cd081ee974f77ba5f1688d007d2f371fa9b278b --- /dev/null +++ b/easybuild/easyconfigs/m/mysqlclient/mysqlclient-1.3.7-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'mysqlclient' +version = '1.3.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/PyMySQL/mysqlclient-python' +description = """Python interface to MySQL""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('MariaDB', '10.1.13'), +] + +# enable static linking to fix problem with unresolved symbols in mysql.so +prebuildopts = "sed -i 's/static = False/static = True/g' site.cfg && " + +options = {'modulename': 'MySQLdb'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.10b1-ictce-5.5.0-ibverbs.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.10b1-ictce-5.5.0-ibverbs.eb index ca095349484e359d8f91076fdc8fb9a205ec0e31..007dda5df82e4924167da663bd29dafd0a93bdbd 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.10b1-ictce-5.5.0-ibverbs.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.10b1-ictce-5.5.0-ibverbs.eb @@ -3,7 +3,8 @@ version = '2.10b1' versionsuffix = '-ibverbs' homepage = 'http://www.ks.uiuc.edu/Research/namd/' -description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'opt': True, 'pic': True} @@ -15,6 +16,9 @@ dependencies = [ ('FFTW', '3.3.4'), ] +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + charm_arch = "net-linux-x86_64 ibverbs" moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.10b1-ictce-5.5.0-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.10b1-ictce-5.5.0-mpi.eb index 8c61d5ae85813c9dc211e5978c225a3a41b6fcab..cb852fe76dd3677a02c18f0ad604ff0e2a0a0f53 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.10b1-ictce-5.5.0-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.10b1-ictce-5.5.0-mpi.eb @@ -3,7 +3,8 @@ version = '2.10b1' versionsuffix = '-mpi' homepage = 'http://www.ks.uiuc.edu/Research/namd/' -description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'opt': True, 'pic': True, 'usempi': True} @@ -15,6 +16,9 @@ dependencies = [ ('FFTW', '3.3.4'), ] +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + charm_arch = 'mpi-linux-x86_64' moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-goolf-1.4.10-ibverbs.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.9-goolf-1.4.10-ibverbs.eb index 1bbb708c5e660a513c48098b2571fa9c3648a105..b2ccba3358c16c2eb440b6e115042e524df8d360 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-goolf-1.4.10-ibverbs.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.9-goolf-1.4.10-ibverbs.eb @@ -3,7 +3,8 @@ version = '2.9' versionsuffix = '-ibverbs' homepage = 'http://www.ks.uiuc.edu/Research/namd/' -description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'opt': True, 'pic': True} @@ -14,6 +15,9 @@ dependencies = [ ('Tcl', '8.5.12'), ] +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + charm_arch = "net-linux-x86_64 ibverbs" moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-ictce-5.5.0-ibverbs.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.9-ictce-5.5.0-ibverbs.eb index b18bbca8a4bc9d8e1d058f7724ee95b035e919cf..05806930d28439ca79b3fdb48aea8f23d456d36e 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-ictce-5.5.0-ibverbs.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.9-ictce-5.5.0-ibverbs.eb @@ -3,7 +3,8 @@ version = '2.9' versionsuffix = '-ibverbs' homepage = 'http://www.ks.uiuc.edu/Research/namd/' -description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'opt': True, 'pic': True} @@ -15,6 +16,9 @@ dependencies = [ ('FFTW', '3.3.4'), ] +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + charm_arch = "net-linux-x86_64 ibverbs" moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-ictce-5.5.0-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.9-ictce-5.5.0-mpi.eb index 2fbdf0552929ef1cadedd580b8fa8d01398aef1e..427a25848b61ad2a43707b2203c934b1b3b41def 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.9-ictce-5.5.0-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.9-ictce-5.5.0-mpi.eb @@ -3,7 +3,8 @@ version = '2.9' versionsuffix = '-mpi' homepage = 'http://www.ks.uiuc.edu/Research/namd/' -description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'opt': True, 'pic': True, 'usempi': True} @@ -15,6 +16,9 @@ dependencies = [ ('FFTW', '3.3.4'), ] +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + charm_arch = 'mpi-linux-x86_64' moduleclass = 'chem' 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/NASM/NASM-2.12.02-foss-2016a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0ef2b03e67e146f336e255ea33f977debf47b3ad --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-foss-2016a.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.12.02' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +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/NASM/NASM-2.12.02-foss-2016b.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..1c877d704551f890f8ff6d2f404533e6e1b440cb --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-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 = '2.12.02' + +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/NASM/NASM-2.12.02-intel-2016b.eb b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..daeffdca98a1fc5643be51cb0f6a9e7bd8874658 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.12.02-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 +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.12.02' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'intel', 'version': '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/NCO/NCO-4.6.0-foss-2016a.eb b/easybuild/easyconfigs/n/NCO/NCO-4.6.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..49b3ccedf7b516ec0a724ce12db964a61a4fa11f --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-4.6.0-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '4.6.0' + +homepage = "http://nco.sourceforge.net" +description = """manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://nco.sourceforge.net/src'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('Bison', '3.0.4'), + ('flex', '2.6.0'), +] + +dependencies = [ + ('UDUNITS', '2.2.20'), + ('expat', '2.1.1'), + ('ANTLR', '2.7.7', '-Python-2.7.11'), + ('libdap', '3.18.1', '-Python-2.7.11'), + ('GSL', '2.1'), + ('netCDF', '4.4.0'), +] + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap', 'ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' 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="$CXX -c" -C ngs-java' + +installopts = "-C ngs-sdk && make install -C ngs-java" + +parallel = 1 + +sanity_check_paths = { + 'files': ['jar/ngs-java.jar', ('lib/libngs-sdk.%s' % SHLIB_EXT, 'lib64/libngs-sdk.%s' % SHLIB_EXT), + ('lib/libngs-adapt-c++.a', 'lib64/libngs-adapt-c++.a'), ('lib/libngs-c++.a', 'lib64/libngs-c++.a')], + 'dirs': ['include/ngs', 'share'], +} + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/NTL/NTL-9.8.1-CrayGNU-2016.03.eb b/easybuild/easyconfigs/n/NTL/NTL-9.8.1-CrayGNU-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..184f6052148665fd85d076406ba7e11772337263 --- /dev/null +++ b/easybuild/easyconfigs/n/NTL/NTL-9.8.1-CrayGNU-2016.03.eb @@ -0,0 +1,30 @@ +# contributed by Guilherme Peretti-Pezzi (CSCS) +easyblock = 'ConfigureMake' + +name = 'NTL' +version = '9.8.1' + +homepage = 'http://www.shoup.net/ntl/' +description = """NTL is a high-performance, portable C++ library providing data structures and algorithms +for manipulating signed, arbitrary length integers, and for vectors, matrices, and polynomials over the +integers and over finite fields.""" + +toolchain = {'name': 'CrayGNU', 'version': '2016.03'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.shoup.net/ntl/'] + +dependencies = [('GMP', '6.1.0')] + +prefix_opt = 'PREFIX=' + +configopts = 'CXX="$CXX" GMP_PREFIX=$EBROOTGMP' + +start_dir = 'src/' + +sanity_check_paths = { + 'files': ["lib/libntl.a"], + 'dirs': ["include/"], +} + +moduleclass = 'math' 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/nco/nco-0.0.2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/n/nco/nco-0.0.2-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..a661d2786bdd76ea012fa9a46bde9dfb533c4c8c --- /dev/null +++ b/easybuild/easyconfigs/n/nco/nco-0.0.2-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'nco' +version = '0.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nco/pynco' +description = """Python bindings for NCO""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.10'), + ('NCO', '4.5.1', versionsuffix), + ('numpy', '1.10.4', versionsuffix), + ('scipy', '0.16.1', versionsuffix), + ('netcdf4-python', '1.2.2', versionsuffix), + +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' 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 new file mode 100644 index 0000000000000000000000000000000000000000..307af92999e6a5ffb1b85295ef784a91bf05bf77 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-CrayGNU-2016.03.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': 'CrayGNU', 'version': '2016.03'} +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", "ncurses6-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-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..7d6659abd11b9fc4c609c05d7f71df94cecdb71d --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-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': 'GCC', 'version': '4.9.3-2.25'} +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', + # 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-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..a13213588d3cf9f0a0a1114489555f8d751453c4 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCC-5.4.0-2.26.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': 'GCC', 'version': '5.4.0-2.26'} +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', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-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-GCCcore-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-5.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..84498506a6104b88163ae8606025852cd6e19b10 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-5.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'GCCcore', 'version': '5.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_gcc-5.patch'] + +builddependencies = [('binutils', '2.26')] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-5.4.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..afda72a745e2b8735608a8f3667b8795a18d3e5d --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-5.4.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_gcc-5.patch'] + +builddependencies = [('binutils', '2.26')] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..a573fe0099a0d93cbeea583c79b33127266c9e33 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-GCCcore-6.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.0' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'GCCcore', 'version': '6.2.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_gcc-5.patch'] + +builddependencies = [('binutils', '2.27')] + +configopts = [ + # default build + '--with-shared --enable-overwrite', + # the UTF-8 enabled version (ncursesw) + '--with-shared --enable-overwrite --enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/' +] + +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.0-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-2016.04.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..8b51018ccdb60d11c51decb527bf907cf0c728af --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016.04.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': 'foss', 'version': '2016.04'} +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', + # 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-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 new file mode 100644 index 0000000000000000000000000000000000000000..2e3653e592f93e9244b892ab5e4c421faf95c045 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-foss-2016b.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': 'foss', 'version': '2016b'} +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-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 new file mode 100644 index 0000000000000000000000000000000000000000..d3393acd5476ff8f11fd75a91f4ef6888c12eed6 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0-intel-2016b.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': 'intel', 'version': '2016b'} +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-2016.07.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/ncurses/ncurses-6.0_gcc-5.patch b/easybuild/easyconfigs/n/ncurses/ncurses-6.0_gcc-5.patch new file mode 100644 index 0000000000000000000000000000000000000000..be362111f4deac7262a3033895df73c785145a40 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.0_gcc-5.patch @@ -0,0 +1,33 @@ +Patch is taken from ncurses upstream repository. + +The problem it solves is that gcc 5.1 and later adds spurios #line +markers into the preprocessor output (see comment in the actual patch). + +diff --git a/ncurses/base/MKlib_gen.sh b/ncurses/base/MKlib_gen.sh +index b91398c..9e41cea 100755 +--- a/ncurses/base/MKlib_gen.sh ++++ b/ncurses/base/MKlib_gen.sh +@@ -66,6 +66,23 @@ preprocessor="$1 -DNCURSES_INTERNALS -I../include" + AWK="$2" + USE="$3" + ++# A patch discussed here: ++# https://gcc.gnu.org/ml/gcc-patches/2014-06/msg02185.html ++# introduces spurious #line markers into the preprocessor output. The result ++# appears in gcc 5.0 and (with modification) in 5.1, making it necessary to ++# determine if we are using gcc, and if so, what version because the proposed ++# solution uses a nonstandard option. ++PRG=`echo "$1" | sed -e 's/[[:space:]].*$//'` ++FSF=`"$PRG" --version 2>/dev/null | fgrep "Free Software Foundation" | head -n 1` ++ALL=`"$PRG" -dumpversion 2>/dev/null ` ++ONE=`echo "$ALL" | sed -e 's/\..*$//'` ++if test -n "$FSF" && test -n "$ALL" && test -n "$ONE" ; then ++ if test $ONE -ge 5 ; then ++ echo ".. adding -P option to work around $PRG $ALL" >&2 ++ preprocessor="$preprocessor -P" ++ fi ++fi ++ + PID=$$ + ED1=sed1_${PID}.sed + ED2=sed2_${PID}.sed 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/ne/ne-3.0.1-foss-2015a.eb b/easybuild/easyconfigs/n/ne/ne-3.0.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..489806193093c601569fb92766a3408be3ab4760 --- /dev/null +++ b/easybuild/easyconfigs/n/ne/ne-3.0.1-foss-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'ne' +version = '3.0.1' + +homepage = 'http://ne.di.unimi.it/' +description = """ne is a free (GPL'd) text editor based on the POSIX standard +that runs (we hope) on almost any UN*X machine. ne is easy to use for the +beginner, but powerful and fully configurable for the wizard, and most sparing +in its resource usage.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://ne.di.unimi.it/'] +sources = [SOURCELOWER_TAR_GZ] + +skipsteps = ['configure'] +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/ne'], + 'dirs': ['share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2016b.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e30ec19416c51d31b54d0a946e657d2f074d46e0 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.0-intel-2016b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.0' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('netCDF', '4.4.1')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-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-intel-2016b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..83d8e2b0a22fb3cbbcf39cf40147a487a47e3705 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.4-intel-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': 'intel', '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-foss-2016a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8e1936bec645b81f4e4f11e549ba5f0afd1744c3 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-foss-2016a.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.4.1' + +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': '2016a'} +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/netCDF/netCDF-4.4.1-foss-2016b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..f688f2156e4260455aea9b0b44ec7d0a57879691 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-foss-2016b.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.4.1' + +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/netCDF/netCDF-4.4.1-intel-2016a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e66c2bd0e4e45341038dacea37820a176287ab3f --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-intel-2016a.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.4.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +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/netCDF/netCDF-4.4.1-intel-2016b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..98351330435ac8cfbf840baba308e8d1ebad26a4 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.4.1-intel-2016b.eb @@ -0,0 +1,34 @@ +name = 'netCDF' +version = '4.4.1' + +homepage = 'http://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = [ + 'https://github.com/Unidata/netcdf-c/archive/' +] + +dependencies = [ + ('HDF5', '1.8.17'), + ('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/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/netcdf4-python/netcdf4-python-1.2.2-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.2.2-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..1c992d8b514f633fab1a24221970060c6d47d0d8 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.2.2-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,24 @@ +name = 'netcdf4-python' +version = '1.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf4-python/archive/'] +sources = ['v%(version)srel.tar.gz'] + +patches = ['netcdf4-python-1.1.8-avoid-diskless-test.patch'] + +dependencies = [ + ('Python', '2.7.10'), + ('numpy', '1.10.4', versionsuffix), + ('HDF5', '1.8.15'), + ('netCDF', '4.3.3.1'), + ('cURL', '7.43.0'), +] + +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/nodejs/nodejs-4.4.7-foss-2016a.eb b/easybuild/easyconfigs/n/nodejs/nodejs-4.4.7-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..1ae5d48e2a9e992eb3c53b9a2706e120a442ed21 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-4.4.7-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '4.4.7' + +homepage = 'http://nodejs.org' + +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://nodejs.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] + +builddependencies = [('Python', '2.7.11')] + +sanity_check_paths = { + 'files': ["bin/node", "bin/npm"], + 'dirs': ["lib/node_modules", "include/node"] +} + +moduleclass = 'lang' 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-5.2.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..2c6aa67bd45512331b0f066ca2334ca03656b577 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.2.0.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': '5.2.0'} + +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-5.4.0-2.26.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..0c9f60c6e0037217bc8fb6de1d6cf8538e3a67ff --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCC-5.4.0-2.26.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': '5.4.0-2.26'} + +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-6.1.0-2.27.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-GCCcore-5.4.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..61ae200dde801c185b5ebc98e6330ff674da11d8 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-GCCcore-5.4.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.11' + +homepage = 'http://oss.sgi.com/projects/libnuma/' +description = """The numactl program allows you to run your application program on specific cpu's and memory nodes. + It does this by supplying a NUMA memory policy to the operating system before running your program. + The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.""" + +toolchain = {'name': 'GCCcore', 'version': '5.4.0'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +checksums = ['d3bc88b7ddb9f06d60898f4816ae9127'] + +builddependencies = [('binutils', '2.26')] + +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-foss-2016a.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8e5c5971f0c63d06dc844f576fbb4ce83546b246 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-foss-2016a.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': 'foss', 'version': '2016a'} + +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/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..fb308c3df39e7ebf859707329e00f2b1fb4be314 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-iccifort-2016.3.210-GCC-5.4.0-2.26.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-5.4.0-2.26'} + +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/numactl/numactl-2.0.11-intel-2016b.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..0c6c854f4aab6f3fe28e910af53988e685746b01 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.11-intel-2016b.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': 'intel', 'version': '2016b'} + +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/numba/llvmlite-0.11.0_fix-ffi-Makefile.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.11.0_fix-ffi-Makefile.patch new file mode 100644 index 0000000000000000000000000000000000000000..4e67738a76d044d95753eaef5fa4d451a39a1ec6 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.11.0_fix-ffi-Makefile.patch @@ -0,0 +1,17 @@ +don't use -static-libstdc++, causing problems like "glibc detected *** python: free(): invalid pointer" +cfr. https://github.com/numba/llvmlite/issues/93; +diff --git a/llvmlite-0.11.0/ffi/Makefile.linux.orig b/llvmlite-0.11.0/ffi/Makefile.linux +index 68181f6..b899127 100644 +--- a/llvmlite-0.11.0/ffi/Makefile.linux.orig ++++ b/llvmlite-0.11.0/ffi/Makefile.linux +@@ -17,9 +17,7 @@ OUTPUT = libllvmlite.so + all: $(OUTPUT) + + $(OUTPUT): $(SRC) $(INCLUDE) +- # static-libstdc++ avoids runtime dependencies on a +- # particular libstdc++ version. +- $(CXX) -static-libstdc++ -shared $(CXXFLAGS) $(SRC) -o $(OUTPUT) $(LDFLAGS) $(LIBS) ++ $(CXX) -shared $(CXXFLAGS) $(SRC) -o $(OUTPUT) $(LDFLAGS) $(LIBS) + + clean: + rm -rf test $(OUTPUT) diff --git a/easybuild/easyconfigs/n/numba/numba-0.26.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numba/numba-0.26.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..87ffd27d522db1a9203d56836dd933f7f9610f76 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.26.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,41 @@ +easyblock = 'Bundle' + +name = 'numba' +version = '0.26.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, + Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [ + ('Python', '2.7.11'), + ('LLVM', '3.7.1'), +] + +exts_list = [ + ('llvmlite', '0.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'], + 'patches': ['llvmlite-0.11.0_fix-ffi-Makefile.patch'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/n/numba/'], + }), +] + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': ['bin/numba', 'bin/pycc'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/numexpr/numexpr-2.6.1-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/n/numpy/numpy-1.10.4-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/n/numpy/numpy-1.10.4-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..d197dabcbd26defba3db2fa652c766e9884966b9 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.10.4-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.10.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = [ + 'numpy-1.8.0-mkl.patch', + 'numpy-%(version)s-sse42.patch', +] + +dependencies = [ + ('Python', '2.7.10'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.11.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.11.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..cd8041b190bbc55bea89b39fb5a8e44ed6397fbe --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.11.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.11.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = [ + 'numpy-1.8.0-mkl.patch', + 'numpy-%(version)s-sse42.patch', +] + +dependencies = [ + ('Python', '2.7.11'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.11.0-sse42.patch b/easybuild/easyconfigs/n/numpy/numpy-1.11.0-sse42.patch new file mode 100644 index 0000000000000000000000000000000000000000..75ffeaa0d5939995de089410a1dd77d8bce4e74c --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.11.0-sse42.patch @@ -0,0 +1,25 @@ +#Remove hard coded -xSSE4.2 compilation flag for Intel compilers (add the usual -xHOST) +#compilation would fail on non-SSE4.2 CPUs, and for further CPUs/compilers it would restrict the generated code to SSE4.2 +# February 19th, 2016 by B. Hajgato - Free University Brussels (VUB) +--- ./numpy/distutils/intelccompiler.py.orig 2016-01-06 22:07:54.000000000 +0100 ++++ ./numpy/distutils/intelccompiler.py 2016-02-19 15:07:00.438235792 +0100 +@@ -54,7 +54,7 @@ + def __init__(self, verbose=0, dry_run=0, force=0): + UnixCCompiler.__init__(self, verbose, dry_run, force) + self.cc_exe = ('icc -m64 -fPIC -fp-model strict -O3 ' +- '-fomit-frame-pointer -openmp -xSSE4.2') ++ '-fomit-frame-pointer -openmp -xHOST') + compiler = self.cc_exe + if platform.system() == 'Darwin': + shared_flag = '-Wl,-undefined,dynamic_lookup' +--- ./numpy/distutils/fcompiler/intel.py.orig 2016-01-07 03:16:25.000000000 +0100 ++++ ./numpy/distutils/fcompiler/intel.py 2016-02-19 15:07:16.424220745 +0100 +@@ -123,7 +123,7 @@ + return ['-openmp -fp-model strict'] + + def get_flags_arch(self): +- return ['-xSSE4.2'] ++ return ['-xHOST'] + + # Is there no difference in the version string between the above compilers + # and the Visual compilers? diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.8.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..a912f46a87bfb3f563144e904d64fc52f0fd7a70 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +name = 'numpy' +version = '1.8.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.1-mkl.patch'] + +dependencies = [ + ('Python', '2.7.11'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..b0f7a1aaf19bb612f53ab0ae7bc42ca7d01f12b6 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,32 @@ +name = 'numpy' +version = '1.9.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package for scientific computing with Python. It contains among other things: + a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran + code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, + NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be + defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +dependencies = [ + ('Python', '2.7.12'), +] + +# need to use pip rather than regular 'setup.py install,' +# to ensure that this numpy wins over the one in the Python installation; +# using easy_install does not work... +use_pip = True + +# install as zipped egg to get a .pth file in lib/python*/site-packages; +# this enables shadowing of the numpy that is part of the Python installation +zipped_egg = True + +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 new file mode 100644 index 0000000000000000000000000000000000000000..3879abb7bd9c821c86536f8d6d9b8618ffac1643 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-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': '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_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=.:$PATH lapack-timing' + +sanity_check_paths = { + 'files': ['include/cblas.h', 'include/f77blas.h', 'include/lapacke_config.h', 'include/lapacke.h', + 'include/lapacke_mangling.h', 'include/lapacke_utils.h', 'include/openblas_config.h', + 'lib/libopenblas.a', 'lib/libopenblas.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..21a2a7c81548f8ba57987b857d046a7a7f52ac03 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1.eb @@ -0,0 +1,55 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.18' + +lapackver = '3.6.1' +versionsuffix = '-LAPACK-%s' % lapackver + +homepage = 'http://xianyi.github.com/OpenBLAS/' +description = """OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.""" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' + +lapack_unpack_cmd = 'cd %(name)s-%(version)s; rm -rf lapack-netlib;' +lapack_unpack_cmd += 'mkdir lapack-netlib;' +lapack_unpack_cmd += 'tar -C lapack-netlib --strip-components=1 -zxf %s; cd -' + +sources = [ + 'v%(version)s.tar.gz', + (lapack_src, lapack_unpack_cmd), + large_src, + timing_src, +] +source_urls = [ + # order matters, trying to download the LAPACK tarball from GitHub causes trouble + "http://www.netlib.org/lapack/", + "http://www.netlib.org/lapack/timing/", + "https://github.com/xianyi/OpenBLAS/archive/", +] + +patches = [ + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +buildopts = 'BINARY=64 USE_THREAD=1 CC="$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-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-2016a.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b12504dd19f0c5c0cd0cc30ec5e909a5d6cd3e2e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016a.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': '2016a'} + +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', '2.7.11'), + ('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'), +] + +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=$EBROOTJASPER/include ' +configopts += '-DWITH_IPP=ON ' +configopts += '-DENABLE_SSE=ON -DENABLE_SSE2=ON -DENABLE_SSE3=ON ' +configopts += '-DWITH_CUDA=OFF ' + +sanity_check_paths = { + 'files': ['lib/libopencv_core.%s' % SHLIB_EXT ] + + ['lib/python%%(pyshortver)s/site-packages/cv2.%s' % SHLIB_EXT ] + + ['bin/opencv_%s' % x for x in ['annotation', 'createsamples', 'traincascade']], + 'dirs': ['include'] +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CLASSPATH': 'share/OpenCV/java', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..896ae67a98a2e8d242e0323bb40ae44172f07c17 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0-intel-2016b.eb @@ -0,0 +1,69 @@ +easyblock = 'CMakeMake' + +name = 'OpenCV' +version = '3.1.0' + +homepage = 'http://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/Itseez/opencv/archive/'] +sources = ['%(version)s.zip'] + +patches = ['OpenCV-%(version)s_with_IPP.patch'] + +builddependencies = [ + ('CMake', '3.5.2'), +] + +dependencies = [ + ('Python', '2.7.12'), + ('zlib', '1.2.8'), + ('FFmpeg', '3.1.3'), + ('libjpeg-turbo', '1.5.0'), + ('libpng', '1.6.24'), + ('LibTIFF', '4.0.6'), + ('JasPer', '1.900.1'), + ('Java', '1.8.0_92', '', True), + ('ant', '1.9.7', '-Java-%(javaver)s', True), + ('GLib', '2.49.5'), + ('GTK+', '2.24.31'), +] + +preconfigopts = 'export IPPROOT=$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/OpenCV/OpenCV-3.1.0_with_IPP.patch b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0_with_IPP.patch new file mode 100644 index 0000000000000000000000000000000000000000..37ff51e0c5d7d976c99d49d0ed0f0fd3724997ac --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-3.1.0_with_IPP.patch @@ -0,0 +1,14 @@ +#By defualt OpenCV looks IPP lib dir in $IPPROOT../lib +# In our setup it is at $IPPROOT/lib +# By B. Hajgato July 14th 2016 +--- cmake/OpenCVFindIPP.cmake.orig 2015-12-18 16:02:16.000000000 +0100 ++++ cmake/OpenCVFindIPP.cmake 2016-07-14 13:12:21.541285380 +0200 +@@ -191,7 +191,7 @@ + _ipp_add_library(m) + + if(UNIX) +- get_filename_component(INTEL_COMPILER_LIBRARY_DIR ${IPP_ROOT_DIR}/../lib REALPATH) ++ get_filename_component(INTEL_COMPILER_LIBRARY_DIR ${IPP_ROOT_DIR}/lib REALPATH) + if(NOT EXISTS ${INTEL_COMPILER_LIBRARY_DIR}) + get_filename_component(INTEL_COMPILER_LIBRARY_DIR ${IPP_ROOT_DIR}/../compiler/lib REALPATH) + endif() diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.2.0-intel-2016b.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.2.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..479f9021cea48fd4b77f603ffbdf1568400402d9 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-2.2.0-intel-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '2.2.0' + +homepage = 'http://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/openexr/openexr/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.6.1')] + +env_vars = "CPATH=%(installdir)s/include/OpenEXR:$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-2.2.2-intel-2016a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..76426c6c9bbbef9990d73d28022ade2fa07f5e3c --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2016a.eb @@ -0,0 +1,40 @@ +name = 'OpenFOAM' +version = '2.2.2' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + 'OpenFOAM-2.2.0_libreadline.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +dependencies = [ + ('libreadline', '6.3'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0', '-32bitIDX'), + ('ncurses', '6.0'), + ('SCOTCH', '6.0.4'), + ('Boost', '1.60.0'), +] + + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + ('CMake', '3.5.2'), +] + +moduleclass = 'cae' 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/OpenFOAM/cleanup-OpenFOAM-2.2.2.patch b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.2.2.patch index 14ebe59f75cccbff51f5b1757778057f2212716d..135329c5290c57d129b45c44d9981f319cc1c791 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.2.2.patch +++ b/easybuild/easyconfigs/o/OpenFOAM/cleanup-OpenFOAM-2.2.2.patch @@ -83,28 +83,6 @@ diff -ru OpenFOAM-2.2.2.orig/etc/config/settings.sh OpenFOAM-2.2.2/etc/config/se *) export FOAM_MPI=dummy ;; -diff -ru OpenFOAM-2.2.2.orig/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C OpenFOAM-2.2.2/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C ---- OpenFOAM-2.2.2.orig/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C 2013-10-03 12:28:16.000000000 +0200 -+++ OpenFOAM-2.2.2/src/parallel/decompose/ptscotchDecomp/lnInclude/ptscotchDecomp.C 2015-03-03 10:39:07.827538901 +0100 -@@ -112,6 +112,8 @@ - - \*---------------------------------------------------------------------------*/ - -+#include "mpi.h" -+ - #include "ptscotchDecomp.H" - #include "addToRunTimeSelectionTable.H" - #include "Time.H" -@@ -121,8 +123,8 @@ - - extern "C" - { --#include - #include "mpi.h" -+#include - #include "ptscotch.h" - } - diff -ru OpenFOAM-2.2.2.orig/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-2.2.2/src/parallel/decompose/ptscotchDecomp/Make/options --- OpenFOAM-2.2.2.orig/src/parallel/decompose/ptscotchDecomp/Make/options 2013-10-03 12:28:16.000000000 +0200 +++ OpenFOAM-2.2.2/src/parallel/decompose/ptscotchDecomp/Make/options 2015-03-03 10:39:07.827538901 +0100 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-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..1f3b3eb045a32bb6eee203811bd3e0f942373c7b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-GCC-5.4.0-2.26.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': 'GCC', 'version': '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', '1.11.3')] + +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-1.10.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..ed7694b56fd30e8ab92077451e47f3bee7607d4f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.3-iccifort-2016.3.210-GCC-5.4.0-2.26.eb @@ -0,0 +1,39 @@ +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': 'iccifort', 'version': '2016.3.210-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'] + + +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=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +dependencies = [('hwloc', '1.11.3')] + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +sanity_check_commands = [ + ('mpicc --version | grep icc', ''), + ('mpicxx --version | grep icpc', ''), + ('mpifort --version | grep ifort', ''), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..fd6bb36c388a4243691b6754ce1cc9e76edf6050 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.10.4-PGI-16.7-GCC-5.4.0-2.26.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.10.4' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'PGI', 'version': '16.7-GCC-5.4.0-2.26'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +checksums = ['fb2fdb6a5b65c80d7dfa4bc9a0caf665'] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$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=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +dependencies = [('hwloc', '1.11.3')] + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_cxx", "mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +sanity_check_commands = [ + ('mpicc --version | grep icc', ''), + ('mpicxx --version | grep icpc', ''), + ('mpifort --version | grep ifort', ''), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..23deffc8f49aedb19732a82aea0c0d51bdda155e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-2.0.0-GCC-5.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '2.0.0' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '5.2.0'} + +sources = [SOURCELOWER_TAR_GZ] + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads',] + +dependencies = [('hwloc', '1.11.3')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel'),] + +# VampirTrace is no longer used : https://www.open-mpi.org/community/lists/announce/2016/07/0085.php +libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] +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"], +} + +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/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb index 34c308ea5d735fe2189865b2b34ea6f5fd43ee3b..2ae64198e6a2ee6836c8d245d4ce5d948f8dbda4 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb @@ -12,9 +12,11 @@ description = """OpenPGM is an open source implementation of the Pragmatic Gener toolchain = {'name': 'foss', 'version': '2015a'} -source_urls = [GOOGLECODE_SOURCE] +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['libpgm-%(version)s.tar.gz'] +checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] + configopts = '--with-pic' start_dir = 'pgm' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb index 5f92dedd69fcbe5d7cf3d8c3116e2e238cebf41e..a3d2763924b5dea9844318cb9174f508dc41539a 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016a.eb @@ -12,9 +12,11 @@ description = """OpenPGM is an open source implementation of the Pragmatic Gener toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = [GOOGLECODE_SOURCE] +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['libpgm-%(version)s.tar.gz'] +checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] + configopts = '--with-pic' start_dir = 'pgm' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016b.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..3584a3c7051d34512cd7ba687141d3e79772390a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'http://code.google.com/p/openpgm/' +description = """OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) + specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol + that enables receivers to detect loss, request retransmission of lost data, or notify an application + of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception responsibility.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] +sources = ['libpgm-%(version)s.tar.gz'] + +checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] + +configopts = '--with-pic' + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-goolf-1.4.10.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-goolf-1.4.10.eb index da4b481d25e32d00cbf146c52295aa5d70a3f1c0..ba0d34665722a85f4128766d8ba325bcb1f533e3 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-goolf-1.4.10.eb @@ -12,9 +12,11 @@ for ensuring all data is received, absolving the sender of reception responsibil toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://%s.googlecode.com/files/' % (name.lower())] +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['%s-%s.tar.gz' % ('libpgm', version)] +checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] + configopts = '--with-pic' start_dir = 'pgm' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-goolf-1.7.20.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-goolf-1.7.20.eb index 367fbc744cca3fe43e6a4142f30614b4c6c646c1..34fa9dd22fab0473513908262eccb8bd916f569e 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-goolf-1.7.20.eb @@ -12,9 +12,11 @@ description = """OpenPGM is an open source implementation of the Pragmatic Gener toolchain = {'name': 'goolf', 'version': '1.7.20'} -source_urls = [GOOGLECODE_SOURCE] +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['libpgm-%(version)s.tar.gz'] +checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] + configopts = '--with-pic' start_dir = 'pgm' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.3.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.3.0.eb index 8aaab1f337b9a781a368d61da25af2594dbb3e75..5c73a02ebe4dd4b84788cf9f8aa33dfa6798014e 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.3.0.eb @@ -13,9 +13,11 @@ description = """OpenPGM is an open source implementation of the Pragmatic Gener toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://%s.googlecode.com/files/' % (name.lower())] +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['%s-%s.tar.gz' % ('libpgm', version)] +checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] + configopts = '--with-pic' start_dir = 'pgm' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.5.0.eb index e0719d72e6c3b534a04075363a09879c69ace82b..d10ebd9897231c0c9195f1e20d42a9974b343161 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-ictce-5.5.0.eb @@ -12,9 +12,11 @@ description = """OpenPGM is an open source implementation of the Pragmatic Gener toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['http://%s.googlecode.com/files/' % (name.lower())] +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['%s-%s.tar.gz' % ('libpgm', version)] +checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] + configopts = '--with-pic' start_dir = 'pgm' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb index 690b4d99ca2bee029a64d78938be52a5302df775..b7949218e215d8ae0ae831f08813fcb606fce38a 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb @@ -12,9 +12,11 @@ description = """OpenPGM is an open source implementation of the Pragmatic Gener toolchain = {'name': 'intel', 'version': '2015a'} -source_urls = [GOOGLECODE_SOURCE] +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['libpgm-%(version)s.tar.gz'] +checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] + configopts = '--with-pic' start_dir = 'pgm' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015b.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015b.eb index 26e1420fdaffd92f0979b43a83d48f3696cb5264..abec09000c3953a807078df83d53372a4d04d67c 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015b.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015b.eb @@ -13,9 +13,11 @@ description = """OpenPGM is an open source implementation of the Pragmatic Gener toolchain = {'name': 'intel', 'version': '2015b'} toolchainopts = {'pic': True} -source_urls = [GOOGLECODE_SOURCE] +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['libpgm-%(version)s.tar.gz'] +checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] + configopts = '--with-pic' start_dir = 'pgm' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb index d391dfe9fd9c8b9e58e28eb4d7a2d8d01c2facfd..803b19d70ef1fea456633bb5750fec4094127426 100644 --- a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016a.eb @@ -13,7 +13,7 @@ description = """OpenPGM is an open source implementation of the Pragmatic Gener toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} -source_urls = [GOOGLECODE_SOURCE] +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] sources = ['libpgm-%(version)s.tar.gz'] configopts = '--with-pic' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016b.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..f8d13d08343e5856009d0b259a627d2a8fe001cf --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2016b.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'http://code.google.com/p/openpgm/' +description = """OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) + specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol + that enables receivers to detect loss, request retransmission of lost data, or notify an application + of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception responsibility.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] +sources = ['libpgm-%(version)s.tar.gz'] + +checksums = ['d7673e9ff6cc33cf42fe9fb9a7bfbffa'] + +configopts = '--with-pic' + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.2h-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/PAPI/PAPI-5.4.1-foss-2015a.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b5babf4529e2f11a63dff30a4740b5cd67f16da7 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.1-foss-2015a.eb @@ -0,0 +1,46 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: 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_07-02.html +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '5.4.1' + +homepage = 'http://icl.cs.utk.edu/projects/papi/' +description = """PAPI provides the tool designer and application engineer with a consistent interface and + methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables + software engineers to see, in near real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and software stack.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +# Example download URL, for reference: http://icl.cs.utk.edu/projects/papi/downloads/papi-5.0.0.tar.gz +source_urls = ['http://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] + +start_dir = 'src' + +# parallel build doesn't always work +parallel = 1 + +runtest = 'fulltest' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", "version", + "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b46c6bff0df559bcee258baccb94884dfd406432 --- /dev/null +++ b/easybuild/easyconfigs/p/PARI-GP/PARI-GP-2.7.6-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'PARI-GP' +version = '2.7.6' + +homepage = 'http://pari.math.u-bordeaux.fr' +description = """PARI/GP is a widely used computer algebra system designed for fast computations in number theory + (factorizations, algebraic number theory, elliptic curves...), but also contains a large number of other useful + functions to compute with mathematical entities such as matrices, polynomials, power series, algebraic numbers etc., + and a lot of transcendental functions. PARI is also available as a C library to allow for faster computations. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['pari-%(version)s.tar.gz'] +source_urls = ['http://pari.math.u-bordeaux.fr/pub/pari/unix/'] + +skipsteps = ['configure'] + +prebuildopts = './Configure --prefix=%(installdir)s &&' + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '6.0'), +] + +sanity_check_paths = { + 'files': + ["bin/%s" % binfile for binfile in ['gp','gp-2.7','gphelp','tex2mail']] + + [ "include/pari/%s" % incfile for incfile in ['pari.h','genpari.h']], + 'dirs': ["bin","include"] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.1.4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.1.4-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..cc1a8741b219a0a4297da401e20e91b3fffe6bbe --- /dev/null +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.1.4-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'PCMSolver' +version = '1.1.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pcmsolver.readthedocs.org' +description = """An API for the Polarizable Continuum Model.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'cstd': 'c99'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/PCMSolver/pcmsolver/archive/'] + +dependencies = [ + ('Python', '2.7.11'), + ('zlib', '1.2.8'), + ('Boost', '1.61.0', versionsuffix), +] + +builddependencies = [ + ('CMake', '3.5.2'), + ('Eigen', '3.2.7'), +] + +configopts = '-DCMAKE_BUILD_TYPE=Release -DEIGEN3_ROOT=$EBROOTEIGEN' +configopts += ' -DCMAKE_CXX_FLAGS="$CXXFLAGS $LIBLAPACK_MT -DEIGEN_USE_MKL_ALL"' + +separate_build_dir = True + +runtest = 'test' + +postinstallcmds = ["chmod +x %(installdir)s/bin/pcmsolver.py"] + +sanity_check_paths = { + 'files': ['bin/pcmsolver.py', 'lib/libpcm.a', 'lib/libpcm.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016b.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..89975bad5142c3a6b131e5ef4b3d9e3375c73bfc --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-foss-2016b.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.38' + +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/PCRE/PCRE-8.38-intel-2016b.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..40a976496d32984ee6431e5ca2103e3da20d8b38 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.38-intel-2016b.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.38' + +homepage = 'http://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.39-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/PCRE/PCRE-8.39-intel-2016b.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.39-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..70c4f5b359ff24a1d6d1a86c50d4f418837e7517 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.39-intel-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': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-utf --enable-unicode-properties" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..03cdf3c1c3579232f1288d0911f495a7b3ee51e0 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE2' +version = '10.21' + +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': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://download.sourceforge.net/pcre'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp --enable-jit" + +sanity_check_paths = { + 'files': ["bin/pcre2-config", "bin/pcre2grep", "bin/pcre2test", "lib/libpcre2-8.a"], + 'dirs': [], +} + +moduleclass = 'devel' \ No newline at end of file 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/PETSc/PETSc-3.7.2-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.2-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..87f6653d3b5c77e7ff03b0a32eea1471f583aa29 --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.2-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,32 @@ +name = 'PETSc' +version = '3.7.2' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['PETSc_ranlib-fix.patch'] + +parmetis = 'ParMETIS' +parmetis_ver = '4.0.3' +dependencies = [ + ('Boost', '1.61.0', versionsuffix), + ('ScientificPython', '2.9.4', versionsuffix), + ('FIAT', '1.6.0', versionsuffix), + ('METIS', '5.1.0'), + (parmetis, parmetis_ver), + ('SCOTCH', '6.0.4'), + ('SuiteSparse', '4.5.3', '-%s-%s' % (parmetis, parmetis_ver)), + ('Hypre', '2.11.1'), +] + +builddependencies = [('CMake', '3.5.2')] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..7988df358235da5762ba758a6bdbe619cd11ac28 --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.7.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +name = 'PETSc' +version = '3.7.3' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['http://ftp.mcs.anl.gov/pub/petsc/release-snapshots'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['PETSc_ranlib-fix.patch'] + +parmetis = 'ParMETIS' +parmetis_ver = '4.0.3' +dependencies = [ + ('Boost', '1.61.0', versionsuffix), + ('ScientificPython', '2.9.4', versionsuffix), + ('FIAT', '1.6.0', versionsuffix), + ('METIS', '5.1.0'), + (parmetis, parmetis_ver), + ('SCOTCH', '6.0.4'), + ('SuiteSparse', '4.5.3', '-%s-%s' % (parmetis, parmetis_ver)), + ('Hypre', '2.11.1'), +] + +builddependencies = [('CMake', '3.5.2')] + +configopts = '--LIBS="$LIBS -lrt"' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb b/easybuild/easyconfigs/p/PGDSpider/PGDSpider-2.1.0.3-Java-1.7.0_80.eb 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/PGI/PGI-16.7-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/p/PGI/PGI-16.7-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..4517a84694d8b46bd325234c410b43ebc9922982 --- /dev/null +++ b/easybuild/easyconfigs/p/PGI/PGI-16.7-GCC-5.4.0-2.26.eb @@ -0,0 +1,25 @@ +name = 'PGI' +version = '16.7' + +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 = ['5594e5cab050bba07ed5f7741bc4c5e8'] + +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/PHASE/PHASE-2.1.1.eb b/easybuild/easyconfigs/p/PHASE/PHASE-2.1.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..9a71ee57a7aa7b03d334d982cdc362317e9bea79 --- /dev/null +++ b/easybuild/easyconfigs/p/PHASE/PHASE-2.1.1.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 = "BinariesTarball" + +name = 'PHASE' +version = '2.1.1' + +homepage = 'http://stephenslab.uchicago.edu/phase/download.html' +description = """ The program PHASE implements a Bayesian statistical +method for reconstructing haplotypes from population genotype data. +Documentation: http://stephenslab.uchicago.edu/assets/software/phase/instruct2.1.pdf""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://stephenslab.uchicago.edu/assets/software/phase/phasecode/'] +sources = ['phase.%(version)s.linux.tar.gz'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ["bin/PHASE", "bin/README"], + 'dirs': [] +} + +moduleclass = 'bio' 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/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb new file mode 100644 index 0000000000000000000000000000000000000000..bb22d3db40840b53c75eb924b164fcc68691e9b6 --- /dev/null +++ b/easybuild/easyconfigs/p/PLAST/PLAST-2.3.1-foss-2016a-Java-1.8.0_92.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'PLAST' +version = '2.3.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = "http://www.irisa.fr/symbiose/projects/plast/" +description = """PLAST is a parallel alignment search tool for comparing large protein banks""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/PLAST-software/plast-library/releases/download/v%(version)s/'] +sources=['%(namelower)s_source_v%(version)s.tar.gz'] + +builddependencies = [ + ('CMake', '3.5.2'), + ('Perl', '5.22.1') +] + +dependencies = [ + ('Java', '1.8.0_92', '', True), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'include/algo', 'include/alignment', 'include/misc'], +} + +moduleclass = 'bio' \ No newline at end of file diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016a.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3a9a5a29e93ad257e3ac850417097f09f0575f33 --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016a.eb @@ -0,0 +1,51 @@ +# 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: Adam Huffman +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'PLINK' +version = '1.07' + +homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' +description = """ PLINK is a free, open-source whole genome association analysis toolset, + designed to perform a range of basic, large-scale analyses in a computationally efficient manner. + The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for + steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). + Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, + annotation and storage of results. """ + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'openmp': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] + +patches = ['PLINK-1.07_redeclaration.patch'] + +dependencies = [('zlib', '1.2.8')] + +# plink makefile is a little bit tricky so we pass every options as arguments +# review plink original makefile for details +# if you want "new version check" change to WITH_WEBCHECK="1", but if your compute nodes +# have no internet access better leave it as is +buildopts = ' CXX_UNIX="$CXX $CXXFLAGS" WITH_R_PLUGINS=1 WITH_WEBCHECK="" WITH_ZLIB=1 ' +buildopts += ' WITH_LAPACK=1 FORCE_DYNAMIC=1 LIB_LAPACK=$EBROOTOPENBLAS/lib/libopenblas.%s' % SHLIB_EXT + +files_to_copy = [ + (["plink", "gPLINK.jar"], 'bin'), + "test.map", + "test.ped", + "COPYING.txt", + "README.txt", +] + +sanity_check_paths = { + 'files': ["bin/plink", "bin/gPLINK.jar", "test.map", "test.ped", "COPYING.txt", "README.txt"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016b.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..8d5a6d2eb62ed53d9542a2a09cdd66a255e6111a --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-foss-2016b.eb @@ -0,0 +1,51 @@ +# 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: Adam Huffman +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'PLINK' +version = '1.07' + +homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' +description = """ PLINK is a free, open-source whole genome association analysis toolset, + designed to perform a range of basic, large-scale analyses in a computationally efficient manner. + The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for + steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). + Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, + annotation and storage of results. """ + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'openmp': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] + +patches = ['PLINK-1.07_redeclaration.patch'] + +dependencies = [('zlib', '1.2.8')] + +# plink makefile is a little bit tricky so we pass every options as arguments +# review plink original makefile for details +# if you want "new version check" change to WITH_WEBCHECK="1", but if your compute nodes +# have no internet access better leave it as is +buildopts = ' CXX_UNIX="$CXX $CXXFLAGS" WITH_R_PLUGINS=1 WITH_WEBCHECK="" WITH_ZLIB=1 ' +buildopts += ' WITH_LAPACK=1 FORCE_DYNAMIC=1 LIB_LAPACK=$EBROOTOPENBLAS/lib/libopenblas.%s' % SHLIB_EXT + +files_to_copy = [ + (["plink", "gPLINK.jar"], 'bin'), + "test.map", + "test.ped", + "COPYING.txt", + "README.txt", +] + +sanity_check_paths = { + 'files': ["bin/plink", "bin/gPLINK.jar", "test.map", "test.ped", "COPYING.txt", "README.txt"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-goolf-1.7.20.eb b/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..1ed4041bd8385c13811cd42a9cf74b31d1d2b26d --- /dev/null +++ b/easybuild/easyconfigs/p/PLINKSEQ/PLINKSEQ-0.10-goolf-1.7.20.eb @@ -0,0 +1,39 @@ +# 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 = 'MakeCp' + +name = 'PLINKSEQ' +version = '0.10' + +homepage = 'https://atgu.mgh.harvard.edu/plinkseq/' +description = """ PLINK/SEQ is an open-source C/C++ library for working with human + genetic variation data. The specific focus is to provide a platform for analytic tool + development for variation data from large-scale resequencing and genotyping projects, + particularly whole-exome and whole-genome studies. It is independent of (but designed + to be complementary to) the existing PLINK package. """ + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://psychgen.u.hpc.mssm.edu/plinkseq_downloads/'] +sources = ['%(namelower)s-src-%(version)s.tgz'] + +dependencies = [ + ('protobuf', '2.5.0'), + ('zlib', '1.2.8'), +] + +parallel = 1 + +binary_files = ["behead", "browser", "gcol", "mm", "mongoose", "pdas", "pseq", "smp", "tab2vcf"] + +files_to_copy = [(["build/execs/%s" % x for x in binary_files], "bin")] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binary_files], + 'dirs': [], +} + +moduleclass = 'bio' 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 $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.so', 'lib/libplumed.so'], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.so', + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.2-intel-2016a.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.2-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f7b809de916e469e308273dd01f3ee215d15bff1 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.2-intel-2016a.eb @@ -0,0 +1,42 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.2.2' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '2.1'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.3-intel-2016b.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.3-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..f53ad8b7b8e72602083a5570951fb14be34cee45 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.2.3-intel-2016b.eb @@ -0,0 +1,42 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.2.3' + +homepage = 'http://www.plumed-code.org' +description = """PLUMED is an open source library for free energy calculations in molecular systems which + works together with some of the most popular molecular dynamics engines. Free energy calculations can be + performed as a function of many order parameters with a particular focus on biological problems, using + state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. + The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. +""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': 'True'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '2.1'), + ('libmatheval', '1.1.11'), +] + +preconfigopts = 'env FC=$MPIF90 LIBS="$LIBLAPACK $LIBS" ' +configopts = ' --exec-prefix=%(installdir)s --enable-gsl' +prebuildopts = 'source sourceme.sh && ' + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.%s' % SHLIB_EXT, 'lib/libplumed.%s' % SHLIB_EXT], + 'dirs': ['lib/plumed'] +} + +modextrapaths = { + 'PLUMED_KERNEL': 'lib/libplumedKernel.%s' % SHLIB_EXT, + 'PLUMED_ROOT': 'lib/plumed', +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/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/PROJ/PROJ-4.9.2-foss-2016b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..324f2cd7f8b9dca770e5632ea84d5d371397b25e --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-foss-2016b.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '4.9.2' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-intel-2016b.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..bcb1e2a0d171f9dcda9ae72d70eebdca74be1ce1 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.9.2-intel-2016b.eb @@ -0,0 +1,30 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'PROJ' +version = '4.9.2' + +homepage = 'http://trac.osgeo.org/proj/' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['http://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/cs2cs', 'bin/geod', 'bin/invgeod', 'bin/invproj', + 'bin/nad2bin', 'bin/proj'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PSI/README.md b/easybuild/easyconfigs/p/PSI/README.md new file mode 100644 index 0000000000000000000000000000000000000000..1091a98d5b07a31a066a493d24860eb768e5fa3e --- /dev/null +++ b/easybuild/easyconfigs/p/PSI/README.md @@ -0,0 +1,6 @@ +The developers of PSI decide to rename their project to PSI4. The first version is PSI4/1.0. +To keep up with upstream, we have also stopped adding easyconfigs here and now continue with PSI4 as +program name. Look in the directory 'PSI4' for the latest version of PSI. +More information: +- https://github.com/psi4/psi4/issues/213#issuecomment-182766378 +- https://github.com/psi4/psi4/wiki/Versioning#how-to-get-and-interpret-the-version-number diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.0-disable-ambit.patch b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-disable-ambit.patch new file mode 100644 index 0000000000000000000000000000000000000000..4ce4051cb506cfc6538e7246deec284d8782985e --- /dev/null +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-disable-ambit.patch @@ -0,0 +1,17 @@ +# We don't include it, so don't build the plugin (will fail otherwise) +# Mainlined with https://github.com/psi4/psi4/pull/436 +# wpoely86@gmail.com +diff --git a/plugins/CMakeLists.txt b/plugins/CMakeLists.txt +index 7752eed..ae27cc1 100644 +--- a/plugins/CMakeLists.txt ++++ b/plugins/CMakeLists.txt +@@ -4,7 +4,9 @@ add_subdirectory(mointegrals) + add_subdirectory(mollerplesset2) + add_subdirectory(sointegrals) + add_subdirectory(skeleton) ++if (Ambit_FOUND) + add_subdirectory(skeletonambit) ++endif() + add_subdirectory(skeletonaointegrals) + add_subdirectory(skeletonmointegrals) + add_subdirectory(skeletonsointegrals) 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 new file mode 100644 index 0000000000000000000000000000000000000000..ed0569f10136967d3595406717d9a1186a9b2438 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_PSI' + +name = 'PSI4' +version = '1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.psicode.org/' +description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for + efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform + computations with more than 2500 basis functions running serially or in parallel.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/psi4/psi4/archive/'] +sources = ['%(version)s.tar.gz'] + +patches = [ + 'PSI4-%(version)s-plugin-fix.patch', + 'PSI4-%(version)s-disable-ambit.patch', +] + +dependencies = [ + ('Python', '2.7.11'), + ('Boost', '1.61.0', versionsuffix), + ('PCMSolver', '1.1.4', versionsuffix), + ('CheMPS2', '1.7.2'), +] + +builddependencies = [ + ('CMake', '3.5.2'), +# ('Perl', '5.22.1', '-bare'), # for the test suite +] + +configopts = '-DENABLE_MPI=ON -DENABLE_OMP=ON -DENABLE_UNIT_TESTS=ON -DENABLE_CHEMPS2=ON -DENABLE_PLUGINS=ON' + +# CMake will pick mpiexec by default and this fails with intel MPI +#configopts += ' -DMPIEXEC=$EBROOTIMPI/bin64/mpirun' + +# The tests don't work with MPI (most of them hang or fail) +# ref: https://github.com/psi4/psi4/pull/436#issuecomment-230519769 +runtest = False + +moduleclass = 'chem' 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 new file mode 100644 index 0000000000000000000000000000000000000000..1fcbf7998b7d8041ce3203c7d9ff413bc3f5f2c5 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-intel-2016a-mt-Python-2.7.11.eb @@ -0,0 +1,42 @@ +easyblock = 'EB_PSI' + +name = 'PSI4' +version = '1.0' +pysuff = '-Python-%(pyver)s' +versionsuffix = '-mt%s' % pysuff + +homepage = 'http://www.psicode.org/' +description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for + efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform + computations with more than 2500 basis functions running serially or in parallel.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': False} + +source_urls = ['https://github.com/psi4/psi4/archive/'] +sources = ['%(version)s.tar.gz'] + +patches = [ + 'PSI4-%(version)s-plugin-fix.patch', + 'PSI4-%(version)s-disable-ambit.patch', +] + +dependencies = [ + ('Python', '2.7.11'), + ('Boost', '1.61.0', pysuff), + ('PCMSolver', '1.1.4', pysuff), + ('CheMPS2', '1.7.2'), +] + +builddependencies = [ + ('CMake', '3.5.2'), + ('Perl', '5.22.1', '-bare'), # for the test suite +] + +configopts = '-DENABLE_MPI=OFF -DENABLE_OMP=ON -DENABLE_UNIT_TESTS=ON -DENABLE_PLUGINS=ON -DENABLE_DUMMY_PLUGIN=ON' + +# 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 +runtest = 'ARGS="-V -E \'pubchem1|pubchem2\' -j 4" test' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.0-plugin-fix.patch b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-plugin-fix.patch new file mode 100644 index 0000000000000000000000000000000000000000..1cd68c1a98f7727fe0e48eb516a5d034d611a7ff --- /dev/null +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.0-plugin-fix.patch @@ -0,0 +1,14 @@ +# Let the plugin makefile system work with our install system: patch the +# directory path to correspond with our install directory +# 01/02/2016 - wpoely86@gmail.com +diff -ur psi4public-e4070d0024742579a445e084da9dde078310094d.orig/CMakeLists.txt psi4public-e4070d0024742579a445e084da9dde078310094d/CMakeLists.txt +--- psi4public-e4070d0024742579a445e084da9dde078310094d.orig/CMakeLists.txt 2016-02-01 22:43:36.000000000 +0100 ++++ psi4public-e4070d0024742579a445e084da9dde078310094d/CMakeLists.txt 2016-02-05 12:40:20.375508374 +0100 +@@ -282,6 +282,7 @@ + foreach(dir ${dirs}) + set(PLUGIN_INCLUDE_DIRECTORIES "-I${dir} ${PLUGIN_INCLUDE_DIRECTORIES}") + endforeach() ++set(PLUGIN_INCLUDE_DIRECTORIES "-I$ENV{PSI_SRC_INSTALL_DIR}/include -I$ENV{PSI_SRC_INSTALL_DIR}/src/lib/ -I$ENV{PSI_OBJ_INSTALL_DIR}/include -I$ENV{PSI_OBJ_INSTALL_DIR}/src/lib/ ${PLUGIN_INCLUDE_DIRECTORIES}") + foreach(def ${defs}) + set(PLUGIN_DEFINES "-D${def} ${PLUGIN_DEFINES}") + endforeach() diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..79449c632cffd80d62b4f232d4d822076a8a61bf --- /dev/null +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,44 @@ +easyblock = 'PerlModule' + +name = 'PSORTb' +version = '3.0.4' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'http://psort.org/psortb/index.html' +description = """PSORTb v3.0.4 is the most precise bacterial localization prediction tool available.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://www.psort.org/download/'] +sources = ['bio-tools-psort-all.%(version)s.tar.gz'] + +patches = [ + 'PSORTb-%(version)s-libpsortb.patch', +] + +dependencies = [ + ('Perl', '5.22.1'), + ('libpsortb','1.0'), + ('BioPerl','1.6.924','-Perl-5.22.1'), + ('BLAST','2.2.26', '-Linux_x86_64', True), + ('pftoolsV3','20160324'), +] + +options = {'modulename': 'Bio::Tools::PSort'} + +preconfigopts = "export PSORTROOT=%(installdir)s && " + +prebuildopts = 'sed -i "s/CC = cc/CC ?= gcc/" bio-tools-psort-modhmm/Makefile && ' + +postinstallcmds = [ + "cp -r psort/* %(installdir)s/.", +] + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM.pm', + 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Algorithm/HMM', + 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/Bio/Tools/PSort'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-libpsortb.patch b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-libpsortb.patch new file mode 100644 index 0000000000000000000000000000000000000000..bbc5e91be1d4e684072f1f10cd34c543db0fb3c5 --- /dev/null +++ b/easybuild/easyconfigs/p/PSORTb/PSORTb-3.0.4-libpsortb.patch @@ -0,0 +1,130 @@ +Removed q and a and perl scripting environment set accordingly. +Author: Fokke Dijkstra (University of Groningen) +diff -ru bio-tools-psort-all/lib/Bio/Tools/PSort/Install.pm bio-tools-psort-all.new/lib/Bio/Tools/PSort/Install.pm +--- bio-tools-psort-all/lib/Bio/Tools/PSort/Install.pm 2010-07-29 00:12:43.000000000 +0200 ++++ bio-tools-psort-all.new/lib/Bio/Tools/PSort/Install.pm 2015-11-26 13:50:18.000000000 +0100 +@@ -77,7 +77,12 @@ + } + } + } else { +- $input = ExtUtils::MakeMaker::prompt("\n$lib was not found in the dynamic linker path, is there somewhere else we should check? ", "/usr/local/lib$sixtyfour"); ++ if (exists($ENV{EBROOTLIBPSORTB})) { ++ $input = "$ENV{EBROOTLIBPSORTB}/lib$sixtyfour"; ++ } else { ++ $input = "/usr/local/lib$sixtyfour"; ++ } ++ $input = ExtUtils::MakeMaker::prompt("\n$lib was not found in the dynamic linker path, is there somewhere else we should check? ", $input); + if($path = Bio::Tools::PSort::Install->findLib("-L$input -l$lib")) { + $passed = 1; + $libpath = $input; +diff -ru bio-tools-psort-all/Makefile.PL bio-tools-psort-all.new/Makefile.PL +--- bio-tools-psort-all/Makefile.PL 2010-07-28 23:40:19.000000000 +0200 ++++ bio-tools-psort-all.new/Makefile.PL 2015-11-30 12:03:14.000000000 +0100 +@@ -97,7 +97,12 @@ + } + + sub get_psort_root { +- my $root = prompt("Where do you plan to install the psort configuration files?", '/usr/local/psortb'); ++ if(exists($ENV{PSORTROOT})) { ++ $root = $ENV{PSORTROOT}; ++ } else { ++ $root = '/usr/local/psortb'; ++ } ++ my $root = prompt("Where do you plan to install the psort configuration files?", $root); + $PSORT_ROOT = $root; + } + +Only in bio-tools-psort-all: .Makefile.PL.swp +diff -ru bio-tools-psort-all/psort/bin/check-sig bio-tools-psort-all.new/psort/bin/check-sig +--- bio-tools-psort-all/psort/bin/check-sig 2003-07-25 18:48:03.000000000 +0200 ++++ bio-tools-psort-all.new/psort/bin/check-sig 2015-11-26 13:51:19.000000000 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! /usr/bin/env perl + + use Getopt::Long; + +diff -ru bio-tools-psort-all/psort/bin/psort bio-tools-psort-all.new/psort/bin/psort +--- bio-tools-psort-all/psort/bin/psort 2010-05-26 23:51:55.000000000 +0200 ++++ bio-tools-psort-all.new/psort/bin/psort 2015-11-26 13:50:58.000000000 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! /usr/bin/env perl + + use Bio::Tools::PSort::Report::Formatter; + use Bio::Tools::PSort; +diff -ru bio-tools-psort-all/psort/bin/psort.tmpt bio-tools-psort-all.new/psort/bin/psort.tmpt +--- bio-tools-psort-all/psort/bin/psort.tmpt 2009-11-10 22:46:09.000000000 +0100 ++++ bio-tools-psort-all.new/psort/bin/psort.tmpt 2015-11-26 13:51:01.000000000 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! /usr/bin/env perl + + use Bio::Tools::PSort::Report::Formatter; + use Bio::Tools::PSort; +diff -ru bio-tools-psort-all/psort/conf/analysis/signal/archaea/check-sig bio-tools-psort-all.new/psort/conf/analysis/signal/archaea/check-sig +--- bio-tools-psort-all/psort/conf/analysis/signal/archaea/check-sig 2008-10-01 18:57:37.000000000 +0200 ++++ bio-tools-psort-all.new/psort/conf/analysis/signal/archaea/check-sig 2015-11-26 13:52:00.000000000 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! /usr/bin/env perl + + use Getopt::Long; + +diff -ru bio-tools-psort-all/psort/conf/analysis/signal/gramneg/check-sig bio-tools-psort-all.new/psort/conf/analysis/signal/gramneg/check-sig +--- bio-tools-psort-all/psort/conf/analysis/signal/gramneg/check-sig 2004-02-25 08:50:44.000000000 +0100 ++++ bio-tools-psort-all.new/psort/conf/analysis/signal/gramneg/check-sig 2015-11-26 13:52:02.000000000 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! /usr/bin/env perl + + use Getopt::Long; + +diff -ru bio-tools-psort-all/psort/conf/analysis/signal/grampos/check-sig bio-tools-psort-all.new/psort/conf/analysis/signal/grampos/check-sig +--- bio-tools-psort-all/psort/conf/analysis/signal/grampos/check-sig 2004-04-02 20:23:28.000000000 +0200 ++++ bio-tools-psort-all.new/psort/conf/analysis/signal/grampos/check-sig 2015-11-26 13:52:05.000000000 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/perl ++#! /usr/bin/env perl + + use Getopt::Long; + +diff -ru bio-tools-psort-all/psort/server/rpc/classify.xpl bio-tools-psort-all.new/psort/server/rpc/classify.xpl +--- bio-tools-psort-all/psort/server/rpc/classify.xpl 2004-03-05 20:47:06.000000000 +0100 ++++ bio-tools-psort-all.new/psort/server/rpc/classify.xpl 2015-11-26 13:52:20.000000000 +0100 +@@ -14,7 +14,7 @@ + + + +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +name = "Paraver" +version = "4.4.5" + +homepage = 'http://www.bsc.es/computer-sciences/performance-tools/paraver' +description = """A very powerful performance visualization and analysis tool based on + traces that can be used to analyse any information that is expressed on its input trace format. + Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.""" + +toolchain = {'name': 'GCC', 'version': '4.7.3'} + +dependencies = [ + ('zlib', '1.2.8'), + ('wxPropertyGrid', '1.4.15'), + ('Boost', '1.53.0', '-serial'), +] + +# http://www.bsc.es/computer-sciences/performance-tools/downloads +# Requires input of email address for download +sources = ['%(namelower)s-' + "sources" +'-%(version)s.tar.bz2'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..646562570d220047a1e520a1277312c97fc5b21a --- /dev/null +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.5.6-foss-2015a.eb @@ -0,0 +1,32 @@ +# 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 = "Paraver" +version = "4.5.6" + +homepage = 'http://www.bsc.es/computer-sciences/performance-tools/paraver' +description = """A very powerful performance visualization and analysis tool based on + traces that can be used to analyse any information that is expressed on its input trace format. + Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +compname = 'GCC' +compver = '4.9.2' + +dependencies = [ + ('zlib', '1.2.8', '', (compname, compver)), + ('wxPropertyGrid', '1.4.15', "", (compname, compver)), + ('Boost', '1.58.0', '-serial', (compname, compver)), +] + +# http://www.bsc.es/computer-sciences/performance-tools/downloads +# Requires input of email address for download +sources = ['%(namelower)s-' + "sources" +'-%(version)s.tar.gz'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-5.5.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-5.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..6d7b68ab454852e10e38b28d91e778f390473b0e --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.16.3-ictce-5.5.0.eb @@ -0,0 +1,225 @@ +name = 'Perl' +version = '5.16.3' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['exitcode_error.patch'] + +runtest = 'test' + +exts_list = [ + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('Data::Stag', '0.11', { + 'source_tmpl': 'Data-Stag-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CM/CMUNGALL/'], + }), + ('DB_File', '1.827', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PM/PMQS/'], + }), + ('DBI', '1.625', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TI/TIMB/'], + }), + ('Bio::Perl', '1.6.901', { + 'source_tmpl': 'BioPerl-1.6.901.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'patches': ['BioPerl_disable-broken-test.patch'], + }), + ('Sub::Uplevel', '0.24', { + 'source_tmpl': 'Sub-Uplevel-0.24.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'], + }), + ('Tree::DAG_Node', '1.11', { + 'source_tmpl': 'Tree-DAG_Node-1.11.tgz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/'], + }), + ('Try::Tiny', '0.12', { + 'source_tmpl': 'Try-Tiny-0.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], + }), + ('Test::Fatal', '0.010', { + 'source_tmpl': 'Test-Fatal-0.010.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Test::Exception', '0.31', { + 'source_tmpl': 'Test-Exception-0.31.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADIE/'], + }), + ('Test::Warn', '0.24', { + 'source_tmpl': 'Test-Warn-0.24.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], + }), + ('Test::Requires', '0.06', { + 'source_tmpl': 'Test-Requires-0.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM/'], + }), + ('Test::Tester', '0.108', { + 'source_tmpl': 'Test-Tester-0.108.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FD/FDALY/'], + }), + ('Params::Util', '1.07', { + 'source_tmpl': 'Params-Util-1.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('Sub::Install', '0.926', { + 'source_tmpl': 'Sub-Install-0.926.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Data::OptList', '0.107', { + 'source_tmpl': 'Data-OptList-0.107.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Sub::Exporter', '0.985', { + 'source_tmpl': 'Sub-Exporter-0.985.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/R/RJ/RJBS/'], + }), + ('Test::Output', '1.01', { + 'source_tmpl': 'Test-Output-1.01.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BD/BDFOY/'], + }), + ('Module::Runtime', '0.013', { + 'source_tmpl': 'Module-Runtime-0.013.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM/'], + }), + ('Module::Implementation', '0.06', { + 'source_tmpl': 'Module-Implementation-0.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('List::MoreUtils', '0.33', { + 'source_tmpl': 'List-MoreUtils-0.33.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('Package::DeprecationManager', '0.13', { + 'source_tmpl': 'Package-DeprecationManager-0.13.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Dist::CheckConflicts', '0.02', { + 'source_tmpl': 'Dist-CheckConflicts-0.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], + }), + ('Package::Stash', '0.34', { + 'source_tmpl': 'Package-Stash-0.34.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], + }), + ('Class::Load', '0.20', { + 'source_tmpl': 'Class-Load-0.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BO/BOBTFISH/'], + }), + ('Sub::Name', '0.05', { + 'source_tmpl': 'Sub-Name-0.05.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FL/FLORA/'], + }), + ('Eval::Closure', '0.08', { + 'source_tmpl': 'Eval-Closure-0.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DO/DOY/'], + }), + ('Sub::Exporter::Progressive', '0.001010', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001010.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/F/FR/FREW/'], + }), + ('Devel::GlobalDestruction', '0.11', { + 'source_tmpl': 'Devel-GlobalDestruction-0.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/H/HA/HAARG/'], + }), + ('boolean', '0.30', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/I/IN/INGY/'], + }), + ('Tie::IxHash', '1.23', { + 'source_tmpl': 'Tie-IxHash-1.23.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CH/CHORNY/'], + }), + ('Moose', '2.0801', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/E/ET/ETHER/'], + }), + ('Params::Validate', '1.07', { + 'source_tmpl': 'Params-Validate-1.07.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('DateTime::Locale', '0.45', { + 'source_tmpl': 'DateTime-Locale-0.45.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Class::Singleton', '1.4', { + 'source_tmpl': 'Class-Singleton-1.4.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AB/ABW/'], + }), + ('DateTime::TimeZone', '1.58', { + 'source_tmpl': 'DateTime-TimeZone-1.58.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('DateTime', '1.01', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/D/DW/DWHEELER/'], + }), + ('DateTime::Tiny', '1.04', { + 'source_tmpl': 'DateTime-Tiny-1.04.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/A/AD/ADAMK/'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/U/UR/URI/'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('IO::HTML', '1.00', { + 'source_tmpl': 'IO-HTML-1.00.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/C/CJ/CJM/'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('URI', '1.60', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('HTTP::Request', '6.06', { + 'source_tmpl': 'HTTP-Message-6.06.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PETDANCE/'], + }), + ('HTML::Entities', '3.70', { + 'source_tmpl': 'HTML-Parser-3.70.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GA/GAAS/'], + }), + ('AnyEvent', '7.04', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/M/ML/MLEHMANN/'], + }), + ('Mouse', '1.05', { + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GF/GFUJI/'], + }), + ('XML::NamespaceSupport', '1.11', { + 'source_tmpl': 'XML-NamespaceSupport-1.11.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/'], + }), + ('XML::SAX::Base', '1.08', { + 'source_tmpl': 'XML-SAX-Base-1.08.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM/'], + }), + ('XML::SAX', '0.99', { + 'source_tmpl': 'XML-SAX-0.99.tar.gz', + 'source_urls': ['http://cpan.metacpan.org/authors/id/G/GR/GRANTM/'], + }), +] + +moduleclass = 'lang' 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/Perl/Perl-5.22.2-intel-2016a.eb b/easybuild/easyconfigs/p/Perl/Perl-5.22.2-intel-2016a.eb index c1290fa071cce4263598f1f24de5fb43ac107afa..c8a4524d45495f7604bbbaab39da8b8cd3f3653d 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.22.2-intel-2016a.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.22.2-intel-2016a.eb @@ -881,6 +881,5 @@ exts_list = [ 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], }), ] -exts_list = [] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..dc1a3cef69a3f9ded529556c250fcaa9c11478ce --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-GCCcore-4.9.3.eb @@ -0,0 +1,886 @@ +name = 'Perl' +version = '5.24.0' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('binutils', '2.25')] + +exts_list = [ + ('Config::General', '2.61', { + 'source_tmpl': 'Config-General-2.61.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-6.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.022', { + 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Test::Harness', '3.36', { + 'source_tmpl': 'Test-Harness-3.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.09', { + 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2016060801', { + 'source_tmpl': 'Regexp-Common-2016060801.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-5.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.026', { + 'source_tmpl': 'Test-Warnings-0.026.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '1.05', { + 'source_tmpl': 'DateTime-Locale-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '2.00', { + 'source_tmpl': 'DateTime-TimeZone-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Build', '0.4218', { + 'source_tmpl': 'Module-Build-0.4218.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.24', { + 'source_tmpl': 'Try-Tiny-0.24.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Params::Validate', '1.24', { + 'source_tmpl': 'Params-Validate-1.24.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.416', { + 'source_tmpl': 'List-MoreUtils-0.416.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.042', { + 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-1.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.34', { + 'source_tmpl': 'DateTime-1.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Readonly', '2.05', { + 'source_tmpl': 'Readonly-2.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-0.41.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.29', { + 'source_tmpl': 'Tree-DAG_Node-1.29.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + }), + ('DBI', '1.636', { + 'source_tmpl': 'DBI-1.636.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.50', { + 'source_tmpl': 'DBD-SQLite-1.50.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.76', { + 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-0.73.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', '3.62', { + 'source_tmpl': 'PathTools-3.62.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('ExtUtils::MakeMaker', '7.18', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.18.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Simple', '1.302037', { + 'source_tmpl': 'Test-Simple-1.302037.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', 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['https://cpan.metacpan.org/authors/id/S/SU/SULLR'], + }), + ('Fennec::Lite', '0.004', { + 'source_tmpl': 'Fennec-Lite-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Meta::Builder', '0.003', { + 'source_tmpl': 'Meta-Builder-0.003.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Exporter::Declare', '0.114', { + 'source_tmpl': 'Exporter-Declare-0.114.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Getopt::Long', '2.48', { + 'source_tmpl': 'Getopt-Long-2.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + }), + ('Log::Message', '0.08', { + 'source_tmpl': 'Log-Message-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Mouse', 'v2.4.5', { + 'source_tmpl': 'Mouse-v2.4.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Test::Version', '2.04', { + 'source_tmpl': 'Test-Version-2.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.01', { + 'source_tmpl': 'DBIx-Admin-TableInfo-3.01.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.09', { + 'source_tmpl': 'Net-HTTP-6.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Test::Deep', '1.120', { + 'source_tmpl': 'Test-Deep-1.120.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], + }), + ('Moo', '2.002004', { + 'source_tmpl': 'Moo-2.002004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_tmpl': 'Hash-Merge-0.200.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.09', { + 'source_tmpl': 'HTML-Entities-Interpolate-1.09.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.34', { + 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.64', { + 'source_tmpl': 'Test-Differences-0.64.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.058', { + 'source_tmpl': 'HTTP-Tiny-0.058.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.17', { + 'source_tmpl': 'Package-DeprecationManager-0.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('version', '0.9917', { + 'source_tmpl': 'version-0.9917.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-0.53.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + }), + ('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', '0.15', { + 'source_tmpl': 'Sub-Name-0.15.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', '2011', { + 'source_tmpl': 'Canary-Stability-2011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.12', { + 'source_tmpl': 'AnyEvent-7.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-1.221.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-1.51.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Net::SMTP::SSL', '1.03', { + 'source_tmpl': 'Net-SMTP-SSL-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-2.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-5.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Devel::GlobalDestruction', '0.13', { + 'source_tmpl': 'Devel-GlobalDestruction-0.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Expect', '1.33', { + 'source_tmpl': 'Expect-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JA/JACOBY/'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-v6.0.1.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('Statistics::Descriptive', '3.0612', { + 'source_tmpl': 'Statistics-Descriptive-3.0612.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-0.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.15', { + 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['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', { + 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['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001011', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-2.022.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-1.1903.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000003', { + 'source_tmpl': 'strictures-2.000003.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-2.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('File::Which', '1.21', { + 'source_tmpl': 'File-Which-1.21.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Error', '0.17024', { + 'source_tmpl': 'Error-0.17024.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Mock::Quick', '1.111', { + 'source_tmpl': 'Mock-Quick-1.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::CSV', '1.33', { + 'source_tmpl': 'Text-CSV-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Test::Output', '1.03', { + 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + }), + ('Class::DBI', '3.0.17', { + 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.11', { + 'source_tmpl': 'List-AllUtils-0.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.40', { + 'source_tmpl': 'Exception-Class-1.40.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.14', { + 'source_tmpl': 'Eval-Closure-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-6.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.22', { + 'source_tmpl': 'XML-Simple-2.22.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-0.928.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.01', { + 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.007', { + 'source_tmpl': 'Test-Exception-LessClever-0.007.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', '1.45', { + 'source_tmpl': 'Scalar-List-Utils-1.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::HomeDir', '1.00', { + 'source_tmpl': 'File-HomeDir-1.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-1.002005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.06', { + 'source_tmpl': 'DateTime-Tiny-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.59', { + 'source_tmpl': 'Text-Format-0.59.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.06', { + 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.84', { + 'source_tmpl': 'Log-Handler-0.84.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Devel::StackTrace', '2.01', { + 'source_tmpl': 'Devel-StackTrace-2.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.33', { + 'source_tmpl': 'TermReadKey-2.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.1804', { + 'source_tmpl': 'Moose-2.1804.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-1.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.05', { + 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.34', { + 'source_tmpl': 'File-Find-Rule-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.410', { + 'source_tmpl': 'SQL-Statement-1.410.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-0.37.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.110', { + 'source_tmpl': 'Data-OptList-0.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9160', { + 'source_tmpl': 'CPANPLUS-0.9160.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.05', { + 'source_tmpl': 'Text-Soundex-3.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.18', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-0.18.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.29', { + 'source_tmpl': 'Want-0.29.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.05', { + 'source_tmpl': 'Cwd-Guard-0.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.18', { + 'source_tmpl': 'MailTools-2.18.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..05c6f2b9c0a6158b7682cfb6c93f0c70c119ac65 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b-bare.eb @@ -0,0 +1,17 @@ +name = 'Perl' +version = '5.24.0' +versionsuffix = '-bare' + +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] + +# bare, no extensions +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..77e0aab0f1306032ff1e441370a12720e669a297 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-foss-2016b.eb @@ -0,0 +1,884 @@ +name = 'Perl' +version = '5.24.0' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] + +exts_list = [ + ('Config::General', '2.61', { + 'source_tmpl': 'Config-General-2.61.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-6.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.022', { + 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Test::Harness', '3.36', { + 'source_tmpl': 'Test-Harness-3.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.09', { + 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2016060801', { + 'source_tmpl': 'Regexp-Common-2016060801.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-5.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.026', { + 'source_tmpl': 'Test-Warnings-0.026.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '1.05', { + 'source_tmpl': 'DateTime-Locale-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '2.00', { + 'source_tmpl': 'DateTime-TimeZone-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Build', '0.4218', { + 'source_tmpl': 'Module-Build-0.4218.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.24', { + 'source_tmpl': 'Try-Tiny-0.24.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Params::Validate', '1.24', { + 'source_tmpl': 'Params-Validate-1.24.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.416', { + 'source_tmpl': 'List-MoreUtils-0.416.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.042', { + 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-1.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.34', { + 'source_tmpl': 'DateTime-1.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Readonly', '2.05', { + 'source_tmpl': 'Readonly-2.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-0.41.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.29', { + 'source_tmpl': 'Tree-DAG_Node-1.29.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + }), + ('DBI', '1.636', { + 'source_tmpl': 'DBI-1.636.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.50', { + 'source_tmpl': 'DBD-SQLite-1.50.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.76', { + 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-0.73.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', '3.62', { + 'source_tmpl': 'PathTools-3.62.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('ExtUtils::MakeMaker', '7.18', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.18.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Simple', '1.302037', { + 'source_tmpl': 'Test-Simple-1.302037.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', { + 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['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', '2.029', { + 'source_tmpl': 'IO-Socket-SSL-2.029.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', '2.04', { + 'source_tmpl': 'Test-Version-2.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.01', { + 'source_tmpl': 'DBIx-Admin-TableInfo-3.01.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.09', { + 'source_tmpl': 'Net-HTTP-6.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Test::Deep', '1.120', { + 'source_tmpl': 'Test-Deep-1.120.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], + }), + ('Moo', '2.002004', { + 'source_tmpl': 'Moo-2.002004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_tmpl': 'Hash-Merge-0.200.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.09', { + 'source_tmpl': 'HTML-Entities-Interpolate-1.09.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.34', { + 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.64', { + 'source_tmpl': 'Test-Differences-0.64.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.058', { + 'source_tmpl': 'HTTP-Tiny-0.058.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.17', { + 'source_tmpl': 'Package-DeprecationManager-0.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('version', '0.9917', { + 'source_tmpl': 'version-0.9917.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-0.53.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + }), + ('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', '0.15', { + 'source_tmpl': 'Sub-Name-0.15.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', 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['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', { 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['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.15', { + 'source_tmpl': 'libwww-perl-6.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('GD::Graph', '1.52', { + 'source_tmpl': 'GDGraph-1.52.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('boolean', '0.45', { + 'source_tmpl': 'boolean-0.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-1.75.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-2.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-5.72.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Class::Inspector', '1.28', { + 'source_tmpl': 'Class-Inspector-1.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Parse::RecDescent', '1.967013', { + 'source_tmpl': 'Parse-RecDescent-1.967013.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + }), + ('Carp', '1.38', { + 'source_tmpl': 'Carp-1.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::XPath', '1.37', { + 'source_tmpl': 'XML-XPath-1.37.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + }), + ('Capture::Tiny', '0.42', { + 'source_tmpl': 'Capture-Tiny-0.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-2.90.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001011', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-2.022.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-1.1903.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000003', { + 'source_tmpl': 'strictures-2.000003.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-2.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('File::Which', '1.21', { + 'source_tmpl': 'File-Which-1.21.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Error', '0.17024', { + 'source_tmpl': 'Error-0.17024.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Mock::Quick', '1.111', { + 'source_tmpl': 'Mock-Quick-1.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::CSV', '1.33', { + 'source_tmpl': 'Text-CSV-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Test::Output', '1.03', { + 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + }), + ('Class::DBI', '3.0.17', { + 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.11', { + 'source_tmpl': 'List-AllUtils-0.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.40', { + 'source_tmpl': 'Exception-Class-1.40.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.14', { + 'source_tmpl': 'Eval-Closure-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-6.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.22', { + 'source_tmpl': 'XML-Simple-2.22.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-0.928.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.01', { + 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.007', { + 'source_tmpl': 'Test-Exception-LessClever-0.007.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', '1.45', { + 'source_tmpl': 'Scalar-List-Utils-1.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::HomeDir', '1.00', { + 'source_tmpl': 'File-HomeDir-1.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-1.002005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.06', { + 'source_tmpl': 'DateTime-Tiny-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.59', { + 'source_tmpl': 'Text-Format-0.59.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.06', { + 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.84', { + 'source_tmpl': 'Log-Handler-0.84.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Devel::StackTrace', '2.01', { + 'source_tmpl': 'Devel-StackTrace-2.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.33', { + 'source_tmpl': 'TermReadKey-2.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.1804', { + 'source_tmpl': 'Moose-2.1804.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-1.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.05', { + 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.34', { + 'source_tmpl': 'File-Find-Rule-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.410', { + 'source_tmpl': 'SQL-Statement-1.410.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-0.37.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.110', { + 'source_tmpl': 'Data-OptList-0.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9160', { + 'source_tmpl': 'CPANPLUS-0.9160.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.05', { + 'source_tmpl': 'Text-Soundex-3.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.18', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-0.18.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.29', { + 'source_tmpl': 'Want-0.29.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.05', { + 'source_tmpl': 'Cwd-Guard-0.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.18', { + 'source_tmpl': 'MailTools-2.18.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.24.0-intel-2016b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..087478fa1ff46f1285c7fc2d59b3ec0ad6a6ae3f --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.24.0-intel-2016b.eb @@ -0,0 +1,885 @@ +name = 'Perl' +version = '5.24.0' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] + +exts_list = [ + ('Config::General', '2.61', { + 'source_tmpl': 'Config-General-2.61.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], + }), + ('File::Listing', '6.04', { + 'source_tmpl': 'File-Listing-6.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('ExtUtils::InstallPaths', '0.011', { + 'source_tmpl': 'ExtUtils-InstallPaths-0.011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Helpers', '0.022', { + 'source_tmpl': 'ExtUtils-Helpers-0.022.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Test::Harness', '3.36', { + 'source_tmpl': 'Test-Harness-3.36.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('ExtUtils::Config', '0.008', { + 'source_tmpl': 'ExtUtils-Config-0.008.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Build::Tiny', '0.039', { + 'source_tmpl': 'Module-Build-Tiny-0.039.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('aliased', '0.34', { + 'source_tmpl': 'aliased-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Text::Glob', '0.09', { + 'source_tmpl': 'Text-Glob-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('Regexp::Common', '2016060801', { + 'source_tmpl': 'Regexp-Common-2016060801.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABIGAIL'], + }), + ('GO::Utils', '0.15', { + 'source_tmpl': 'go-perl-0.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Module::Pluggable', '5.2', { + 'source_tmpl': 'Module-Pluggable-5.2.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SI/SIMONW'], + }), + ('Test::Fatal', '0.014', { + 'source_tmpl': 'Test-Fatal-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warnings', '0.026', { + 'source_tmpl': 'Test-Warnings-0.026.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('DateTime::Locale', '1.05', { + 'source_tmpl': 'DateTime-Locale-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('DateTime::TimeZone', '2.00', { + 'source_tmpl': 'DateTime-TimeZone-2.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Test::Requires', '0.10', { + 'source_tmpl': 'Test-Requires-0.10.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOKUHIROM'], + }), + ('Module::Implementation', '0.09', { + 'source_tmpl': 'Module-Implementation-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Module::Build', '0.4218', { + 'source_tmpl': 'Module-Build-0.4218.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Module::Runtime', '0.014', { + 'source_tmpl': 'Module-Runtime-0.014.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/Z/ZE/ZEFRAM'], + }), + ('Try::Tiny', '0.24', { + 'source_tmpl': 'Try-Tiny-0.24.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Params::Validate', '1.24', { + 'source_tmpl': 'Params-Validate-1.24.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('List::MoreUtils', '0.416', { + 'source_tmpl': 'List-MoreUtils-0.416.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Exporter::Tiny', '0.042', { + 'source_tmpl': 'Exporter-Tiny-0.042.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TOBYINK'], + }), + ('Class::Singleton', '1.5', { + 'source_tmpl': 'Class-Singleton-1.5.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('DateTime', '1.34', { + 'source_tmpl': 'DateTime-1.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::Find::Rule::Perl', '1.15', { + 'source_tmpl': 'File-Find-Rule-Perl-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Readonly', '2.05', { + 'source_tmpl': 'Readonly-2.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SA/SANKO'], + }), + ('Git', '0.41', { + 'source_tmpl': 'Git-0.41.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MS/MSOUTH'], + }), + ('Tree::DAG_Node', '1.29', { + 'source_tmpl': 'Tree-DAG_Node-1.29.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Template', '2.26', { + 'source_tmpl': 'Template-Toolkit-2.26.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('FreezeThaw', '0.5001', { + 'source_tmpl': 'FreezeThaw-0.5001.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IL/ILYAZ/modules'], + }), + ('DBI', '1.636', { + 'source_tmpl': 'DBI-1.636.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], + }), + ('DBD::SQLite', '1.50', { + 'source_tmpl': 'DBD-SQLite-1.50.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], + }), + ('Math::Bezier', '0.01', { + 'source_tmpl': 'Math-Bezier-0.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AB/ABW'], + }), + ('Archive::Extract', '0.76', { + 'source_tmpl': 'Archive-Extract-0.76.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('DBIx::Simple', '1.35', { + 'source_tmpl': 'DBIx-Simple-1.35.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JU/JUERD'], + }), + ('Shell', '0.73', { + 'source_tmpl': 'Shell-0.73.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FE/FERREIRA'], + }), + ('File::Spec', '3.62', { + 'source_tmpl': 'PathTools-3.62.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('ExtUtils::MakeMaker', '7.18', { + 'source_tmpl': 'ExtUtils-MakeMaker-7.18.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Test::Simple', '1.302037', { + 'source_tmpl': 'Test-Simple-1.302037.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', '2.029', { + 'source_tmpl': 'IO-Socket-SSL-2.029.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', '2.04', { + 'source_tmpl': 'Test-Version-2.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('DBIx::Admin::TableInfo', '3.01', { + 'source_tmpl': 'DBIx-Admin-TableInfo-3.01.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Net::HTTP', '6.09', { + 'source_tmpl': 'Net-HTTP-6.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Test::Deep', '1.120', { + 'source_tmpl': 'Test-Deep-1.120.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Warn', '0.30', { + 'source_tmpl': 'Test-Warn-0.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('MRO::Compat', '0.12', { + 'source_tmpl': 'MRO-Compat-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BO/BOBTFISH'], + }), + ('Moo', '2.002004', { + 'source_tmpl': 'Moo-2.002004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Hash::Merge', '0.200', { + 'source_tmpl': 'Hash-Merge-0.200.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RI/RIBASUSHI'], + }), + ('HTML::Form', '6.03', { + 'source_tmpl': 'HTML-Form-6.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::Copy::Recursive', '0.38', { + 'source_tmpl': 'File-Copy-Recursive-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DM/DMUEY'], + }), + ('Number::Compare', '0.03', { + 'source_tmpl': 'Number-Compare-0.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('HTML::Entities::Interpolate', '1.09', { + 'source_tmpl': 'HTML-Entities-Interpolate-1.09.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('Test::ClassAPI', '1.06', { + 'source_tmpl': 'Test-ClassAPI-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Test::Most', '0.34', { + 'source_tmpl': 'Test-Most-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/O/OV/OVID'], + }), + ('Class::Accessor', '0.34', { + 'source_tmpl': 'Class-Accessor-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Test::Differences', '0.64', { + 'source_tmpl': 'Test-Differences-0.64.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTTP::Tiny', '0.058', { + 'source_tmpl': 'HTTP-Tiny-0.058.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('Package::DeprecationManager', '0.17', { + 'source_tmpl': 'Package-DeprecationManager-0.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Digest::SHA1', '2.13', { + 'source_tmpl': 'Digest-SHA1-2.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Date::Language', '2.30', { + 'source_tmpl': 'TimeDate-2.30.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('version', '0.9917', { + 'source_tmpl': 'version-0.9917.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JP/JPEACOCK'], + }), + ('Sub::Uplevel', '0.25', { + 'source_tmpl': 'Sub-Uplevel-0.25.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('XML::Bare', '0.53', { + 'source_tmpl': 'XML-Bare-0.53.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CODECHILD'], + 'patches': ['XML-Bare-0.53_icc.patch'], + }), + ('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', '0.15', { + 'source_tmpl': 'Sub-Name-0.15.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', '2011', { + 'source_tmpl': 'Canary-Stability-2011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('AnyEvent', '7.12', { + 'source_tmpl': 'AnyEvent-7.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/ML/MLEHMANN'], + }), + ('Object::Accessor', '0.48', { + 'source_tmpl': 'Object-Accessor-0.48.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Data::UUID', '1.221', { + 'source_tmpl': 'Data-UUID-1.221.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Test::Pod', '1.51', { + 'source_tmpl': 'Test-Pod-1.51.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('AppConfig', '1.71', { + 'source_tmpl': 'AppConfig-1.71.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB'], + }), + ('Net::SMTP::SSL', '1.03', { + 'source_tmpl': 'Net-SMTP-SSL-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::Tiny', '2.06', { + 'source_tmpl': 'XML-Tiny-2.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DC/DCANTRELL'], + }), + ('HTML::Tagset', '3.20', { + 'source_tmpl': 'HTML-Tagset-3.20.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE'], + }), + ('HTML::Tree', '5.03', { + 'source_tmpl': 'HTML-Tree-5.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJM'], + }), + ('Devel::GlobalDestruction', '0.13', { + 'source_tmpl': 'Devel-GlobalDestruction-0.13.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('WWW::RobotRules', '6.02', { + 'source_tmpl': 'WWW-RobotRules-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Expect', '1.33', { + 'source_tmpl': 'Expect-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JA/JACOBY/'], + }), + ('Term::UI', '0.46', { + 'source_tmpl': 'Term-UI-0.46.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('Net::SNMP', 'v6.0.1', { + 'source_tmpl': 'Net-SNMP-v6.0.1.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DT/DTOWN'], + }), + ('XML::SAX::Writer', '0.56', { + 'source_tmpl': 'XML-SAX-Writer-0.56.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN'], + }), + ('Statistics::Descriptive', '3.0612', { + 'source_tmpl': 'Statistics-Descriptive-3.0612.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Class::Load', '0.23', { + 'source_tmpl': 'Class-Load-0.23.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('LWP::Simple', '6.15', { + 'source_tmpl': 'libwww-perl-6.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Time::Piece::MySQL', '0.06', { + 'source_tmpl': 'Time-Piece-MySQL-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Package::Stash::XS', '0.28', { + 'source_tmpl': 'Package-Stash-XS-0.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('GD::Graph', '1.52', { + 'source_tmpl': 'GDGraph-1.52.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RUZ'], + }), + ('Set::Array', '0.30', { + 'source_tmpl': 'Set-Array-0.30.tgz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RS/RSAVAGE'], + }), + ('boolean', '0.45', { + 'source_tmpl': 'boolean-0.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IN/INGY'], + }), + ('Number::Format', '1.75', { + 'source_tmpl': 'Number-Format-1.75.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/W/WR/WRW'], + }), + ('Data::Stag', '0.14', { + 'source_tmpl': 'Data-Stag-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CM/CMUNGALL'], + }), + ('Test::NoWarnings', '1.04', { + 'source_tmpl': 'Test-NoWarnings-1.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Crypt::DES', '2.07', { + 'source_tmpl': 'Crypt-DES-2.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DP/DPARIS'], + }), + ('Exporter', '5.72', { + 'source_tmpl': 'Exporter-5.72.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Class::Inspector', '1.28', { + 'source_tmpl': 'Class-Inspector-1.28.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Parse::RecDescent', '1.967013', { + 'source_tmpl': 'Parse-RecDescent-1.967013.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JT/JTBRAUN'], + }), + ('Carp', '1.38', { + 'source_tmpl': 'Carp-1.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('XML::XPath', '1.37', { + 'source_tmpl': 'XML-XPath-1.37.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MANWAR'], + }), + ('Capture::Tiny', '0.42', { + 'source_tmpl': 'Capture-Tiny-0.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('JSON', '2.90', { + 'source_tmpl': 'JSON-2.90.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Sub::Exporter', '0.987', { + 'source_tmpl': 'Sub-Exporter-0.987.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Class::Load::XS', '0.09', { + 'source_tmpl': 'Class-Load-XS-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AN/ANDYA'], + }), + ('Sub::Exporter::Progressive', '0.001011', { + 'source_tmpl': 'Sub-Exporter-Progressive-0.001011.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('Data::Dumper::Concise', '2.022', { + 'source_tmpl': 'Data-Dumper-Concise-2.022.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/F/FR/FREW'], + }), + ('File::Slurp::Tiny', '0.004', { + 'source_tmpl': 'File-Slurp-Tiny-0.004.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT'], + }), + ('Algorithm::Diff', '1.1903', { + 'source_tmpl': 'Algorithm-Diff-1.1903.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TY/TYEMQ'], + }), + ('AnyData', '0.12', { + 'source_tmpl': 'AnyData-0.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Iconv', '1.7', { + 'source_tmpl': 'Text-Iconv-1.7.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MP/MPIOTR'], + }), + ('Class::Data::Inheritable', '0.08', { + 'source_tmpl': 'Class-Data-Inheritable-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Text::Balanced', '2.03', { + 'source_tmpl': 'Text-Balanced-2.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHAY'], + }), + ('strictures', '2.000003', { + 'source_tmpl': 'strictures-2.000003.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('Switch', '2.17', { + 'source_tmpl': 'Switch-2.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHORNY'], + }), + ('File::Which', '1.21', { + 'source_tmpl': 'File-Which-1.21.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + }), + ('Email::Date::Format', '1.005', { + 'source_tmpl': 'Email-Date-Format-1.005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Error', '0.17024', { + 'source_tmpl': 'Error-0.17024.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Mock::Quick', '1.111', { + 'source_tmpl': 'Mock-Quick-1.111.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('Text::CSV', '1.33', { + 'source_tmpl': 'Text-CSV-1.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA'], + }), + ('Test::Output', '1.03', { + 'source_tmpl': 'Test-Output-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BD/BDFOY'], + }), + ('Class::DBI', '3.0.17', { + 'source_tmpl': 'Class-DBI-v3.0.17.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('List::AllUtils', '0.11', { + 'source_tmpl': 'List-AllUtils-0.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('UNIVERSAL::moniker', '0.08', { + 'source_tmpl': 'UNIVERSAL-moniker-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KASEI'], + }), + ('Exception::Class', '1.40', { + 'source_tmpl': 'Exception-Class-1.40.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('File::CheckTree', '4.42', { + 'source_tmpl': 'File-CheckTree-4.42.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Math::VecStat', '0.08', { + 'source_tmpl': 'Math-VecStat-0.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AS/ASPINELLI'], + }), + ('Pod::LaTeX', '0.61', { + 'source_tmpl': 'Pod-LaTeX-0.61.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TJ/TJENNESS'], + }), + ('Eval::Closure', '0.14', { + 'source_tmpl': 'Eval-Closure-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('HTTP::Request', '6.11', { + 'source_tmpl': 'HTTP-Message-6.11.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIROD'], + }), + ('IO::String', '1.08', { + 'source_tmpl': 'IO-String-1.08.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('XML::Simple', '2.22', { + 'source_tmpl': 'XML-Simple-2.22.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GR/GRANTM'], + }), + ('Sub::Install', '0.928', { + 'source_tmpl': 'Sub-Install-0.928.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('HTTP::Cookies', '6.01', { + 'source_tmpl': 'HTTP-Cookies-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Pod::Plainer', '1.04', { + 'source_tmpl': 'Pod-Plainer-1.04.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RM/RMBARKER'], + }), + ('Test::Exception::LessClever', '0.007', { + 'source_tmpl': 'Test-Exception-LessClever-0.007.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], + }), + ('LWP::MediaTypes', '6.02', { + 'source_tmpl': 'LWP-MediaTypes-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Scalar::Util', '1.45', { + 'source_tmpl': 'Scalar-List-Utils-1.45.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PEVANS'], + }), + ('Data::Section::Simple', '0.07', { + 'source_tmpl': 'Data-Section-Simple-0.07.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('Class::Trigger', '0.14', { + 'source_tmpl': 'Class-Trigger-0.14.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MI/MIYAGAWA'], + }), + ('HTTP::Daemon', '6.01', { + 'source_tmpl': 'HTTP-Daemon-6.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('File::HomeDir', '1.00', { + 'source_tmpl': 'File-HomeDir-1.00.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('HTTP::Date', '6.02', { + 'source_tmpl': 'HTTP-Date-6.02.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GAAS'], + }), + ('Authen::SASL', '2.16', { + 'source_tmpl': 'Authen-SASL-2.16.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], + }), + ('Clone', '0.38', { + 'source_tmpl': 'Clone-0.38.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GA/GARU'], + }), + ('Data::Types', '0.09', { + 'source_tmpl': 'Data-Types-0.09.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DW/DWHEELER'], + }), + ('Import::Into', '1.002005', { + 'source_tmpl': 'Import-Into-1.002005.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG'], + }), + ('DateTime::Tiny', '1.06', { + 'source_tmpl': 'DateTime-Tiny-1.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + }), + ('DBD::AnyData', '0.110', { + 'source_tmpl': 'DBD-AnyData-0.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('Text::Format', '0.59', { + 'source_tmpl': 'Text-Format-0.59.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF'], + }), + ('Devel::CheckCompiler', '0.06', { + 'source_tmpl': 'Devel-CheckCompiler-0.06.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SY/SYOHEX'], + }), + ('Log::Handler', '0.84', { + 'source_tmpl': 'Log-Handler-0.84.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BL/BLOONIX'], + }), + ('DBIx::ContextualFetch', '1.03', { + 'source_tmpl': 'DBIx-ContextualFetch-1.03.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TM/TMTM'], + }), + ('Devel::StackTrace', '2.01', { + 'source_tmpl': 'Devel-StackTrace-2.01.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], + }), + ('Term::ReadKey', '2.33', { + 'source_tmpl': 'TermReadKey-2.33.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JS/JSTOWE'], + }), + ('Set::IntSpan', '1.19', { + 'source_tmpl': 'Set-IntSpan-1.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SW/SWMCD'], + }), + ('Moose', '2.1804', { + 'source_tmpl': 'Moose-2.1804.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], + }), + ('Algorithm::Dependency', '1.110', { + 'source_tmpl': 'Algorithm-Dependency-1.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AD/ADAMK'], + }), + ('Font::TTF', '1.05', { + 'source_tmpl': 'Font-TTF-1.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MH/MHOSKEN'], + }), + ('IPC::Run3', '0.048', { + 'source_tmpl': 'IPC-Run3-0.048.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('File::Find::Rule', '0.34', { + 'source_tmpl': 'File-Find-Rule-0.34.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RC/RCLAMP'], + }), + ('SQL::Statement', '1.410', { + 'source_tmpl': 'SQL-Statement-1.410.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RE/REHSACK'], + }), + ('File::Slurp', '9999.19', { + 'source_tmpl': 'File-Slurp-9999.19.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/U/UR/URI'], + }), + ('Package::Stash', '0.37', { + 'source_tmpl': 'Package-Stash-0.37.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DO/DOY'], + }), + ('Data::OptList', '0.110', { + 'source_tmpl': 'Data-OptList-0.110.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('CPANPLUS', '0.9160', { + 'source_tmpl': 'CPANPLUS-0.9160.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BI/BINGOS'], + }), + ('IO::Tty', '1.12', { + 'source_tmpl': 'IO-Tty-1.12.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + }), + ('Text::Soundex', '3.05', { + 'source_tmpl': 'Text-Soundex-3.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + }), + ('Lingua::EN::PluralToSingular', '0.18', { + 'source_tmpl': 'Lingua-EN-PluralToSingular-0.18.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BK/BKB'], + }), + ('Want', '0.29', { + 'source_tmpl': 'Want-0.29.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN'], + }), + ('Cwd::Guard', '0.05', { + 'source_tmpl': 'Cwd-Guard-0.05.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KA/KAZEBURO'], + }), + ('Bundle::BioPerl', '2.1.9', { + 'source_tmpl': 'Bundle-BioPerl-2.1.9.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS'], + }), + ('Mail::Util', '2.18', { + 'source_tmpl': 'MailTools-2.18.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MARKOV'], + }), +] + +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-3.2.0-intel-2016a-Python-2.7.11-freetype-2.6.3.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11-freetype-2.6.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..11a471d767ea7f872e359cad7492c401fdbecaf3 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11-freetype-2.6.3.eb @@ -0,0 +1,29 @@ +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': 'intel', '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'), + ('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-3.2.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb index e08e25c6bb796ad36128af14b5a76989d5443ead..085a2ad289344aaf13dc532fa343b8a298c01888 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-3.2.0-intel-2016a-Python-2.7.11.eb @@ -16,6 +16,7 @@ sources = [SOURCE_TAR_GZ] dependencies = [ ('Python', '2.7.11'), ('libjpeg-turbo', '1.4.2'), + ('libpng', '1.6.21'), ('zlib', '1.2.8'), ('LibTIFF', '4.0.6'), ('freetype', '2.6.2'), 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/Platanus/Platanus-1.2.4-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..9f312bdd69bf415550fa81552a37fb2561557e74 --- /dev/null +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.4-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'Platanus' +version = '1.2.4' + +homepage = 'http://platanus.bio.titech.ac.jp/' +description = """PLATform for Assembling NUcleotide Sequences""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'openmp': True} + +# the download cannot be automated because it points to a PHP form +# http://platanus.bio.titech.ac.jp/?ddownload=150 +sources = ['%(name)s_v%(version)s.tar.gz'] + +buildopts = 'CXX="$CXX"' + +files_to_copy = [(["platanus"],'bin'), "README", "LICENSE"] + +sanity_check_paths = { + 'files': ["bin/platanus"], + 'dirs': [""], +} + +moduleclass = 'bio' 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/ProbABEL/ProbABEL-0.5.0.eb b/easybuild/easyconfigs/p/ProbABEL/ProbABEL-0.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..379bdbc80d26a5bd396b36c4d57679323ad71484 --- /dev/null +++ b/easybuild/easyconfigs/p/ProbABEL/ProbABEL-0.5.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'ProbABEL' +version = '0.5.0' + +homepage = "http://www.genabel.org/packages/ProbABEL" +description = """Tool for genome-wide association +analysis of imputed genetic data.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.genabel.org/sites/default/files/software/'] +sources = ['probabel-%(version)s.tar.gz'] + +dependencies = [ + ('Eigen', '3.2.6') +] + +configopts = '--disable-latex-doc' + +postinstallcmds = ["mv %(installdir)s/etc/probabel_config.cfg.example %(installdir)s/etc/probabel_config.cfg"] + +sanity_check_paths = { + 'files': ['bin/probabel', 'bin/pacoxph', 'bin/palinear', 'bin/palogist','etc/probabel_config.cfg'], + 'dirs': ['share'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyCogent/PyCogent-1.5.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyCogent/PyCogent-1.5.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..a1f5a8ace427b76b56eb133f137ab60cdb76efc5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCogent/PyCogent-1.5.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyCogent' +version = '1.5.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pycogent/pycogent/' +description = """PyCogent includes connectors to remote databases, built-in generalized probabilistic techniques +for working with biological sequences, and controllers for 3rd party applications.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/pycogent/pycogent/archive/'] +sources = ['%(version)s-release.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), +] + +options = {'modulename': 'cogent'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyCogent/PyCogent-1.9-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyCogent/PyCogent-1.9-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..bcf748bc3882c72e41f4d8cf7c9baf8b09eab14d --- /dev/null +++ b/easybuild/easyconfigs/p/PyCogent/PyCogent-1.9-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyCogent' +version = '1.9' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pycogent/pycogent/' +description = """PyCogent includes connectors to remote databases, built-in generalized probabilistic techniques +for working with biological sequences, and controllers for 3rd party applications.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/pycogent/pycogent/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), +] + +options = {'modulename': 'cogent'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..b961fbd0a432bb2a602a59e54bcb5dc2d4c81c0e --- /dev/null +++ b/easybuild/easyconfigs/p/PyGTS/PyGTS-0.3.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyGTS' +version = '0.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://sourceforge.net/projects/pygts/' +description = """ PyGTS is a python package used to construct, manipulate, + and perform computations on triangulated surfaces. + It is a hand-crafted and pythonic binding for the GNU Triangulated Surface (GTS) Library. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('GLib', '2.49.5'), + ('GTS' ,'0.7.6'), +] + +options = {'modulename': 'gts'} + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/gts/_gts.%s' % SHLIB_EXT], + 'dirs':[], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..874abcf752d41e9b8975dde7532d0f9d684fbda6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyNAST/PyNAST-1.2.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'PyNAST' +version = '1.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/qiime/pynast/' +description = """Python Nearest Alignment Space Termination tool""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/biocore/pynast/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), + ('PyCogent', '1.5.3', versionsuffix), + ('UCLUST', '1.2.22q', '-i86linux64', True), +] + +options = {'modulename': 'pynast'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'bio' 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-15.3.0-foss-2016a-Python-2.7.11-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.3.0-foss-2016a-Python-2.7.11-zmq4.eb new file mode 100644 index 0000000000000000000000000000000000000000..a2bc171fd9ef84e679f327913878902c2290b81d --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.3.0-foss-2016a-Python-2.7.11-zmq4.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '15.3.0' +zmqversion = '4.1.4' +versionsuffix = '-Python-%%(pyver)s-zmq%s' % zmqversion.split('.')[0] + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('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/PyZMQ/PyZMQ-15.3.0-foss-2016a-Python-3.5.1-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.3.0-foss-2016a-Python-3.5.1-zmq4.eb new file mode 100644 index 0000000000000000000000000000000000000000..31aca465ba3dc446766f0b0f1961b4e149891e4f --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.3.0-foss-2016a-Python-3.5.1-zmq4.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '15.3.0' +zmqversion = '4.1.4' +versionsuffix = '-Python-%%(pyver)s-zmq%s' % zmqversion.split('.')[0] + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), + ('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/PyZMQ/PyZMQ-15.4.0-intel-2016b-Python-2.7.12-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.4.0-intel-2016b-Python-2.7.12-zmq4.eb new file mode 100644 index 0000000000000000000000000000000000000000..df4a2aa3e95fde71395fce7df5fe1b66e8c151b3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-15.4.0-intel-2016b-Python-2.7.12-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', '2.7.12'), + ('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/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/PyZMQ/PyZMQ-16.0.2-foss-2016b-Python-2.7.12-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2016b-Python-2.7.12-zmq4.eb new file mode 100644 index 0000000000000000000000000000000000000000..2ae02cf97537598eb3e5060976ed26a5a5a1baf5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2016b-Python-2.7.12-zmq4.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '16.0.2' +zmqversion = '4.2.0' +versionsuffix = '-Python-%%(pyver)s-zmq%s' % zmqversion.split('.')[0] + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['9a8768b00a566a400d70318f8c359cfe'] + +dependencies = [ + ('Python', '2.7.12'), + ('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/PyZMQ/PyZMQ-16.0.2-foss-2016b-Python-3.5.2-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2016b-Python-3.5.2-zmq4.eb new file mode 100644 index 0000000000000000000000000000000000000000..a6d0276b239704a651c22711234f31ac483fb104 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-foss-2016b-Python-3.5.2-zmq4.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '16.0.2' +zmqversion = '4.2.0' +versionsuffix = '-Python-%%(pyver)s-zmq%s' % zmqversion.split('.')[0] + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +checksums = ['9a8768b00a566a400d70318f8c359cfe'] + +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/PyZMQ/PyZMQ-16.0.2-intel-2016b-Python-2.7.12-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2016b-Python-2.7.12-zmq4.eb new file mode 100644 index 0000000000000000000000000000000000000000..83db644170c41b2bd00f723d50bfcf43887202f4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2016b-Python-2.7.12-zmq4.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '16.0.2' +zmqversion = '4.2.0' +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] + +checksums = ['9a8768b00a566a400d70318f8c359cfe'] + +dependencies = [ + ('Python', '2.7.12'), + ('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/PyZMQ/PyZMQ-16.0.2-intel-2016b-Python-3.5.2-zmq4.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2016b-Python-3.5.2-zmq4.eb new file mode 100644 index 0000000000000000000000000000000000000000..0d5d945f584d3a3c5b5b4bad8ba51266e12dbfd8 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-16.0.2-intel-2016b-Python-3.5.2-zmq4.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '16.0.2' +zmqversion = '4.2.0' +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] + +checksums = ['9a8768b00a566a400d70318f8c359cfe'] + +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-2.7.11.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..29f7e2e571d818f6a6c3796a63ae02c55ab92c43 --- /dev/null +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.1.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,26 @@ +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', '2.7.11'), +] + +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/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-0.9.0-goolf-1.7.20-Python-2.7.11.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb index 61ca6bdf2868fed5919597be3f8f7d77efb5c020..f0889a65b2bc239ad7bc4a87956f2eac9746a6d6 100644 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.9.0-goolf-1.7.20-Python-2.7.11.eb @@ -30,10 +30,10 @@ exts_filter = ("python -c 'import %(ext_name)s'", '') exts_list = [ ('Cython', '0.23.4', { - 'source_urls': ['http://cython.org/release/'], + 'source_urls': ['http://cython.org/release/'], }), ('pysam', version, { - 'source_tmpl': 'v%(version)s.tar.gz', + 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/pysam-developers/pysam/archive/'], }), ] 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..3deabf6808af1926cd63354940e49ba4ae0a1613 --- /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 new file mode 100644 index 0000000000000000000000000000000000000000..d69b594b089801a7bd59378bb50da618d38a2fda --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2015.11.eb @@ -0,0 +1,139 @@ +# @author: Luca Marsella (CSCS) +# @author: Guilherme Peretti-Pezzi (CSCS) + +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': 'CrayGNU', 'version': '2015.11'} +toolchainopts = {'pic': True} + +numpyversion = '1.10.4' +scipyversion = '0.16.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# patch needed for building h5py +patches = ['h5py-CrayGNU-Python-2.7.patch'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.9.2'), + ('Tk', '8.6.4', '-no-X11'), # this requires a full X11 stack + ('GMP', '6.1.0'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated Mar 1st 2016 +exts_list = [ + ('setuptools', '20.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '8.0.3', { + '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-CrayGNU-2016.03.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..ab13993dcf3d948857fd3edf0ea84defe533da8a --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-CrayGNU-2016.03.eb @@ -0,0 +1,139 @@ +# @author: Luca Marsella (CSCS) +# @author: Guilherme Peretti-Pezzi (CSCS) + +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': 'CrayGNU', 'version': '2016.03'} +toolchainopts = {'pic': True} + +numpyversion = '1.10.4' +scipyversion = '0.16.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# patch needed for building h5py +patches = ['h5py-CrayGNU-Python-2.7.patch'] + +# 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 + ('GMP', '6.1.0'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated Mar 1st 2016 +exts_list = [ + ('setuptools', '20.2.2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '8.0.3', { + '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-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 51bd3f9ff0716514a0cb998468b655febe4273e0..c5fe86070e7d3f66c813b221f9a2f4ce09b133de 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 @@ -67,7 +67,7 @@ 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-2.7.11-foss-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-foss-2016a.eb index 80212964f1b2a37029523317c832db73e5e048f8..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 @@ -67,7 +67,7 @@ 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-2.7.11-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-gimkl-2.11.5.eb index a99feb707857dd99fa8791a129d889148caffd94..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 @@ -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-2.7.11-goolf-1.7.20.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-goolf-1.7.20.eb index bfec054fb2abb4335000f7a7dbcabea4fa51ebaa..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 @@ -68,7 +68,7 @@ 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-2.7.11-intel-2015b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2015b.eb index bce00fd447f743c572c23d9aea8be2016dae4308..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 @@ -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-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 b8a12d273e580d7c81b90133443002d66fe60aff..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 @@ -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-2.7.11-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb index 0965b7d1e961653868fce97a1d8870269f869e4b..8b707bfd80fa9086066d264a6fea0cc9ec580998 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a-libX11-1.6.3.eb @@ -72,7 +72,7 @@ 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-2.7.11-intel-2016a.eb b/easybuild/easyconfigs/p/Python/Python-2.7.11-intel-2016a.eb index 14683881485dc775e9381eb4570023302941f884..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 @@ -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-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 new file mode 100644 index 0000000000000000000000000000000000000000..abfcbbf934634e4ace5d77d23dfee715d6e5bd50 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCC-5.4.0-2.26-bare.eb @@ -0,0 +1,31 @@ +name = 'Python' +version = '2.7.12' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.13.0'), + ('Tk', '8.6.5'), # this requires a full X11 stack + ('GMP', '6.1.1'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..62cd674cc5b11902dc649594835e9667c198ba26 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-GCCcore-4.9.3-bare.eb @@ -0,0 +1,37 @@ +name = 'Python' +version = '2.7.12' +versionsuffix = '-bare' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +builddependencies = [ + ('binutils', '2.25'), +] + +dependencies = [ + ('zlib', '1.2.8'), + ('bzip2', '1.0.6'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.14.1'), + # ('OpenSSL', '1.0.1k'), # OS dependency should be preferred if the os version is more recent then this version, it's + # nice to have an up to date openssl for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# We hide this by default since users should not use it in production, high-performance Python should be delivered at +# compiler level with a default extension set +#hidden = True + +# bare installation: only known module deps for GCCcore tools included +exts_list =[] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ba6ada1467237aadd0d98828506e50c9df09c353 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-foss-2016b.eb @@ -0,0 +1,133 @@ +name = 'Python' +version = '2.7.12' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.13.0'), + ('Tk', '8.6.5'), # this requires a full X11 stack + ('GMP', '6.1.1'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '23.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '8.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', '1.11.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'patches': ['numpy-1.8.0-mkl.patch'], + }), + ('scipy', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('pbr', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.24', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.5.3', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.10', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('cryptography', '1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + }), + ('paramiko', '2.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2016.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.18.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.6', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.5', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), + ('virtualenv', '15.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb b/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..f39ab1c05674d776d582c462884cdb54b6e8a21c --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.12-intel-2016b.eb @@ -0,0 +1,133 @@ +name = 'Python' +version = '2.7.12' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('SQLite', '3.13.0'), + ('Tk', '8.6.5'), # this requires a full X11 stack + ('GMP', '6.1.1'), + ('libffi', '3.2.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '23.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '8.1.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.7', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', '1.11.1', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy'], + 'patches': ['numpy-1.8.0-mkl.patch'], + }), + ('scipy', '0.17.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy'], + }), + ('blist', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], + }), + ('mpi4py', '1.3.1', { + 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('pbr', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.12.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.24', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cython/'], + }), + ('six', '1.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.5.3', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '4.0.10', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.1.0', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['http://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('cryptography', '1.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cryptography/'], + }), + ('paramiko', '2.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), + ('netifaces', '0.10.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netifaces'], + }), + ('netaddr', '0.7.18', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('funcsigs', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/funcsigs'], + }), + ('mock', '2.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2016.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.18.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('enum34', '1.1.6', { + 'modulename': 'enum', + 'source_urls': ['https://pypi.python.org/packages/source/e/enum34'], + }), + ('bitstring', '3.1.5', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/b/bitstring'], + }), + ('virtualenv', '15.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/v/virtualenv'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/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 new file mode 100644 index 0000000000000000000000000000000000000000..f40c4aab551a331325e3f14f233d4673bd4a6ae4 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-foss-2016b.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': '2016b'} +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-intel-2016b.eb b/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..805061ab30b31af53ad2e6564cfa0550060d6e4f --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.5.2-intel-2016b.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': 'intel', 'version': '2016b'} +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/h5py-CrayGNU-Python-2.7.patch b/easybuild/easyconfigs/p/Python/h5py-CrayGNU-Python-2.7.patch new file mode 100644 index 0000000000000000000000000000000000000000..f63000e2632e4fd7602ff71e161423ec921ea1b2 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/h5py-CrayGNU-Python-2.7.patch @@ -0,0 +1,17 @@ +The Cray wrappers are not detected as 'gcc' here and +therefore we need the fix below in order to get the correct compilation flags: "-Wl,-R" + +@author: Christopher Bignamini (CSCS) +@author: Guilherme Peretti-Pezzi (CSCS) + +--- EasyBuildTesting/Python-2.7.9/Lib/distutils.orig/unixccompiler.py 2014-12-10 16:59:34.000000000 +0100 ++++ EasyBuildTesting/Python-2.7.9/Lib/distutils/unixccompiler.py 2015-06-12 16:02:06.000000000 +0200 +@@ -237,7 +237,7 @@ + elif self._is_gcc(compiler): + return "-Wl,-R" + dir + else: +- return "-R" + dir ++ return "-Wl,-R " + dir + + def library_option(self, lib): + return "-l" + lib diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..9fd43e27cf1b1c064d6a1ea0b384e41f322409d6 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.18.0' +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': '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 = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..a23b70abdac674c68b9c07ae743eac5f59e25876 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.0-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.18.0' +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': '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 = 'lib' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..127a463ca2e7c8e1f17c9f5f97d360fb2d055596 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.18.1' +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-0.18.1-intel-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..11324cd1bf1e5fcdeb47fe3dcfbf3f61b84bcbff --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.18.1-intel-2016b-Python-3.5.2.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '0.18.1' +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/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/parallel/parallel-20160622-foss-2016a.eb b/easybuild/easyconfigs/p/parallel/parallel-20160622-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a142b93a8f0f46f5ec1ea664bda4ed71c29e1dcc --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20160622-foss-2016a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20160622' + +homepage = 'http://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('Perl', '5.22.1', '-bare'), +] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/patchelf/patchelf-0.9-foss-2016a.eb b/easybuild/easyconfigs/p/patchelf/patchelf-0.9-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e8f6bc4d9e1cab9186ab0186d3294f8898d3c17d --- /dev/null +++ b/easybuild/easyconfigs/p/patchelf/patchelf-0.9-foss-2016a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'patchelf' +version = '0.9' + +homepage = 'http://nixos.org/patchelf.html' +description = """PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/NixOS/patchelf/archive/'] +sources = ['%(version)s.tar.gz'] + +preconfigopts = "sh bootstrap.sh && " + +sanity_check_paths = { + 'files': ['bin/patchelf'], + 'dirs': ['share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/path.py/path.py-8.2.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/path.py/path.py-8.2.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..82ba3e59253cb3181beb26415c02c57ce1333cca --- /dev/null +++ b/easybuild/easyconfigs/p/path.py/path.py-8.2.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'path.py' +version = '8.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jaraco/path.py' +description = """path.py is a Python library implementing path objects as first-class entities, + allowing common operations on files to be invoked on those path objects directly.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://pypi.python.org/packages/fc/fc/dcae2146aed6becbea77158eddb4e437718170efeade0f7fdf0aebe46b94/'] +sources = ['path.py-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '2.7.11'), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/path.py'], + 'dirs': [], +} + +options = {'modulename': 'path'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/path.py/path.py-8.2.1-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/path.py/path.py-8.2.1-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..af0413a4f2feeba6dbfa1048ba230ea6c664a86d --- /dev/null +++ b/easybuild/easyconfigs/p/path.py/path.py-8.2.1-foss-2016a-Python-3.5.1.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': 'foss', 'version': '2016a'} + +source_urls = ['https://pypi.python.org/packages/fc/fc/dcae2146aed6becbea77158eddb4e437718170efeade0f7fdf0aebe46b94/'] +sources = ['path.py-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '3.5.1'), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/path.py'], + 'dirs': [], +} + +options = {'modulename': 'path'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/path.py/path.py-8.2.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/path.py/path.py-8.2.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..e118b5f02038befc696a586589eb86e13ab39c7e --- /dev/null +++ b/easybuild/easyconfigs/p/path.py/path.py-8.2.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'path.py' +version = '8.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jaraco/path.py' +description = """path.py is a Python library implementing path objects as first-class entities, + allowing common operations on files to be invoked on those path objects directly.""" + +toolchain = {'name': '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', '2.7.12'), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/path.py'], + 'dirs': [], +} + +options = {'modulename': 'path'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/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/pbs_python/pbs_python-4.6.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..7299050947c34edb594ff978aeeac31e2550ad4b --- /dev/null +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'pbs_python' +version = '4.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://oss.trac.surfsara.nl/pbs_python' +description = """The pbs_python package is a wrapper class for the Torque C library. With this package you now can + write utilities/extensions in Python instead of C. We developed this package because we want to replace xpbsmon by + an ascii version named pbsmon. PBSQuery is also included in this package. This is a python module build on top of + the pbs python module to simplify querying the batch server, eg: how many jobs, how many nodes, ...""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['http://ftp.sara.nl/pub/outgoing/'] +sources = [SOURCE_TAR_GZ] + +patches = [ + 'pbs_python-%(version)s_CC.patch', + 'pbs_python-%(version)s_remove-printf.patch', +] + +dependencies = [('Python', '2.7.12')] + +osdependencies = ['torque-devel'] + +# this is needed for setup.py script +configopts = "--datarootdir=%(installdir)s --docdir=%(installdir)s" +prebuildopts = 'export CFLAGS="$CFLAGS -I/usr/include/torque/" && ' +preinstallopts = prebuildopts + +pythonpath = 'lib/python%(pyshortver)s/site-packages' +modextrapaths = {'PYTHONPATH': pythonpath} + +sanity_check_paths = { + 'files': [], + 'dirs': ["%s/pbs" % pythonpath] +} + +moduleclass = 'tools' 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/pftoolsV3/pftoolsV3-20160324-foss-2016a.eb b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-20160324-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8d5302dd6c83b5b456b349eac2d04efb40e1e2e2 --- /dev/null +++ b/easybuild/easyconfigs/p/pftoolsV3/pftoolsV3-20160324-foss-2016a.eb @@ -0,0 +1,22 @@ +easyblock='ConfigureMake' + +name = 'pftoolsV3' +version = '20160324' + +homepage = 'http://web.expasy.org/pftools/' +description = """The pftools package contains all the software necessary to build protein and DNA generalized profiles and use + them to scan and align sequences, and search databases. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = ['%(name)s.tar.gz'] +source_urls = ['ftp://ftp.lausanne.isb-sib.ch/pub/software/unix/pftools/%(name)s/'] +checksums = ['ef1d3c7583d764cff06861fca75be455'] + +sanity_check_paths = { + 'files': ['bin/ptof', 'bin/htop', 'bin/6ft', 'bin/2ft', 'bin/pfdump', 'bin/pfscan', 'bin/pfsearch'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb b/easybuild/easyconfigs/p/picard/picard-2.1.1-Java-1.8.0_112.eb 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/pip/pip-8.1.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pip/pip-8.1.2-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..32c9404b0075752bfb801c07c0e2a5fdfd64abd3 --- /dev/null +++ b/easybuild/easyconfigs/p/pip/pip-8.1.2-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,19 @@ +easyblock = 'PythonPackage' + +name = 'pip' +version = '8.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pip.pypa.io' +description = """The PyPA recommended tool for installing Python packages.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pip/pip-8.1.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pip/pip-8.1.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..ffdebb2121957ad3da730b4426abb7346ccd9f06 --- /dev/null +++ b/easybuild/easyconfigs/p/pip/pip-8.1.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,19 @@ +easyblock = 'PythonPackage' + +name = 'pip' +version = '8.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pip.pypa.io' +description = """The PyPA recommended tool for installing Python packages.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.34.0-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-0.27.1-foss-2015b.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-foss-2015b.eb index 73c06e7f1b0ec40c631a6591bb99bf9ea97db0b9..d7052c1c1bc9a58551db16dd58c09e3606fbb2ed 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-foss-2015b.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-foss-2015b.eb @@ -15,7 +15,7 @@ tar_config_opts = True toolchain = {'name': 'foss', 'version': '2015b'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] configopts = " --with-internal-glib" diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-goolf-1.4.10.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-goolf-1.4.10.eb index 0b6b8bc92789a6c447bdc5a5a87b75bf6c0c4b5c..79931f690ca6644da80ebc6a359580f846e3d8c8 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-goolf-1.4.10.eb @@ -12,7 +12,7 @@ for instance, rather than hard-coding values on where to find glib (or other lib toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] configopts = " --with-internal-glib" diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-ictce-5.3.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-ictce-5.3.0.eb index 206bdee24407f8e0c7b95be60f7f184b690e78cb..61f51a72889c4f4a3882c31990a0bc4ecadae717 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-ictce-5.3.0.eb @@ -13,7 +13,7 @@ description = """pkg-config is a helper tool used when compiling applications an toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] configopts = " --with-internal-glib" diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-ictce-5.5.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-ictce-5.5.0.eb index fee25e4441373b4bd33a2cbc1da44a0976f4b45e..2b116605832cc7f08d8feeedb848249ebd962ca4 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-ictce-5.5.0.eb @@ -15,7 +15,7 @@ tar_config_opts = True toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] configopts = " --with-internal-glib" diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015a.eb index ddfabeac319be3fb4087d9d16b23eb25aa74df47..d3711e40bd238f9a2e7c8ec45fe097beb83c52e6 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015a.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015a.eb @@ -15,7 +15,7 @@ tar_config_opts = True toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] configopts = " --with-internal-glib" diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015b.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015b.eb index f271d1a6738954507f5984ca406b763ef39e8e28..853d2fd1aa5cf6437dd06b3c1f9ca80f93a74ab4 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015b.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015b.eb @@ -15,7 +15,7 @@ tar_config_opts = True toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] configopts = " --with-internal-glib" diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-GCC-4.8.2.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-GCC-4.8.2.eb index b4996e7af35594a442f250ed7216ad9956a97e00..8373b491c48e358e1c3b58f789da8d8a90657ac6 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-GCC-4.8.2.eb @@ -15,7 +15,7 @@ tar_config_opts = True toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] configopts = " --with-internal-glib" diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-GCC-4.9.2.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-GCC-4.9.2.eb index 68447b95f4358432cea3381f857dcf81c1f0aba5..db1a5eb0a1b90e5ed9b2f93dd99a85ebc18a46d9 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-GCC-4.9.2.eb @@ -15,7 +15,7 @@ tar_config_opts = True toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] configopts = " --with-internal-glib" diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-GNU-4.9.3-2.25.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-GNU-4.9.3-2.25.eb index a3cc058e1f1bafbc0c9deec7b04b1755de70e267..acc7f7d1bf13be3f5ab81c47383be7eb8710ccd1 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-GNU-4.9.3-2.25.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-GNU-4.9.3-2.25.eb @@ -15,7 +15,7 @@ tar_config_opts = True toolchain = {'name': 'GNU', 'version': '4.9.3-2.25'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] configopts = " --with-internal-glib" diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-ictce-5.5.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-ictce-5.5.0.eb index 7c85168da3f6be663efeaad3e125e139b0af5f44..bbe881a34b5fcb43827054b8dbaefc036020c76b 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-ictce-5.5.0.eb @@ -15,7 +15,7 @@ tar_config_opts = True toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] configopts = " --with-internal-glib" diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-intel-2015a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-intel-2015a.eb index f5981f1368671b6e0497edaafb918579f99a93da..2bcff32be771e8405302e1a22496b5a7e9d65bda 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-intel-2015a.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.28-intel-2015a.eb @@ -15,7 +15,7 @@ tar_config_opts = True toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] configopts = " --with-internal-glib" diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb index 2796515752da9aa5f57dc829609f683fe184a9db..d4b7b3f1ddc002493af0ae5eba46cadca62cc490 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-foss-2016a.eb @@ -12,7 +12,7 @@ description = """pkg-config is a helper tool used when compiling applications an toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] # don't use PAX, it might break. tar_config_opts = True diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-gimkl-2.11.5.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-gimkl-2.11.5.eb index c593a8d395d0547c2db1f9323d67f4c06894e721..e9844ad8e6238d29d88cba73e3d4941ffc182525 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-gimkl-2.11.5.eb @@ -12,7 +12,7 @@ description = """pkg-config is a helper tool used when compiling applications an toolchain = {'name': 'gimkl', 'version': '2.11.5'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] # don't use PAX, it might break. tar_config_opts = True diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2015a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2015a.eb index 55e66932e222da03ab889a915fb6dae72b893bc0..de196014299b1c9bff0ca8fa118fc0655c37edba 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2015a.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2015a.eb @@ -12,7 +12,7 @@ description = """pkg-config is a helper tool used when compiling applications an toolchain = {'name': 'intel', 'version': '2015a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] # don't use PAX, it might break. tar_config_opts = True diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2015b.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2015b.eb index 245547ce08d9be50b45632bf690a26db4ad10fae..4ffff0c4e5a7498d21495b1f2bb9465c244516c6 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2015b.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2015b.eb @@ -12,7 +12,7 @@ description = """pkg-config is a helper tool used when compiling applications an toolchain = {'name': 'intel', 'version': '2015b'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] # don't use PAX, it might break. tar_config_opts = True diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2016a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2016a.eb index cc9d6a1ec7323073bd61b4e523b8a2c814ecb151..4b47af4546da3098a4308f4620e6b63960942b02 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2016a.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29-intel-2016a.eb @@ -12,7 +12,7 @@ description = """pkg-config is a helper tool used when compiling applications an toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] # don't use PAX, it might break. tar_config_opts = True diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..3fb349d523a4710b6a612d63233582dc310f8344 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-GCCcore-4.9.3.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.1' + +homepage = 'http://www.freedesktop.org/wiki/Software/pkg-config/' +description = """pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the + correct compiler options on the command line so an application can use + gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other libraries).""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] + +builddependencies = [('binutils', '2.25')] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016a.eb index bb2fea6cae6d26a2621d6a087fb567e6be5a6ea0..a8da4a98c874b4b2b6b086f683b9e45a520eaaec 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016a.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-foss-2016a.eb @@ -12,7 +12,7 @@ description = """pkg-config is a helper tool used when compiling applications an toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] # don't use PAX, it might break. tar_config_opts = True 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..2449f8de681cacc1ae5be0615e02c4c19e9a9ec1 --- /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 = ['https://pkg-config.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016a.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016a.eb index eeb50eabb138ec6a49adf5c33a0d6238ff5ede9b..647242172eea42a08b04b207f8074065a1b2d883 100644 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016a.eb +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016a.eb @@ -12,7 +12,7 @@ description = """pkg-config is a helper tool used when compiling applications an toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://pkgconfig.freedesktop.org/releases/'] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] # don't use PAX, it might break. tar_config_opts = True diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016b.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..0ae50de1d19211889fca9e69bc91eec97805aab7 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.1-intel-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': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pkg-config.freedesktop.org/releases/'] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..8ac0d86b7412557a014059fc2552cdd66b19004c --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016a-Python-2.7.11.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': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('pkg-config', '0.29'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..74658315efd06e0373399ecdab14d750a7a4cb43 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016a-Python-3.5.1.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': 'foss', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), + ('pkg-config', '0.29'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..6e76927dc1408c78c264a09696437bdc0cfdeefd --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016b-Python-2.7.12.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': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('pkg-config', '0.29.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016b-Python-3.5.2.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-2016b-Python-3.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..f2590ee0e4bbb30cc91d61f1a74ff59348ff5c8b --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-foss-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': 'foss', '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/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..5be193eb6bdc9a43418dfb21cf8affecd10b3adf --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.1.0-intel-2016b-Python-2.7.12.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', '2.7.12'), + ('pkg-config', '0.29.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'data' 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-1.0.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..fe4231de3be298e8bb2000592bd12d0fb8eb1105 --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'prompt-toolkit' +version = '1.0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' +description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://pypi.python.org/packages/4d/1f/5f5a3831006a1e9799d418e32d02c01529d6fa292851e381bd7df4908079/'] +sources = ['prompt_toolkit-%(version)s-py2-none-any.whl'] + +dependencies = [ + ('Python', '2.7.11'), + ('wcwidth', '0.1.7', versionsuffix), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/prompt_toolkit'], +} + +options = {'modulename': 'prompt_toolkit'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..4b1aefd0e6d20baec80e5283086b752ed62c218a --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.3-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'prompt-toolkit' +version = '1.0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' +description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://pypi.python.org/packages/1b/5b/6a1c5e6b9ad024a32b93abaeb49f517079f0fd9539aba2c2f36d8a76a1cf/'] +sources = ['prompt_toolkit-%(version)s-py3-none-any.whl'] + +dependencies = [ + ('Python', '3.5.1'), + ('wcwidth', '0.1.7', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/prompt_toolkit'], +} + +options = {'modulename': 'prompt_toolkit'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..a4fd060e9c31ef79e696908b3e1e2b0b0ddd860d --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'prompt-toolkit' +version = '1.0.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' +description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/eb/81/a7ad3c223f323d05381208c262889bd09577852bd5044a13965a9a13f5ed/'] +sources = ['prompt_toolkit-%(version)s-py2-none-any.whl'] + +dependencies = [ + ('Python', '2.7.12'), + ('wcwidth', '0.1.7', versionsuffix), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/prompt_toolkit'], +} + +options = {'modulename': 'prompt_toolkit'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-1.0.6-intel-2016b-Python-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-2.5.0-goolf-1.7.20.eb b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..56627b2c07ddb222c1be024ad477ddf1d62a2d0d --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-2.5.0-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'protobuf' +version = '2.5.0' + +homepage = 'https://code.google.com/p/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GOOGLECODE_SOURCE] + +sanity_check_paths = { + 'files': ['bin/protoc'], + 'dirs': [], +} + +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/psmc/psmc-0.6.5-foss-2016a.eb b/easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..59517cb97857238994bf4e5742780ddfedde5539 --- /dev/null +++ b/easybuild/easyconfigs/p/psmc/psmc-0.6.5-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'psmc' +version = '0.6.5' + +homepage = 'https://github.com/lh3/psmc' +description = """This software package infers population size history from a diploid sequence +using the Pairwise Sequentially Markovian Coalescent (PSMC) model.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/lh3/psmc/archive/'] +sources = ['%(version)s.tar.gz'] + +buildopts = '&& cd utils && make' + +utils = [ + 'avg.pl', 'calD', 'cntcpg', 'ctime_plot.pl', 'dec2ctime.pl', 'decode2bed.pl', 'fq2psmcfa', 'history2ms.pl', + 'ms2psmcfa.pl', 'mutDiff', 'pcnt_bezier.lua', 'psmc2history.pl', 'psmc_plot.pl', 'psmc_trunc.pl', 'splitfa', +] + +files_to_copy = [ + (['psmc'], 'bin'), + (['utils/%s' % util for util in utils], 'bin') +] + +sanity_check_paths = { + 'files': ['bin/psmc'] + ['bin/%s' % util for util in utils], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/psutil/psutil-4.2.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/psutil/psutil-4.2.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..4ad57c66abb44cfb11af997bb1c6dfc48ab9a0c9 --- /dev/null +++ b/easybuild/easyconfigs/p/psutil/psutil-4.2.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'psutil' +version = '4.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/giampaolo/psutil' +description = """A cross-platform process and system utilities module for Python""" + +toolchain = {'name': 'intel', '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 = 'lib' diff --git a/easybuild/easyconfigs/p/psutil/psutil-4.3.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/psutil/psutil-4.3.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..1230de05aa209ea7a590bdf490cbde73e198a5cf --- /dev/null +++ b/easybuild/easyconfigs/p/psutil/psutil-4.3.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'psutil' +version = '4.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/giampaolo/psutil' +description = """A cross-platform process and system utilities module for Python""" + +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 = 'lib' diff --git a/easybuild/easyconfigs/p/psutil/psutil-4.3.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/psutil/psutil-4.3.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..c74074ba5c7bd964e0062e5aa04aaa068bac57d3 --- /dev/null +++ b/easybuild/easyconfigs/p/psutil/psutil-4.3.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'psutil' +version = '4.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/giampaolo/psutil' +description = """A cross-platform process and system utilities module for Python""" + +toolchain = {'name': 'intel', '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 = 'lib' diff --git a/easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..7bd9dcc8b81005297d76988a0aa6922bf9bccde8 --- /dev/null +++ b/easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'py' +version = '1.4.31' +versionsuffix = '-Python-%(pyver)s' + +homepage = ' http://pylib.readthedocs.org/' +description = """library with cross-python path, ini-parsing, io, code, log facilities""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_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/p/py/py-1.4.31-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..80574f225442b4fc3ce8fb88a083ee365497c997 --- /dev/null +++ b/easybuild/easyconfigs/p/py/py-1.4.31-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'py' +version = '1.4.31' +versionsuffix = '-Python-%(pyver)s' + +homepage = ' http://pylib.readthedocs.org/' +description = """library with cross-python path, ini-parsing, io, code, log facilities""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_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/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..908370bc3a1e18f11f9cd6d9eac0f912d7762334 --- /dev/null +++ b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,68 @@ +easyblock = 'CMakeMake' + +name = 'pyGIMLi' +version = '20160803' +commit_id = 'a190c53' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pygimli.org/' +description = """pyGIMLi is an open-source multi-method library for solving inverse + and forward tasks related to geophysical problems. Written in C++ and Python, + it offers both efficiency and flexibility allowing you to quickly build + your own robust inversion applications for the geophysical problem at hand.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/gimli-org/gimli/archive/'] +sources = ['%s.tar.gz' % commit_id] + +patches = ['%(name)s-%(version)s_openblas.patch'] + +#pyGIMLi is picky about the version of CastXML/pygccxml/pyplusplus +#Check scripts/buildThirdParty.sh +builddependencies = [ + ('CMake', '3.4.3'), + ('CastXML', '20160617'), + ('pygccxml', '20160706', versionsuffix), + ('pyplusplus', '20160707', versionsuffix), +] + +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', versionsuffix), + ('pytest', '3.0.1', versionsuffix), + ('Clang', '3.7.1'), + ('Boost', '1.60.0', versionsuffix), + ('zlib', '1.2.8'), + ('Triangle', '1.6'), + ('CppUnit', '1.12.1'), + ('SuiteSparse', '4.5.3', '-METIS-5.1.0'), +] + +separate_build_dir = True + +configopts = '-DBOOST_ROOT=$EBROOTBOOST ' +configopts += '-DBLAS_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.%s ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.%s ' % SHLIB_EXT +configopts += '-DCASTXML_EXECUTABLE=$EBROOTCASTXML/bin/castxml ' +configopts += '-DPYGCCXML_PATH=$EBROOTPYGCCXML/lib/python%(pyshortver)s/site-packages/ ' +configopts += '-DPYPLUSPLUS_PATH=$EBROOTPYPLUSPLUS/lib/python%(pyshortver)s/site-packages/ ' + +buildopts = 'gimli pygimli apps' + +installopts = ' && mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages ' +installopts += '&& cp -a ../gimli*/python/. %(installdir)s/lib/python%(pyshortver)s/site-packages ' +installopts += '&& mkdir %(installdir)s/bin ' +installopts += '&& cp ../easybuild_obj/bin/* %(installdir)s/bin' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bms2vtk', 'dc1dinv', 'dc1dsmooth', 'fdem1dinv', 'fdem1dsmooth', + 'harmfit', 'invlinearmat', 'mrs1dblock', 'mrs1dsmooth', + 'mt1dinv', 'mt1dsmooth', 'polyfit', 'ttinv', 'ttmod']]+ + ['lib/libgimli.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/pygimli.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..bf649cda81c20497028cda994d98f1ee73e4efe5 --- /dev/null +++ b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,68 @@ +easyblock = 'CMakeMake' + +name = 'pyGIMLi' +version = '20160803' +commit_id = 'a190c53' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pygimli.org/' +description = """pyGIMLi is an open-source multi-method library for solving inverse + and forward tasks related to geophysical problems. Written in C++ and Python, + it offers both efficiency and flexibility allowing you to quickly build + your own robust inversion applications for the geophysical problem at hand.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/gimli-org/gimli/archive/'] +sources = ['%s.tar.gz' % commit_id] + +patches = ['%(name)s-%(version)s_openblas.patch'] + +#pyGIMLi is picky about the version of CastXML/pygccxml/pyplusplus +#Check scripts/buildThirdParty.sh +builddependencies = [ + ('CMake', '3.4.3'), + ('CastXML', '20160617'), + ('pygccxml', '20160706', versionsuffix), + ('pyplusplus', '20160707', versionsuffix), +] + +dependencies = [ + ('Python', '3.5.1'), + ('matplotlib', '1.5.1', versionsuffix), + ('pytest', '3.0.1', versionsuffix), + ('Clang', '3.7.1'), + ('Boost', '1.60.0', versionsuffix), + ('zlib', '1.2.8'), + ('Triangle', '1.6'), + ('CppUnit', '1.12.1'), + ('SuiteSparse', '4.5.3', '-METIS-5.1.0'), +] + +separate_build_dir = True + +configopts = '-DBOOST_ROOT=$EBROOTBOOST ' +configopts += '-DBLAS_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.%s ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES=$EBROOTOPENBLAS/lib/libopenblas.%s ' % SHLIB_EXT +configopts += '-DCASTXML_EXECUTABLE=$EBROOTCASTXML/bin/castxml ' +configopts += '-DPYGCCXML_PATH=$EBROOTPYGCCXML/lib/python%(pyshortver)s/site-packages/ ' +configopts += '-DPYPLUSPLUS_PATH=$EBROOTPYPLUSPLUS/lib/python%(pyshortver)s/site-packages/ ' + +buildopts = 'gimli pygimli apps' + +installopts = ' && mkdir -p %(installdir)s/lib/python%(pyshortver)s/site-packages ' +installopts += '&& cp -a ../gimli*/python/. %(installdir)s/lib/python%(pyshortver)s/site-packages ' +installopts += '&& mkdir %(installdir)s/bin ' +installopts += '&& cp ../easybuild_obj/bin/* %(installdir)s/bin' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bms2vtk', 'dc1dinv', 'dc1dsmooth', 'fdem1dinv', 'fdem1dsmooth', + 'harmfit', 'invlinearmat', 'mrs1dblock', 'mrs1dsmooth', + 'mt1dinv', 'mt1dsmooth', 'polyfit', 'ttinv', 'ttmod']]+ + ['lib/libgimli.%s' % SHLIB_EXT, 'lib/python%(pyshortver)s/site-packages/pygimli.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803_openblas.patch b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803_openblas.patch new file mode 100644 index 0000000000000000000000000000000000000000..b8d7de57eff6a77684298ddaf933fb58d37fd015 --- /dev/null +++ b/easybuild/easyconfigs/p/pyGIMLi/pyGIMLi-20160803_openblas.patch @@ -0,0 +1,13 @@ +# OpenBLAS cblas.h is loacted at include/cblas.h and not include/openblas/cblas.h +# Aug 04th 2016 by B. Hajgato (Free University Brussels - VUB) +--- gimli/src/gimli.cpp.orig 2016-08-04 08:53:28.000000000 +0200 ++++ gimli/src/gimli.cpp 2016-08-04 14:19:26.570541693 +0200 +@@ -28,7 +28,7 @@ + #include + + #if OPENBLAS_FOUND && !CONDA_BUILD +- #include ++ #include + // #else + // #include + #endif diff --git a/easybuild/easyconfigs/p/pygccxml/pygccxml-20160706-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pygccxml/pygccxml-20160706-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..9f63786f27c5a6ec0ee2dc1b85d50f02855cbb07 --- /dev/null +++ b/easybuild/easyconfigs/p/pygccxml/pygccxml-20160706-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'pygccxml' +version = '20160706' +commit_id = '648e8da' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/pygccxml' +description = """Python package for easy C++ declarations navigation.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/gccxml/pygccxml/archive/'] +sources = ['%s.tar.gz' % commit_id] + +builddependencies = [('pip', '8.1.2', versionsuffix)] + +dependencies = [ + ('Python', '2.7.11'), + ('CastXML', '20160617'), +] + +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +options = {'modulename': '%(name)s'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pygccxml/pygccxml-20160706-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pygccxml/pygccxml-20160706-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..be70419f92331a558a1e2bf2ff22d777d5f2b68a --- /dev/null +++ b/easybuild/easyconfigs/p/pygccxml/pygccxml-20160706-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'pygccxml' +version = '20160706' +commit_id = '648e8da' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/pygccxml' +description = """Python package for easy C++ declarations navigation.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/gccxml/pygccxml/archive/'] +sources = ['%s.tar.gz' % commit_id] + +dependencies = [ + ('Python', '3.5.1'), + ('CastXML', '20160617'), +] + +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +options = {'modulename': '%(name)s'} + +moduleclass = 'tools' 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/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..695617390c7ef20fd3803cdda85cf7fc1ec7e7b5 --- /dev/null +++ b/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'pyplusplus' +version = '20160707' +commit_id = '2c6c05b7a7d2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/ompl/pyplusplus' +description = """Py++ is a code generator for Boost.Python that simplifies + writing Python bindings of a C/C++ library + The tool is implemented as a Python module which is controlled by a user script.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://bitbucket.org/ompl/pyplusplus/get/'] +sources = ['%s.zip' % commit_id] + +builddependencies = [('pip', '8.1.2', versionsuffix)] + +dependencies = [ + ('Python', '2.7.11'), + ('pygccxml', '20160706', '-Python-%(pyver)s'), +] + +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +options = {'modulename': '%(name)s'} + +moduleclass = 'tools' + diff --git a/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..98760a6c19b4b09008b9954f63970153a95996c8 --- /dev/null +++ b/easybuild/easyconfigs/p/pyplusplus/pyplusplus-20160707-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'pyplusplus' +version = '20160707' +commit_id = '2c6c05b7a7d2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://bitbucket.org/ompl/pyplusplus' +description = """Py++ is a code generator for Boost.Python that simplifies + writing Python bindings of a C/C++ library + The tool is implemented as a Python module which is controlled by a user script.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://bitbucket.org/ompl/pyplusplus/get/'] +sources = ['%s.zip' % commit_id] + +dependencies = [ + ('Python', '3.5.1'), + ('pygccxml', '20160706', '-Python-%(pyver)s'), +] + +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +options = {'modulename': '%(name)s'} + +moduleclass = 'tools' + diff --git a/easybuild/easyconfigs/p/pysqlite/pysqlite-2.8.2-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.8.2-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..0387ef7b1e9c66e6da98863cd2b2d7876d9461fc --- /dev/null +++ b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.8.2-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'pysqlite' +version = '2.8.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/pysqlite' +description = """pysqlite is an interface to the SQLite 3.x embedded relational database engine. + It is almost fully compliant with the Python database API version 2.0 also exposes the unique features of SQLite.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('SQLite', '3.9.2'), # also dependency for Python itself +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s%(version_major)s'], +} + +options = {'modulename': '%(name)s%(version_major)s'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..a816b7e71ea3fb19d9755224d605adc32ef60941 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,25 @@ +easyblock = "PythonPackage" + +name = 'pytest' +version = '3.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytest.org' +description = """pytest: simple powerful testing with Python""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('py', '1.4.31', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..85ae51712a4a9e343a33c7e8bd90fdec519f9ad5 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-3.0.1-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,25 @@ +easyblock = "PythonPackage" + +name = 'pytest' +version = '3.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pytest.org' +description = """pytest: simple powerful testing with Python""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), + ('py', '1.4.31', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' 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-3.3.8-intel-2016a.eb b/easybuild/easyconfigs/q/Qt/Qt-3.3.8-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3e1447d59473b8362827c1528c83434a2cca3cb8 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-3.3.8-intel-2016a.eb @@ -0,0 +1,12 @@ +name = 'Qt' +version = '3.3.8' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://download.qt.io/archive/qt/%(version_major)s/'] +sources = ['qt-x11-free-%(version)s.tar.gz'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb index 8616257c5ce38ea0cda53270f0bf98ad2eb115ad..fca5be42427ef9cb0704c375077536bc7f1fdb7a 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016a-GLib-2.48.0.eb @@ -17,11 +17,40 @@ patches = ['Qt-%(version)s_phonon-export.patch'] glib_ver = '2.48.0' versionsuffix = '-GLib-%s' % glib_ver +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', glib_ver), ('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'), ] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016b.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..b274210da05ff5c16b8b0b1cfe3e56b0952e87fc --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-foss-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': 'foss', '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/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb index ada4c2ab36a8aa16eab3d62cae7de1badb20fa1b..30a0fdb71960af6721da0cb7c512c825d0df1775 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.7-intel-2016a-GLib-2.48.0.eb @@ -17,11 +17,40 @@ patches = ['Qt-%(version)s_phonon-export.patch'] glib_ver = '2.48.0' versionsuffix = '-GLib-%s' % glib_ver +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', glib_ver), ('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'), ] moduleclass = 'devel' 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/Qt5-5.6.0-foss-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb index 27b1514a37daac0be65a9152ebf4c01ae979b049..80096881146560b9e823b4937c12ceddfc4674c6 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-foss-2016a.eb @@ -14,6 +14,20 @@ source_urls = [ ] 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'), diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb index f4f0ab35bde7c33b7925cac361f0fef7b8095f19..e402c568f37c7a0b42e14e88289806d4ef89503b 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.6.0-intel-2016a.eb @@ -14,6 +14,20 @@ source_urls = [ ] 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'), 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-5.1.2-ictce-7.3.5.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..d453b22ecbafcdb07de1ac703a58b9e400d0a9ab --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.1.2-ictce-7.3.5.eb @@ -0,0 +1,46 @@ +name = 'QuantumESPRESSO' +version = '5.1.2' + +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': 'ictce', 'version': '7.3.5'} +toolchainopts = {'usempi': True} + +sources = [ + 'espresso-%(version)s.tar.gz', + 'atomic-%(version)s.tar.gz', + 'neb-%(version)s.tar.gz', + 'PHonon-%(version)s.tar.gz', + 'pwcond-%(version)s.tar.gz', + 'tddfpt-%(version)s.tar.gz', + 'xspectra-%(version)s.tar.gz', + 'GWW-%(version)s.tar.gz', +] + +source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz and GWW*.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/185/753/', # espresso-5.1.2.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/185/754/', # GWW-5.1.2.tar.gz +] + +checksums = [ + '55f766d1c41c8e7994b0d6717a55c3ea', # espresso-5.1.2.tar.gz + '77ec8a5b2106abc080a55463d4fc964b', # atomic-5.1.2.tar.gz + 'b6123aa99f7db958dd635e9837abdf00', # neb-5.1.2.tar.gz + '49c65d222449c5fcea539470e8001170', # PHonon-5.1.2.tar.gz + '6a6c8f84d2a3e65d60cf4e5387383b9b', # pwcond-5.1.2.tar.gz + '9790e7d55fc1f08c554a9d0212bc7f9e', # tddfpt-5.1.2.tar.gz + 'c27d6c9515c0ce29462a9b1e8203d118', # xspectra-5.1.2.tar.gz + '681c7f83b4adefbf2da721c4b8210670', # GWW-5.1.2.tar.gz +] + +buildopts = 'all w90 want gipaw' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..7bd4242d316b2c9b07718ebadabc09e5825a5a7b --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,68 @@ +name = 'QuantumESPRESSO' +version = '5.3.0' + +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': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +# major part of this list was determined from espresso/install/plugins_list +sources = [ + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'atomic-%(version)s.tar.gz', + 'neb-%(version)s.tar.gz', + 'PHonon-%(version)s.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', + 'pwcond-%(version)s.tar.gz', + 'tddfpt-%(version)s.tar.gz', + 'want-2.5.1-base.tar.gz', + 'yambo-3.4.2.tgz', + 'xspectra-%(version)s.tar.gz', +] +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/204/912/', # espresso-5.3.0.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-%(version)s_yambo-fixes.patch', + 'QuantumESPRESSO-%(version)s_fftxlib-fixes.patch', +] + +# source checksums +checksums = [ + '6848fcfaeb118587d6be36bd10b7f2c3', # espresso-5.3.0.tar.gz + 'a1e9611b9a82941c23426028d112186e', # wannier90-1.2.tar.gz + 'e713f74b78a04600265e697ca346bea1', # atomic-5.3.0.tar.gz + '91157da66570deb4e7a353a23621a39f', # neb-5.3.0.tar.gz + '994c89e72b5500bceb44dada7134cc12', # PHonon-5.3.0.tar.gz + # 'f094031c6d13a0e00022daf4d7c847c7', # plumed-1.3-qe-r11758.tar.gz + '897753893dc46502de24b81929694ee1', # pwcond-5.3.0.tar.gz + 'ac9d86386f2b2d28a6b00c902668669b', # tddfpt-5.3.0.tar.gz + 'ac365daebbe380bf4019235eacf71079', # want-2.5.1-base.tar.gz + 'f0820a0f42dfc81ce3811af647bed777', # yambo-3.4.2.tgz + 'fc7d9d80e00185afcab44307d3b70a65', # xspectra-5.3.0.tar.gz +] + +# gipaw excluded due to: configure: error: Cannot compile against this version of Quantum-Espresso +# add plumed and uncomment the lines in sources and checksums if the package is downloaded manually +# 'all' not used here because upftools are missing from 5.3.0 package +buildopts = 'pw ph pp pwcond neb cp ld1 tddfpt w90 want yambo xspectra' # plumed + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_fftxlib-fixes.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_fftxlib-fixes.patch new file mode 100644 index 0000000000000000000000000000000000000000..c1fdcc987306e603dc9ef83df55baa390737a40c --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_fftxlib-fixes.patch @@ -0,0 +1,24 @@ +* remove fftw_version, conflicts with the one in mkl's fftw +* http://qe-forge.org/pipermail/q-e-developers/2016-January/001088.html +author: Miguel Dias Costa (National University of Singapore) +--- espresso-5.3.0/FFTXlib/fftw.c.orig 2016-05-26 09:54:35.911733000 +0800 ++++ espresso-5.3.0/FFTXlib/fftw.c 2016-05-26 09:59:43.900568303 +0800 +@@ -345,8 +345,6 @@ + #include + #include + +-char *fftw_version = "FFTW V1.1 ($Id: fftw.c,v 1.3 2010-01-26 14:06:59 giannozz Exp $)"; +- + /* + * This function is called in other files, so we cannot declare + * it as static. +--- espresso-5.3.0/FFTXlib/fftw.h.orig 2016-05-26 09:54:40.566922000 +0800 ++++ espresso-5.3.0/FFTXlib/fftw.h 2016-05-26 09:59:59.822132168 +0800 +@@ -133,7 +133,6 @@ + + extern generic_codelet fftw_twiddle_generic; + extern generic_codelet fftwi_twiddle_generic; +-extern char *fftw_version; + + /***************************** + * Plans diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_yambo-fixes.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_yambo-fixes.patch new file mode 100644 index 0000000000000000000000000000000000000000..b4c96acc606145a173ea68f6eb898f4cefb356e6 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.3.0_yambo-fixes.patch @@ -0,0 +1,71 @@ +* make sure -nofor_main is also used when $FC is defined as mpif90 for yambo +* fix check in yambo configure script w.r.t. preprocessing Fortran code by ignoring harmless warning in stderr output +* force ifort mangling in yambo's netcdf +author: Kenneth Hoste (HPC-UGent), adapted to espresso-5.3.0 and yambo-3.4.2 by Miguel Dias Costa (National University of Singapore) +--- espresso-5.3.0/yambo-3.4.2/configure.orig 2016-05-26 16:18:16.177156000 +0800 ++++ espresso-5.3.0/yambo-3.4.2/configure 2016-05-26 16:20:31.929218336 +0800 +@@ -6238,7 +6238,7 @@ + ;; + *g95*) + ;; +- *ifort*) ++ *ifort*|*mpif90*) + $FC -v >& ver_ + VER_8=`grep 8. ver_ | wc -l` + VER_9=`grep 9. ver_ | wc -l` +@@ -6321,7 +6321,7 @@ + FCMFLAG="" + OMPFLAGS="-fopenmp" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *11* | *12* | *13* |*14* | *15* ) +@@ -6365,7 +6365,7 @@ + UFFLAGS="-g -O0 -fno-second-underscore" + FCMFLAG="" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *1*) +@@ -6413,7 +6413,7 @@ + UFFLAGS="-g -O0 -w" + OMPFLAGS="-openmp" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *1*) +@@ -6472,7 +6472,7 @@ + UFFLAGS="-g -O0 -w -tpp2" + OMPFLAGS="-openmp" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *11* | *12* | *13* |*14* |*15* ) +@@ -7651,7 +7651,7 @@ + + if ! test -s conftest.er1 || test -n "`grep successful conftest.er1`" ; then + eval $CPP $CPPFLAGS conftest.F > conftest.${F90SUFFIX} +- eval $FC $FCFLAGS -c conftest.${F90SUFFIX} 2> conftest.er2 >&5 ++ eval $FC $FCFLAGS -c conftest.${F90SUFFIX} | grep -v "ifort: command line remark" 2> conftest.er2 >&5 + if test -s conftest.er2 ; then + if ! test -n "`grep successful conftest.er2`" ; then + acx_F90_ok=no ; +--- espresso-5.3.0/yambo-3.4.2/lib/netcdf/Makefile.loc.orig 2016-06-02 17:29:53.816844000 +0800 ++++ espresso-5.3.0/yambo-3.4.2/lib/netcdf/Makefile.loc 2016-06-02 17:30:45.579476000 +0800 +@@ -40,7 +40,7 @@ + FC="$(f90)" \ + FCFLAGS="$(f77flags)" \ + FFLAGS="$(f77flags)" \ +- CPPFLAGS="$(netcdf_aux)" \ ++ CPPFLAGS="$(netcdf_aux) -DpgiFortran" \ + F90="$(f90)" \ + F77="$(f77)" \ + INSTALL_DIR="$(INSTALL_DIR)" ); \ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb new file mode 100644 index 0000000000000000000000000000000000000000..57849d2efa21f0c22e9fd5acd09fa19afe1ea6f7 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-foss-2016b-hybrid.eb @@ -0,0 +1,58 @@ +name = 'QuantumESPRESSO' +version = '5.4.0' +versionsuffix = '-hybrid' + +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': 'foss', 'version': '2016b'} +toolchainopts = {'usempi': True, 'openmp': True} + +# this list was determined from QE 5.4.0 version release +sources = [ + # Common source + 'espresso-%(version)s.tar.gz', + 'tddfpt-%(version)s.tar.gz', + # Other sources + 'atomic-%(version)s.tar.gz', + 'neb-%(version)s.tar.gz', + 'PHonon-%(version)s.tar.gz', + 'pwcond-%(version)s.tar.gz', + 'xspectra-%(version)s.tar.gz' , + 'PWgui-%(version)s.tar.gz' , + 'EPW-%(version)s.tar.gz' , + 'test-suite-%(version)s.tar.gz' , + 'GWW-%(version)s.tar.gz' , +] +source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # Almost all + 'http://www.qe-forge.org/gf/download/frsrelease/211/968/', # espresso-5.4.0.tar.gz + # These will not be used because of the 404 signal not found from the previous link. + 'http://www.qe-forge.org/gf/download/frsrelease/211/961/', # PWgui-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/956/', # tddfpt-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/954/', # atomic-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/959/', # neb-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/962/', # PHonon-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/960/', # pwcond-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/958/', # xspectra-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/969/', # EPW-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/963/', # test-suite-5.4.0.tar.gz + 'http://www.qe-forge.org/gf/download/frsrelease/211/957/', # GWW-5.4.0.tar.gz +] + +# Hybrid option exists only for backward compatibility, use toolchain option openmp instead. +hybrid = True +# Patch file to avoid the CPP problem generated by different OSes +patches = ['QuantumESPRESSO-5.4.0_fix-f90rule-gfortran.patch'] + +# packages included in 5.4.0 version of QE. We met errors when try to include gipaw, yambo and someother packages. +buildopts = 'all tddfpt neb xspectra ph ' + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' + diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..8529a9282fa5056c314d81694e907c8364107841 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0-intel-2016.02-GCC-4.9.eb @@ -0,0 +1,66 @@ +name = 'QuantumESPRESSO' +version = '5.4.0' + +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': '2016.02-GCC-4.9'} +toolchainopts = {'usempi': True} + +# major part of this list was determined from espresso/install/plugins_list +sources = [ + 'espresso-%(version)s.tar.gz', + 'wannier90-1.2.tar.gz', + 'atomic-%(version)s.tar.gz', + 'neb-%(version)s.tar.gz', + 'PHonon-%(version)s.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', + 'pwcond-%(version)s.tar.gz', + 'tddfpt-%(version)s.tar.gz', + 'want-2.5.1-base.tar.gz', + 'yambo-3.4.2.tgz', + 'xspectra-%(version)s.tar.gz', +] +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/211/968/', # espresso-5.4.0.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-%(version)s_yambo-fixes.patch', +] + +# source checksums +checksums = [ + '8bb78181b39bd084ae5cb7a512c1cfe7', # espresso-5.4.0.tar.gz + 'a1e9611b9a82941c23426028d112186e', # wannier90-1.2.tar.gz + '24dc0d8bf5cf4eb4dc38e1c18a80b3ee', # atomic-5.4.0.tar.gz + '254f929259fb06036b78c493cf18e5d6', # neb-5.4.0.tar.gz + 'f641fe9dcf0ec8f1e47d74e3c7c39705', # PHonon-5.4.0.tar.gz + # 'f094031c6d13a0e00022daf4d7c847c7', # plumed-1.3-qe-r11758.tar.gz + '31c1cd8cd76752833a9205d456093d0a', # pwcond-5.4.0.tar.gz + '2101533a627644ef467b60d400977eab', # tddfpt-5.4.0.tar.gz + 'ac365daebbe380bf4019235eacf71079', # want-2.5.1-base.tar.gz + 'f0820a0f42dfc81ce3811af647bed777', # yambo-3.4.2.tgz + '95080929c87389cd15cf765048cfc9d2', # xspectra-5.4.0.tar.gz +] + +# gipaw excluded due to: configure: error: Cannot compile against this version of Quantum-Espresso +# add plumed and uncomment the lines in sources and checksums if the package is downloaded manually +buildopts = 'all w90 want yambo xspectra' # plumed + +# parallel build tends to fail +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_fix-f90rule-gfortran.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_fix-f90rule-gfortran.patch new file mode 100644 index 0000000000000000000000000000000000000000..85d62f606be0a23e55ae8a56b71f1463683c48a9 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_fix-f90rule-gfortran.patch @@ -0,0 +1,12 @@ +diff -rupN espresso-5.4.0.orig/install/make.sys.in espresso-5.4.0/install/make.sys.in +--- espresso-5.4.0.orig/install/make.sys.in 2016-04-24 23:19:25.000000000 +0200 ++++ espresso-5.4.0/install/make.sys.in 2016-06-11 15:08:15.869499000 +0200 +@@ -13,7 +13,7 @@ + # remember the tabulator in the first column !!! + + .f90.o: +- @f90rule@ ++ $(MPIF90) $(F90FLAGS) -c $< + + # .f.o and .c.o: do not modify + diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_yambo-fixes.patch b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_yambo-fixes.patch new file mode 100644 index 0000000000000000000000000000000000000000..fd63a363335ced902eb5b3ab8a84f8427c675c28 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.4.0_yambo-fixes.patch @@ -0,0 +1,71 @@ +* make sure -nofor_main is also used when $FC is defined as mpif90 for yambo +* fix check in yambo configure script w.r.t. preprocessing Fortran code by ignoring harmless warning in stderr output +* force ifort mangling in yambo's netcdf +author: Kenneth Hoste (HPC-UGent), adapted to espresso-5.4.0 and yambo-3.4.2 by Miguel Dias Costa (National University of Singapore) +--- espresso-5.4.0/yambo-3.4.2/configure.orig 2016-05-26 16:18:16.177156000 +0800 ++++ espresso-5.4.0/yambo-3.4.2/configure 2016-05-26 16:20:31.929218336 +0800 +@@ -6238,7 +6238,7 @@ + ;; + *g95*) + ;; +- *ifort*) ++ *ifort*|*mpif90*) + $FC -v >& ver_ + VER_8=`grep 8. ver_ | wc -l` + VER_9=`grep 9. ver_ | wc -l` +@@ -6321,7 +6321,7 @@ + FCMFLAG="" + OMPFLAGS="-fopenmp" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *11* | *12* | *13* |*14* | *15* ) +@@ -6365,7 +6365,7 @@ + UFFLAGS="-g -O0 -fno-second-underscore" + FCMFLAG="" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *1*) +@@ -6413,7 +6413,7 @@ + UFFLAGS="-g -O0 -w" + OMPFLAGS="-openmp" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *1*) +@@ -6472,7 +6472,7 @@ + UFFLAGS="-g -O0 -w -tpp2" + OMPFLAGS="-openmp" + ;; +- *ifort*) ++ *ifort*|*mpif90*) + CPU_FLAG="" + case "${FCVERSION}" in + *11* | *12* | *13* |*14* |*15* ) +@@ -7651,7 +7651,7 @@ + + if ! test -s conftest.er1 || test -n "`grep successful conftest.er1`" ; then + eval $CPP $CPPFLAGS conftest.F > conftest.${F90SUFFIX} +- eval $FC $FCFLAGS -c conftest.${F90SUFFIX} 2> conftest.er2 >&5 ++ eval $FC $FCFLAGS -c conftest.${F90SUFFIX} | grep -v "ifort: command line remark" 2> conftest.er2 >&5 + if test -s conftest.er2 ; then + if ! test -n "`grep successful conftest.er2`" ; then + acx_F90_ok=no ; +--- espresso-5.4.0/yambo-3.4.2/lib/netcdf/Makefile.loc.orig 2016-06-02 17:29:53.816844000 +0800 ++++ espresso-5.4.0/yambo-3.4.2/lib/netcdf/Makefile.loc 2016-06-02 17:30:45.579476000 +0800 +@@ -40,7 +40,7 @@ + FC="$(f90)" \ + FCFLAGS="$(f77flags)" \ + FFLAGS="$(f77flags)" \ +- CPPFLAGS="$(netcdf_aux)" \ ++ CPPFLAGS="$(netcdf_aux) -DpgiFortran" \ + F90="$(f90)" \ + F77="$(f77)" \ + INSTALL_DIR="$(INSTALL_DIR)" ); \ 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/Qwt/Qwt-6.1.2-intel-2016a.eb b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.2-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6c0ec84358f7662b3713dcd5a3b5e5434a80047c --- /dev/null +++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.1.2-intel-2016a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Qwt' +version = '6.1.2' + +homepage = 'http://qwt.sourceforge.net/' +description = """The Qwt library contains GUI Components and utility classes which are primarily useful for programs + with a technical background.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('Qt', '4.8.7'), +] + +skipsteps = ['configure'] + +prebuildopts = "sed -i 's@QWT_INSTALL_PREFIX[ ]*=.*@QWT_INSTALL_PREFIX = %(installdir)s@g' qwtconfig.pri && " +prebuildopts += "qmake qwt.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwt.%s' % SHLIB_EXT], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/q/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-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb index 13ad83c7743c43ade92aece403358eff3176e16a..2d99ed5c8860f599789ce6b7dbde7b64641f26f3 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-foss-2016a-R-3.2.3.eb @@ -141,6 +141,8 @@ exts_list = [ ('metagenomeSeq', '1.12.0', bioconductor_options), ('gdsfmt', '1.6.2', bioconductor_options), ('SNPRelate', '1.4.2', bioconductor_options), + ('phyloseq', '1.14.0', bioconductor_options), + ('ALDEx2', '1.2.0', bioconductor_options), ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb index 64a35be205030a61fc66e1a25896026a77a9d632..54239fe955dccb4e9abe14ac9210e02491651a48 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.2-intel-2016a-R-3.2.3.eb @@ -140,6 +140,8 @@ exts_list = [ ('metagenomeSeq', '1.12.0', bioconductor_options), ('gdsfmt', '1.6.2', bioconductor_options), ('SNPRelate', '1.4.2', bioconductor_options), + ('phyloseq', '1.14.0', bioconductor_options), + ('ALDEx2', '1.2.0', bioconductor_options), ] modextrapaths = {'R_LIBS': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.3-intel-2016b-R-3.3.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.3-intel-2016b-R-3.3.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..c43e3ff869c6dc0bc148156b2d577546f7c28601 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.3-intel-2016b-R-3.3.1.eb @@ -0,0 +1,161 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.3' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +dependencies = [ + ('R', '3.3.1'), + ('HDF5', '1.8.17'), # for rhdf5 +] + +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, +} +bioconductor_options = { + 'source_urls': [ + 'http://bioconductor.org/packages/3.3/bioc/src/contrib/', + 'http://bioconductor.org/packages/3.3/data/annotation/src/contrib/', + 'http://bioconductor.org/packages/3.3/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +exts_list = [ + ('BiocGenerics', '0.18.0', bioconductor_options), + ('Biobase', '2.32.0', bioconductor_options), + ('S4Vectors', '0.10.3', bioconductor_options), + ('IRanges', '2.6.1', bioconductor_options), + ('GenomeInfoDb', '1.8.3', bioconductor_options), + ('AnnotationDbi', '1.34.4', bioconductor_options), + ('zlibbioc', '1.18.0', bioconductor_options), + ('XVector', '0.12.1', bioconductor_options), + ('Biostrings', '2.40.2', bioconductor_options), + ('GenomicRanges', '1.24.2', bioconductor_options), + ('BiocParallel', '1.6.6', bioconductor_options), + ('Rsamtools', '1.24.0', bioconductor_options), + ('lambda.r', '1.1.9', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.3', ext_options), + ('SummarizedExperiment', '1.2.3', bioconductor_options), + ('GenomicAlignments', '1.8.4', bioconductor_options), + ('ShortRead', '1.30.0', bioconductor_options), + ('graph', '1.50.0', bioconductor_options), + ('affyio', '1.42.0', bioconductor_options), + ('BiocInstaller', '1.22.3', bioconductor_options), + ('preprocessCore', '1.34.0', bioconductor_options), + ('affy', '1.50.0', bioconductor_options), + ('GO.db', '3.3.0', bioconductor_options), + ('limma', '3.28.19', bioconductor_options), + ('RBGL', '1.48.1', bioconductor_options), + ('org.Hs.eg.db', '3.3.0', bioconductor_options), + ('AnnotationForge', '1.14.2', bioconductor_options), + ('KEGG.db', '3.2.3', bioconductor_options), + ('annaffy', '1.44.0', bioconductor_options), + ('gcrma', '2.44.0', bioconductor_options), + ('oligoClasses', '1.34.0', bioconductor_options), + ('edgeR', '3.14.0', bioconductor_options), + ('PFAM.db', '3.3.0', bioconductor_options), + ('perm', '1.0-0.0', ext_options), + ('baySeq', '2.6.0', bioconductor_options), + ('qvalue', '2.4.2', bioconductor_options), + ('impute', '1.46.0', bioconductor_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.26.0', bioconductor_options), + ('hgu133plus2.db', '3.2.3', bioconductor_options), + ('illuminaio', '0.14.0', bioconductor_options), + ('rtracklayer', '1.32.2', bioconductor_options), + ('biomaRt', '2.28.0', bioconductor_options), + ('GenomicFeatures', '1.24.5', bioconductor_options), + ('bumphunter', '1.12.0', bioconductor_options), + ('multtest', '2.28.0', bioconductor_options), + ('siggenes', '1.46.0', bioconductor_options), + ('DynDoc', '1.50.0', bioconductor_options), + ('genoset', '1.28.2', bioconductor_options), + ('NOISeq', '2.16.0', bioconductor_options), + ('Rgraphviz', '2.16.0', bioconductor_options), + ('RNASeqPower', '1.12.0', bioconductor_options), + ('annotate', '1.50.0', bioconductor_options), + ('GSEABase', '1.34.0', bioconductor_options), + ('genefilter', '1.54.2', bioconductor_options), + ('Category', '2.38.0', bioconductor_options), + ('GOstats', '2.38.1', bioconductor_options), + ('BSgenome', '1.40.1', bioconductor_options), + ('VariantAnnotation', '1.18.7', bioconductor_options), + ('interactiveDisplayBase', '1.10.3', bioconductor_options), + ('AnnotationHub', '2.4.2', bioconductor_options), + ('ensembldb', '1.4.7', bioconductor_options), + ('biovizBase', '1.20.0', bioconductor_options), + ('OrganismDbi', '1.14.1', bioconductor_options), + ('ggbio', '1.20.2', bioconductor_options), + ('geneplotter', '1.50.0', bioconductor_options), + ('DESeq2', '1.12.4', bioconductor_options), + ('ReportingTools', '2.12.2', bioconductor_options), + ('affycoretools', '1.44.3', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.2.2', bioconductor_options), + ('Homo.sapiens', '1.3.1', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), + ('AgiMicroRna', '2.22.0', bioconductor_options), + ('GenomeGraphs', '1.32.0', bioconductor_options), + ('geneLenDataBase', '1.8.0', bioconductor_options), + ('goseq', '1.24.0', bioconductor_options), + ('KEGGREST', '1.12.2', bioconductor_options), + ('KEGGgraph', '1.30.0', bioconductor_options), + ('KEGGprofile', '1.14.0', bioconductor_options), + ('GEOquery', '2.38.4', bioconductor_options), + ('mixOmics', '6.0.0', ext_options), + ('minfi', '1.18.6', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), + ('methylumi', '2.18.2', bioconductor_options), + ('lumi', '2.24.0', bioconductor_options), + ('widgetTools', '1.50.0', bioconductor_options), + ('tkWidgets', '1.50.0', bioconductor_options), + ('Mfuzz', '2.32.0', bioconductor_options), + ('maSigPro', '1.44.0', bioconductor_options), + ('SPIA', '2.24.0', bioconductor_options), + ('Gviz', '1.16.4', bioconductor_options), + ('cummeRbund', '2.14.0', bioconductor_options), + ('GenomicFiles', '1.8.0', bioconductor_options), + ('derfinderHelper', '1.6.3', bioconductor_options), + ('derfinder', '1.6.4', bioconductor_options), + ('polyester', '1.8.3', bioconductor_options), + ('Rsubread', '1.22.3', bioconductor_options), + ('pcaMethods', '1.64.0', bioconductor_options), + ('marray', '1.50.0', bioconductor_options), + ('CGHbase', '1.32.0', bioconductor_options), + ('sigaR', '1.15.0', bioconductor_options), + ('HCsnip', '1.12.0', bioconductor_options), + ('metagenomeSeq', '1.14.2', bioconductor_options), + ('gdsfmt', '1.8.3', bioconductor_options), + ('SNPRelate', '1.6.5', dict(bioconductor_options.items() + [('patches', ['SNPRelate-1.6.5_no-SSE-intr.patch'])])), + ('rhdf5', '2.16.0', bioconductor_options), + ('biomformat', '1.0.2', bioconductor_options), + ('phyloseq', '1.16.2', bioconductor_options), + ('ALDEx2', '1.4.0', bioconductor_options), + ('dada2', '1.0.3', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/SNPRelate-1.6.5_no-SSE-intr.patch b/easybuild/easyconfigs/r/R-bundle-Bioconductor/SNPRelate-1.6.5_no-SSE-intr.patch new file mode 100644 index 0000000000000000000000000000000000000000..cb934b50ee0ec3051eff837f8e6ef6eff469b8e7 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/SNPRelate-1.6.5_no-SSE-intr.patch @@ -0,0 +1,15 @@ +disable SSE intrinsics to avoid error when compiling with Intel C++ compiler: +"error: expression must have integral or enum type" +in genIBS.cpp and genKING.cpp due to use of complement (~) on values of type _m128i +author: Kenneth Hoste; patch suggested by Xiuwen Zheng (SNPRelate maintainer) +--- SNPRelate.orig/src/Makevars 2016-07-29 06:39:00.000000000 +0200 ++++ SNPRelate/src/Makevars 2016-08-26 09:31:44.440787000 +0200 +@@ -3,7 +3,7 @@ + ### ### + + # additional preprocessor options +-PKG_CPPFLAGS = -DUSING_R -I. ++PKG_CPPFLAGS = -DUSING_R -I. -DCOREARRAY_NO_SIMD + + # to set flags for the linker + PKG_LIBS = $(FLIBS) $(BLAS_LIBS) $(LAPACK_LIBS) -lpthread diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb index 966d48e3c9aa0ed601be64d7d66f34c514cdc19e..b54b0f68e9b75c468b2aee4e5825e1f215ba0e4e 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2015b.eb @@ -26,6 +26,7 @@ dependencies = [ ('libxml2', '2.9.2'), # for XML ('GDAL', '2.0.1'), # for rgdal ('PROJ', '4.8.0'), # for rgdal + ('GMP', '6.0.0a', '', ('GNU', '4.9.3-2.25')), # for igraph ] name_tmpl = '%(name)s_%(version)s.tar.gz' @@ -439,6 +440,10 @@ exts_list = [ ('diveRsity', '1.9.89', ext_options), ('doSNOW', '1.0.14', ext_options), ('phangorn', '2.0.2', ext_options), + ('geepack', '1.2-0.1', ext_options), + ('lubridate', '1.5.6', ext_options), + ('biom', '0.3.12', ext_options), + ('pim', '2.0.0.2', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..ffd3ec61bf3d278adca9f8e1ab2ae598ad17577f --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a-bare.eb @@ -0,0 +1,27 @@ +name = 'R' +version = '3.2.3' +versionsuffix = '-bare' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('libpng', '1.6.21'), # for plotting in R + ('libjpeg-turbo', '1.4.2'), # for plottting in R + ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it +] + +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb index 323a1f250777823cc2eb4c9ea7c1607cd157be60..580f74438d2ce591213dd88b066ded2a05049aa8 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016a.eb @@ -26,6 +26,7 @@ dependencies = [ ('libxml2', '2.9.3'), # for XML ('GDAL', '2.0.2'), # for rgdal ('PROJ', '4.9.2'), # for rgdal + ('GMP', '6.1.0'), # for igraph ] name_tmpl = '%(name)s_%(version)s.tar.gz' @@ -439,6 +440,10 @@ exts_list = [ ('diveRsity', '1.9.89', ext_options), ('doSNOW', '1.0.14', ext_options), ('phangorn', '2.0.2', ext_options), + ('geepack', '1.2-0.1', ext_options), + ('lubridate', '1.5.6', ext_options), + ('biom', '0.3.12', ext_options), + ('pim', '2.0.0.2', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..004c178582be56e6841d2bfbf8f2992141629f95 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.3-foss-2016b.eb @@ -0,0 +1,449 @@ +name = 'R' +version = '3.2.3' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$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', '3.17-1', ext_options), + ('fastcluster', '1.1.16', ext_options), + ('chron', '2.3-47', ext_options), + ('data.table', '1.9.6', ext_options), + ('registry', '0.3', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doParallel', '1.0.10', ext_options), + ('gridBase', '0.4-7', ext_options), + ('NMF', '0.20.6', ext_options), + ('irlba', '2.0.0', ext_options), + ('igraph', '1.0.1', ext_options), + ('GeneNet', '1.2.13', ext_options), + ('ape', '3.4', ext_options), + ('htmltools', '0.3', ext_options), + ('RJSONIO', '1.3-0', ext_options), + ('caTools', '1.17.1', ext_options), + ('gplots', '2.17.0', ext_options), + ('ROCR', '1.0-7', ext_options), + ('httpuv', '1.3.3', ext_options), + ('R6', '2.1.1', ext_options), + ('jsonlite', '0.9.19', ext_options), + ('rjson', '0.2.15', ext_options), + ('shiny', '0.12.2', ext_options), + ('seqinr', '3.1-3', ext_options), + ('LearnBayes', '2.15', ext_options), + ('deldir', '0.1-9', ext_options), + ('spdep', '0.5-92', ext_options), + ('assertthat', '0.1', ext_options), + ('lazyeval', '0.1.10', ext_options), + ('dplyr', '0.4.3', ext_options), + ('adegenet', '2.0.0', ext_options), + ('rncl', '0.6.0', ext_options), + ('XML', '3.98-1.3', ext_options), + ('memoise', '0.2.1', ext_options), + ('crayon', '1.3.1', ext_options), + ('praise', '1.0.0', ext_options), + ('testthat', '0.11.0', ext_options), + ('yaml', '2.1.13', ext_options), + ('knitr', '1.11', ext_options), + ('rmarkdown', '0.9.2', ext_options), + ('curl', '0.9.4', ext_options), + ('httr', '1.0.0', ext_options), + ('reshape', '0.8.5', ext_options), + ('bold', '0.3.0', ext_options), + ('taxize', '0.7.0', ext_options), + ('tidyr', '0.3.1', ext_options), + ('uuid', '0.1-2', ext_options), + ('RNeXML', '2.0.5', ext_options), + ('phylobase', '0.8.0', ext_options), + ('adephylo', '1.1-6', ext_options), + ('animation', '2.4', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.5.8', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.5-2', ext_options), + ('dismo', '1.0-12', ext_options), + ('expm', '0.999-0', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.3', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.3-6', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.6', ext_options), + ('glmnet', '2.0-2', ext_options), + ('rgl', '0.95.1441', ext_options), + ('labdsv', '1.7-0', ext_options), + ('stabs', '0.5-1', ext_options), + ('mboost', '2.5-0', ext_options), + ('msm', '1.6', ext_options), + ('nor1mix', '1.2-1', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-8', ext_options), + ('polspline', '1.1.12', ext_options), + ('TH.data', '1.0-6', ext_options), + ('multcomp', '1.4-1', ext_options), + ('rms', '4.4-1', ext_options), + ('RWekajars', '3.7.12-1', ext_options), + ('RWeka', '0.4-24', ext_options), + ('slam', '0.1-32', 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-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..c7a11a43fc768dc70dd75baca5a4e4b0cd4a8cb2 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-bare.eb @@ -0,0 +1,27 @@ +name = 'R' +version = '3.2.3' +versionsuffix = '-bare' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] + +preconfigopts = 'BLAS_LIBS="$LIBBLAS" LAPACK_LIBS="$LIBLAPACK"' +configopts = "--with-lapack --with-blas --with-pic --enable-threads --with-x=no --enable-R-shlib" +configopts += " --with-recommended-packages=no" + +dependencies = [ + ('libreadline', '6.3'), + ('ncurses', '6.0'), + ('libpng', '1.6.21'), # for plotting in R + ('libjpeg-turbo', '1.4.2'), # for plottting in R + ('Java', '1.8.0_72', '', True), # Java bindings are built if Java is found, might as well provide it +] + +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb index 2fead5c7204c579706565f131e803492e1915bf5..1a886a00c96e84d063a6b2cbd8d934ee6c2540c4 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a-libX11-1.6.3.eb @@ -15,8 +15,6 @@ source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] preconfigopts = 'BLAS_LIBS="$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 @@ -39,6 +37,7 @@ dependencies = [ ('libxml2', '2.9.3'), # for XML ('GDAL', '2.0.2'), # for rgdal ('PROJ', '4.9.2'), # for rgdal + ('GMP', '6.1.0'), # for igraph ] name_tmpl = '%(name)s_%(version)s.tar.gz' @@ -451,6 +450,10 @@ exts_list = [ ('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.eb b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb index 91dc12b96403ac3e8230df209a2d11a6f8552e5d..7baa761be0155d372ce09e1a5326058207687901 100644 --- a/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb +++ b/easybuild/easyconfigs/r/R/R-3.2.3-intel-2016a.eb @@ -26,6 +26,7 @@ dependencies = [ ('libxml2', '2.9.3'), # for XML ('GDAL', '2.0.2'), # for rgdal ('PROJ', '4.9.2'), # for rgdal + ('GMP', '6.1.0'), # for igraph ] name_tmpl = '%(name)s_%(version)s.tar.gz' @@ -439,6 +440,10 @@ exts_list = [ ('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-3.3.1-foss-2016a.eb b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9e8837b860fcceaf6d9e1330131e07eac9b26116 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016a.eb @@ -0,0 +1,471 @@ +name = 'R' +version = '3.3.1' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +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'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), + ('zlib', '1.2.8'), + ('SQLite', '3.13.0'), + ('PCRE', '8.38'), + ('libpng', '1.6.23'), # for plotting in R + ('libjpeg-turbo', '1.5.0'), # for plottting in R + ('LibTIFF', '4.0.6'), + ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.5'), # for tcltk + ('Tk', '8.6.5'), # for tcltk + ('cURL', '7.49.1'), # for RCurl + ('libxml2', '2.9.4'), # for XML + ('GDAL', '2.1.0'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal + ('GMP', '6.1.1'), # for igraph + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + + +# !! order of packages is important !! +# packages updated on July 8th 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', '0.6-6', 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', '4.0', 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', '1.4', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.6', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-24', ext_options), + ('mime', '0.5', ext_options), + ('markdown', '0.7.7', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-9', ext_options), + ('mclust', '5.2', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.4', ext_options), + ('som', '0.3-5.1', ext_options), + ('SuppDists', '1.1-9.2', 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', '1.7-4', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-3', ext_options), + ('BH', '1.60.0-2', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', 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('phangorn', '2.0.4', ext_options), + ('geepack', '1.2-0.2', 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-3.3.1-foss-2016b.eb b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ea4614f23dd286995def2626768fed1c6bba17dc --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.3.1-foss-2016b.eb @@ -0,0 +1,471 @@ +name = 'R' +version = '3.3.1' + +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'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), + ('zlib', '1.2.8'), + ('SQLite', '3.13.0'), + ('PCRE', '8.38'), + ('libpng', '1.6.23'), # for plotting in R + ('libjpeg-turbo', '1.5.0'), # for plottting in R + ('LibTIFF', '4.0.6'), + ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.5'), # for tcltk + ('Tk', '8.6.5'), # for tcltk + ('cURL', '7.49.1'), # for RCurl + ('libxml2', '2.9.4'), # for XML + ('GDAL', '2.1.0'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal + ('GMP', '6.1.1'), # for igraph + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + + +# !! order of packages is important !! +# packages updated on July 8th 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', '0.6-6', 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', 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'0.8.2', ext_options), + ('sem', '3.1-7', 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', '1.3.4', ext_options), + ('diveRsity', '1.9.89', ext_options), + ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.0.4', ext_options), + ('geepack', '1.2-0.2', 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-3.3.1-intel-2016b.eb b/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..21471e59851c2251e434818f4d0c4d92ceed55bc --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.3.1-intel-2016b.eb @@ -0,0 +1,471 @@ +name = 'R' +version = '3.3.1' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', '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'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.2'), + ('zlib', '1.2.8'), + ('SQLite', '3.13.0'), + ('PCRE', '8.38'), + ('libpng', '1.6.23'), # for plotting in R + ('libjpeg-turbo', '1.5.0'), # for plottting in R + ('LibTIFF', '4.0.6'), + ('Java', '1.8.0_92', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.5'), # for tcltk + ('Tk', '8.6.5'), # for tcltk + ('cURL', '7.49.1'), # for RCurl + ('libxml2', '2.9.4'), # for XML + ('GDAL', '2.1.0'), # for rgdal + ('PROJ', '4.9.2'), # for rgdal + ('GMP', '6.1.1'), # for igraph + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +name_tmpl = '%(name)s_%(version)s.tar.gz' +ext_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': name_tmpl, +} + + +# !! order of packages is important !! +# packages updated on July 8th 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', '0.6-6', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-6', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), + ('bit', '1.1-12', ext_options), + ('filehash', '2.3', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '4.0', 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', '1.4', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.6', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-24', ext_options), + ('mime', '0.5', ext_options), + ('markdown', '0.7.7', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-9', ext_options), + ('mclust', '5.2', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.4', ext_options), + ('som', '0.3-5.1', ext_options), + ('SuppDists', '1.1-9.2', 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', '1.7-4', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-3', ext_options), + ('BH', '1.60.0-2', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.8', ext_options), + ('longitudinal', '1.1.12', ext_options), + ('backports', '1.0.3', ext_options), + ('checkmate', '1.8.1', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-6', ext_options), + ('digest', '0.6.9', ext_options), + ('fastmatch', '1.0-4', ext_options), + ('ffbase', '0.12.3', ext_options), + ('iterators', '1.0.8', ext_options), + ('maps', '3.1.0', 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', '1.1.1', ext_options), + ('magrittr', '1.5', ext_options), + ('stringr', '1.0.0', ext_options), + ('evaluate', '0.9', ext_options), + ('logspline', '2.1.9', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.9-0', ext_options), + ('plotrix', '3.6-2', ext_options), + ('randomForest', '4.6-12', ext_options), + ('scatterplot3d', '0.3-37', ext_options), + ('SparseM', '1.7', ext_options), + ('tripack', '1.3-7', ext_options), + ('irace', '1.07', ext_options), + ('rJava', '0.9-8', ext_options), + ('lattice', '0.20-33', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-28', ext_options), + ('Matrix', '1.2-6', ext_options), + ('png', '0.1-7', ext_options), + ('Rcpp', '0.12.5', ext_options), + ('RcppArmadillo', '0.7.100.3.1', ext_options), + ('plyr', '1.8.4', 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', '1.0-37', ext_options), + ('pls', '2.5-0', ext_options), + ('class', '7.3-14', ext_options), + ('e1071', '1.6-7', ext_options), + ('nnet', '7.3-12', ext_options), + ('nlme', '3.1-128', ext_options), + ('minqa', '1.2.4', ext_options), + ('RcppEigen', '0.3.2.8.1', ext_options), + ('MatrixModels', '0.4-1', ext_options), + ('quantreg', '5.26', ext_options), + ('mgcv', '1.8-12', ext_options), + ('colorspace', '1.2-6', ext_options), + ('robustbase', '0.92-6', ext_options), + ('sp', '1.2-3', ext_options), + ('zoo', '1.7-13', 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', '2.39-5', ext_options), + ('mice', '2.25', ext_options), + ('urca', '1.2-9', 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', '1.3-18', ext_options), + ('mixtools', '1.0.4', ext_options), + ('cluster', '2.0.4', 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', '0.4-1', ext_options), + ('foreign', '0.8-66', ext_options), + ('gam', '1.12', ext_options), + ('gamlss.data', '4.3-4', ext_options), + ('gamlss.dist', '4.3-6', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-15', ext_options), + ('xts', '0.9-7', ext_options), + ('TTR', '0.23-1', ext_options), + ('quantmod', '0.4-5', ext_options), + ('mnormt', '1.5-4', ext_options), + ('mvtnorm', '1.0-5', ext_options), + ('pcaPP', '1.9-60', ext_options), + ('numDeriv', '2014.2-1', ext_options), + ('lava', '1.4.3', 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', '1.1-0', ext_options), + ('spatial', '7.3-11', ext_options), + ('VGAM', '1.0-2', ext_options), + ('waveslim', '1.7.5', ext_options), + ('xtable', '1.8-2', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.13', ext_options), + ('tseriesChaos', '0.1-13', ext_options), + ('tseries', '0.10-35', ext_options), + ('fastICA', '1.2-0', ext_options), + ('R.methodsS3', '1.7.1', ext_options), + ('R.oo', '1.20.0', ext_options), + ('cgdsr', '1.2.5', ext_options), + ('R.utils', '2.3.0', ext_options), + ('R.matlab', '3.6.0', 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', '0.2.0', ext_options), + ('munsell', '0.4.3', ext_options), + ('labeling', '0.3', ext_options), + ('scales', '0.4.0', ext_options), + ('proto', '0.3-10', ext_options), + ('ggplot2', '2.1.0', ext_options), + ('gridExtra', '2.2.1', ext_options), + ('chron', '2.3-47', ext_options), + ('data.table', '1.9.6', ext_options), + ('Hmisc', '3.17-4', ext_options), + ('fastcluster', '1.1.20', ext_options), + ('registry', '0.3', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doParallel', '1.0.10', ext_options), + ('gridBase', '0.4-7', ext_options), + ('NMF', '0.20.6', ext_options), + ('irlba', '2.0.0', ext_options), + ('igraph', '1.0.1', ext_options), + ('GeneNet', '1.2.13', ext_options), + ('ape', '3.5', ext_options), + ('htmltools', '0.3.5', ext_options), + ('RJSONIO', '1.3-0', ext_options), + ('caTools', '1.17.1', ext_options), + ('gplots', '3.0.1', ext_options), + ('ROCR', '1.0-7', ext_options), + ('httpuv', '1.3.3', ext_options), + ('R6', '2.1.2', ext_options), + ('jsonlite', '1.0', ext_options), + ('rjson', '0.2.15', ext_options), + ('shiny', '0.13.2', ext_options), + ('seqinr', '3.2-0', ext_options), + ('LearnBayes', '2.15', ext_options), + ('deldir', '0.1-12', ext_options), + ('gmodels', '2.16.2', ext_options), + ('spdep', '0.6-5', ext_options), + ('assertthat', '0.1', ext_options), + ('lazyeval', '0.2.0', ext_options), + ('tibble', '1.1', ext_options), + ('dplyr', '0.5.0', ext_options), + ('vegan', '2.4-0', ext_options), + ('adegenet', '2.0.1', ext_options), + ('rncl', '0.6.0', ext_options), + ('XML', '3.98-1.4', ext_options), + ('memoise', '1.0.0', ext_options), + ('crayon', '1.3.2', ext_options), + ('praise', '1.0.0', ext_options), + ('testthat', '1.0.2', ext_options), + ('yaml', '2.1.13', ext_options), + ('knitr', '1.13', ext_options), + ('rmarkdown', '0.9.6', ext_options), + ('curl', '0.9.7', ext_options), + ('openssl', '0.9.4', ext_options), + ('httr', '1.2.1', ext_options), + ('reshape', '0.8.5', ext_options), + ('xml2', '1.0.0', ext_options), + ('bold', '0.3.5', ext_options), + ('rredlist', '0.1.0', ext_options), + ('rentrez', '1.0.2', ext_options), + ('rotl', '3.0.0', ext_options), + ('taxize', '0.7.8', ext_options), + ('tidyr', '0.5.1', ext_options), + ('uuid', '0.1-2', ext_options), + ('RNeXML', '2.0.7', ext_options), + ('phylobase', '0.8.2', ext_options), + ('adephylo', '1.1-6', ext_options), + ('animation', '2.4', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.5.19', dict(ext_options.items() + [('patches', ['bigmemory-4.5.19_icpc-wd308.patch'])])), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.5-8', ext_options), + ('dismo', '1.1-1', ext_options), + ('expm', '0.999-0', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.4', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.4-1', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.6', ext_options), + ('glmnet', '2.0-5', ext_options), + ('rgl', '0.95.1441', ext_options), + ('labdsv', '1.8-0', ext_options), + ('stabs', '0.5-1', ext_options), + ('modeltools', '0.2-21', ext_options), + ('strucchange', '1.5-1', ext_options), + ('TH.data', '1.0-7', ext_options), + ('multcomp', '1.4-5', ext_options), + ('coin', '1.1-2', ext_options), + ('party', '1.0-25', ext_options), + ('mboost', '2.6-0', ext_options), + ('msm', '1.6.1', ext_options), + ('nor1mix', '1.2-1', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-8', ext_options), + ('polspline', '1.1.12', ext_options), + ('rms', '4.5-0', ext_options), + ('RWekajars', '3.9.0-1', ext_options), + ('RWeka', '0.4-29', ext_options), + ('slam', '0.1-35', ext_options), + ('tm', '0.6-2', ext_options), + ('TraMineR', '1.8-12', ext_options), + ('chemometrics', '1.3.9', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-5', ext_options), + ('statmod', '1.4.24', 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', '1.2.0', ext_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('matrixStats', '0.50.2', 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', '1.1-12', ext_options), + ('pbkrtest', '0.4-6', ext_options), + ('car', '2.1-2', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.33', ext_options), + ('flexclust', '1.3-4', ext_options), + ('flexmix', '2.3-13', ext_options), + ('prabclus', '2.2-6', ext_options), + ('diptest', '0.75-7', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-10', ext_options), + ('BiasedUrn', '1.07', ext_options), + ('TeachingDemos', '2.10', ext_options), + ('kohonen', '2.0.19', ext_options), + ('base64', '2.0', ext_options), + ('doRNG', '1.6', ext_options), + ('nleqslv', '3.0.2', 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', '1.6.17', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('forecast', '7.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), + ('fma', '2.2', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), + ('maptools', '0.8-39', ext_options), + ('deldir', '0.1-12', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.5-6', ext_options), + ('goftest', '1.0-3', ext_options), + ('spatstat', '1.46-1', ext_options), + ('rgdal', '1.1-10', ext_options), + ('gdalUtils', '2.0.1.7', ext_options), + ('pracma', '1.9.3', ext_options), + ('RCurl', '1.95-4.8', ext_options), + ('bio3d', '2.2-4', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.4', ext_options), + ('cvAUC', '1.1.0', ext_options), + ('SuperLearner', '2.0-19', ext_options), + ('lpSolve', '5.6.13', ext_options), + ('mediation', '4.4.5', ext_options), + ('caret', '6.0-70', ext_options), + ('adabag', '4.1', ext_options), + ('parallelMap', '1.3', ext_options), + ('ParamHelpers', '1.7', ext_options), + ('ggvis', '0.4.2', ext_options), + ('mlr', '2.8', 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', '0.13', ext_options), + ('tensorA', '0.36', ext_options), + ('EasyABC', '1.5', ext_options), + ('shape', '1.4.2', ext_options), + ('whisker', '0.3-2', ext_options), + ('rstudioapi', '0.6', ext_options), + ('roxygen2', '5.0.1', ext_options), + ('git2r', '0.15.0', ext_options), + ('rversions', '1.0.2', ext_options), + ('withr', '1.0.2', ext_options), + ('devtools', '1.12.0', 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', '1.2-3', 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', dict(ext_options.items() + [('patches', [('multicool-0.1-9_icpc-wd308.patch', 1)])])), + ('ks', '1.10.4', ext_options), + ('logcondens', '2.1.4', ext_options), + ('Iso', '0.0-17', ext_options), + ('penalized', '0.9-47', ext_options), + ('clusterRepro', '0.5-1.1', ext_options), + ('randomForestSRC', '2.2.0', ext_options), + ('sm', '2.2-5.4', ext_options), + ('psych', '1.6.6', 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', '1.0.1', ext_options), + ('DiagrammeR', '0.8.2', ext_options), + ('sem', '3.1-7', ext_options), + ('jpeg', '0.1-8', ext_options), + ('sna', '2.3-2', ext_options), + ('glasso', '1.8', dict(ext_options.items() + [('patches', [('glasso-1.8-ifort-no-fixed.patch', 1)])])), + ('huge', '1.2.7', ext_options), + ('d3Network', '0.5.2.1', ext_options), + ('ggm', '2.3', ext_options), + ('qgraph', '1.3.4', ext_options), + ('diveRsity', '1.9.89', ext_options), + ('doSNOW', '1.0.14', ext_options), + ('phangorn', '2.0.4', ext_options), + ('geepack', '1.2-0.2', 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/bigmemory-4.5.19_icpc-wd308.patch b/easybuild/easyconfigs/r/R/bigmemory-4.5.19_icpc-wd308.patch new file mode 100644 index 0000000000000000000000000000000000000000..dedc605c24bec66fdb05b3a1e53a5e4ea0152dfd --- /dev/null +++ b/easybuild/easyconfigs/r/R/bigmemory-4.5.19_icpc-wd308.patch @@ -0,0 +1,11 @@ +--- bigmemory/MD5.orig 2016-03-28 18:59:53.000000000 +0200 ++++ bigmemory/MD5 2016-07-09 11:10:14.293902207 +0200 +@@ -7,7 +7,7 @@ + 08d8ac748bb99e6cd73cbc851ba24e6f *R/zzz.R + 3d01d7e508b363c81587088af3221fa7 *build/vignette.rds + cff4b0071fbcb3165aaf35c802b46b34 *cleanup +-eb219c5b9917fe3022b63e0296e61953 *configure ++04b3ce27c656a79eded3b3e21bdaa97b *configure + fc5c8f75e424213609b3e3cd9b57f5bf *configure.win + 0cd9765e8adee62083d32a17a6b9aa07 *inst/CITATION + f883e7fbbec7e35f5142805cd80548cf *inst/doc/Overview.R diff --git a/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..b11e63c0268f5a196b848615de2df32315ae26d1 --- /dev/null +++ b/easybuild/easyconfigs/r/RASPA2/RASPA2-2.0.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'RASPA2' +version = '2.0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/numat/RASPA2' +description = """A general purpose classical simulation package that can be used for the simulation of + molecules in gases, fluids, zeolites, aluminosilicates, + metal-organic frameworks, carbon nanotubes and external fields.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://pypi.python.org/packages/source/r/RASPA2/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), +] + +# remove stub loader for libraspa2.so, it causes problems like "invalid ELF header" and is not really needed anyway +postinstallcmds = ["rm %(installdir)s/lib/python*/site-packages/*.egg/RASPA2/simulations/lib/libraspa2.py*"] + +sanity_check_paths = { + 'files': ['bin/raspa-dir', 'bin/simulate'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +options = {'modulename': 'RASPA2'} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-foss-2016a-hybrid-avx2.eb b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-foss-2016a-hybrid-avx2.eb new file mode 100644 index 0000000000000000000000000000000000000000..d8510427bfe236292634565d794e19931b127afe --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML/RAxML-8.2.4-foss-2016a-hybrid-avx2.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'RAxML' +version = '8.2.4' +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/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/RMBlast/RMBlast-2.2.28-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.2.28-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..d6dced35466bc2f64e6c7cc70252fcf4dbb5a485 --- /dev/null +++ b/easybuild/easyconfigs/r/RMBlast/RMBlast-2.2.28-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'RMBlast' +version = '2.2.28' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://www.repeatmasker.org/RMBlast.html' +description = """RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between + this distribution and the NCBI distribution is the addition of a new program 'rmblastn' for use with RepeatMasker and + RepeatModeler.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/%(version)s'] +sources = ['ncbi-rmblastn-%(version)s-src.tar.gz'] +checksums = [('md5', 'fb5f4e2e02ffcb1b17af2e9f206c5c22')] + +dependencies = [ + ('Boost', '1.58.0', versionsuffix), +] + +configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' + +sanity_check_paths = { + 'files': ['bin/blastp', 'bin/blastn', 'bin/deltablast', 'bin/rmblastn'], + 'dirs': ['lib', 'bin'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..e025c77b0277d5835714260a9d4b8acfd594c77e --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.13-ictce-5.5.0.eb @@ -0,0 +1,39 @@ +name = 'ROOT' +version = 'v5.34.13' + +homepage = 'http://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s_%(version)s.source.tar.gz'] +source_urls = ['ftp://root.cern.ch/root/'] +patches = [ + 'configure_FftwFromMkl_28.patch', + 'ROOT-v5_recent-ifort.patch', +] + +python = 'Python' +pyver = '2.7.6' + +dependencies = [ + ('GSL', '1.16'), + ('libxml2', '2.9.1', '-%s-%s' % (python, pyver)), + (python, pyver), +] + +# architecture +arch = 'linuxx8664icc' + +# disable features +configopts = ' --disable-xft --disable-x11 --disable-xrootd --disable-mysql' +# enable features +configopts += ' --enable-unuran --enable-table --enable-explicitlink --enable-minuit2 --enable-roofit' +configopts += ' --with-gsl-incdir=$EBROOTGSL/include/gsl --with-gsl-libdir=$EBROOTGSL/lib' +configopts += ' --with-fftw3-incdir=$MKLROOT/mkl/include/fftw --with-fftw3-libdir=$MKLROOT/mkl/lib/intel64' +configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' +configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..81755cd85648e0302e3b4db8db8bd074be690fda --- /dev/null +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v6.08.02-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'ROOT' +version = 'v6.08.02' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://root.cern.ch/drupal/' +description = """The ROOT system provides a set of OO frameworks with all the functionality + needed to handle and analyze large amounts of data in a very efficient way.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = ['%(namelower)s_%(version)s.source.tar.gz'] +source_urls = ['https://root.cern.ch/download/'] + +builddependencies = [ + ('CMake', '3.4.3'), +] + +dependencies = [ + ('GSL', '2.1'), + ('libxml2', '2.9.3'), + ('PCRE', '8.38'), + ('CFITSIO', '3.38'), + ('freetype', '2.6.3'), + ('Python', '2.7.11'), + ('zlib', '1.2.8'), + ('libX11', '1.6.3'), + ('libXft', '2.3.2', '-freetype-2.6.3'), + ('libXpm', '3.5.11'), + ('libXext', '1.3.3'), + ('Mesa', '11.2.1'), + ('libGLU', '9.0.0', '-Mesa-11.2.1'), + ('GL2PS', '1.3.9', '-Mesa-11.2.1'), +] + +separate_build_dir = True + +configopts = '-Dxrootd=OFF -Dmysql=OFF -Dkrb5=OFF -Dodbc=OFF ' +configopts += '-Doracle=OFF -Dpgsql=OFF -Dqt=OFF -Dsqlite=OFF ' +configopts += '-Dcxx14=ON ' +configopts += '-Dunuran=ON -Dtable=ON -Dexplicitlink=ON -Dminuit2=ON ' + +moduleclass = 'data' 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/RSEM/RSEM-1.3.0-foss-2016b.eb b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.0-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..d01f2f908948cd3c54b3e29a9436d6fbddecda34 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.0-foss-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'RSEM' +version = '1.3.0' + +homepage = 'http://deweylab.github.io/RSEM/' +description = """RNA-Seq by Expectation-Maximization""" + +toolchain = {'name': 'foss', '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'), + ('Perl', '5.24.0'), + ('R', '3.3.1'), +] + +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/RSEM/RSEM-1.3.0_makefiles.patch b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.0_makefiles.patch new file mode 100644 index 0000000000000000000000000000000000000000..4edfe6016556e3a8321c07b9933c8fe1e3c0df56 --- /dev/null +++ b/easybuild/easyconfigs/r/RSEM/RSEM-1.3.0_makefiles.patch @@ -0,0 +1,61 @@ +# Remove preset CXX and CPPFLAGS for each makefile, such that it uses the ones defined by EB. +# Author: Bob Dröge - Rijksuniversiteit Groningen (RUG) +--- RSEM-1.2.30/Makefile 2016-04-20 23:59:26.000000000 +0200 ++++ RSEM-1.2.30.new/Makefile 2016-05-13 16:25:04.000000000 +0200 +@@ -11,12 +11,12 @@ + BOOST = . + + # Compilation variables +-CXX = g++ +-CXXFLAGS = -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) +-CPPFLAGS = ++#CXX = g++ ++CXXFLAGS += -std=gnu++98 -Wall -I. -I$(BOOST) -I$(SAMTOOLS)/$(HTSLIB) ++#CPPFLAGS = + +-LDFLAGS = +-LDLIBS = ++#LDFLAGS = ++#LDLIBS = + + # Installation variables + INSTALL = install +--- RSEM-1.2.30/samtools-1.3/Makefile 2016-04-20 23:59:26.000000000 +0200 ++++ RSEM-1.2.30.new/samtools-1.3/Makefile 2016-05-13 16:25:42.000000000 +0200 +@@ -21,10 +21,10 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-CPPFLAGS = +-CFLAGS = -g -Wall -O2 +-LDFLAGS = ++#CC = gcc ++#CPPFLAGS = ++#CFLAGS = -g -Wall -O2 ++#LDFLAGS = + LIBS = + + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE +--- RSEM-1.2.30/samtools-1.3/htslib-1.3/Makefile 2016-04-20 23:59:26.000000000 +0200 ++++ RSEM-1.2.30.new/samtools-1.3/htslib-1.3/Makefile 2016-05-13 16:26:24.000000000 +0200 +@@ -22,15 +22,15 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc ++#CC = gcc + AR = ar + RANLIB = ranlib + +-CPPFLAGS = ++#CPPFLAGS = + # TODO: probably update cram code to make it compile cleanly with -Wc++-compat +-CFLAGS = -g -Wall -O2 ++#CFLAGS = -g -Wall -O2 + EXTRA_CFLAGS_PIC = -fpic +-LDFLAGS = ++#LDFLAGS = + LIBS = + + # For now these don't work too well as samtools also needs to know to diff --git a/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.4-foss-2016b-Python-2.7.12-R-3.3.1.eb b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.4-foss-2016b-Python-2.7.12-R-3.3.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..f122fed527159c2320b52af4ac2083a6bcb0a355 --- /dev/null +++ b/easybuild/easyconfigs/r/RSeQC/RSeQC-2.6.4-foss-2016b-Python-2.7.12-R-3.3.1.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman +# The Francis Crick Institute + +easyblock = 'PythonPackage' + +name = 'RSeQC' +version = '2.6.4' +basepyversionsuffix = '-Python-%(pyver)s' +versionsuffix = basepyversionsuffix + '-R-%(rver)s' + +homepage = 'http://rseqc.sourceforge.net/' +description = """RSeQC provides a number of useful modules that can + comprehensively evaluate high throughput sequence data especially RNA-seq + data. Some basic modules quickly inspect sequence quality, nucleotide + composition bias, PCR bias and GC bias, while RNA-seq specific modules + evaluate sequencing saturation, mapped reads distribution, coverage + uniformity, strand specificity, transcript level RNA integrity etc.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +dependencies = [ + ('R', '3.3.1'), + ('Python', '2.7.12'), + ('Pysam', '0.9.1.4', basepyversionsuffix), +] + +runtest = "python setup.py test" + +sanity_check_paths = { + 'files': ['bin/bam_stat.py', 'bin/overlay_bigwig.py', 'bin/split_paired_bam.py'], + 'dirs': ["bin", "lib"] +} + +options = {'modulename': 'qcmodule'} + +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/Ruby/Ruby-2.3.3.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..6c9287f577d000319ffc8dc3002ce124f79e0215 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.3.3.eb @@ -0,0 +1,64 @@ +# 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 = '2.3.3' + +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': 'dummy', 'version': 'dummy'} + +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', '1.9.14', ext_options), + ('childprocess', '0.5.9', ext_options), + ('json', '2.0.2', ext_options), + ('cabin', '0.9.0', ext_options), + ('backports', '3.6.8', ext_options), + ('arr-pm', '0.0.10', ext_options), + ('clamp', '1.1.1', ext_options), + ('multipart-post', '2.0.0', ext_options), + ('faraday', '0.10.0', ext_options), + ('faraday_middleware', '0.10.1', 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', '1.12.1', ext_options), + ('public_suffix', '2.0.4', ext_options), + ('addressable', '2.4.0', ext_options), + ('gh', '0.15.0', ext_options), + ('launchy', '2.4.3', ext_options), + ('ethon', '0.10.1', ext_options), + ('typhoeus', '0.6.9', ext_options), + ('websocket', '1.2.3', ext_options), + ('pusher-client', '0.6.2', ext_options), + ('diff-lcs', '1.2.5', ext_options), + ('rspec-support', '3.5.0', ext_options), + ('rspec-mocks', '3.5.0', ext_options), + ('rspec-expectations', '3.5.0', ext_options), + ('rspec-core', '3.5.4', ext_options), + ('rspec', '3.5.0', ext_options), + ('rack', '1.6.5', ext_options), + ('rack-protection', '1.5.3', ext_options), + ('tilt', '2.0.5', 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/rainbow/rainbow-2.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb index c431cc2a4f1f63a6eb90a4db86b69cb47260f1d3..e5d10e806149d54f1907953ff14f3d3142c6147b 100644 --- a/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/rainbow/rainbow-2.0.4-goolf-1.4.10.eb @@ -19,7 +19,7 @@ sources = ['%(name)s_%(version)s.tar.gz'] buildopts = ' CC=$CC' files_to_copy = [(['rainbow', 'ezmsim', 'rbasm', 'select_sec_rbcontig.pl', - 'select_best_rbcontig_plus_read1.pl', 'select_sec_rbcontig.pl', 'select_all_rbcontig.pl'], 'bin')] + 'select_best_rbcontig_plus_read1.pl', 'select_sec_rbcontig.pl', 'select_all_rbcontig.pl'], 'bin')] parallel = 1 diff --git a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb index d480848616fe72d362a6cf60f364809735fbf69f..b2957244c9b0348a77d66f1655d7579e8b6fc301 100644 --- a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb +++ b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-foss-2016a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] +builddependencies = [('xorg-macros', '1.19.0')] + sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['randr.h', 'randrproto.h']], 'dirs': [], diff --git a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb index 563fbfcbf25b676ddf3cb8ee1287f7f415d87d4e..0b878f0ec4880699ab20348335d2c3ba432e66cb 100644 --- a/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb +++ b/easybuild/easyconfigs/r/randrproto/randrproto-1.5.0-intel-2016a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] +builddependencies = [('xorg-macros', '1.19.0')] + sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in ['randr.h', 'randrproto.h']], 'dirs': [], diff --git a/easybuild/easyconfigs/r/requests/requests-2.10.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/r/requests/requests-2.10.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..6eb676993b882725b397203b085c4a5c3279472d --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.10.0-foss-2016a-Python-2.7.11.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', '2.7.11'), +] + +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-2.10.0-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/r/rhdf5/rhdf5-2.16.0-intel-2016a-R-3.2.3.eb b/easybuild/easyconfigs/r/rhdf5/rhdf5-2.16.0-intel-2016a-R-3.2.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..f7d64d2b43242ce64b89bb932be7b5d6fac31cc0 --- /dev/null +++ b/easybuild/easyconfigs/r/rhdf5/rhdf5-2.16.0-intel-2016a-R-3.2.3.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'rhdf5' +version = '2.16.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://bioconductor.org/packages/release/bioc/html/rhdf5.html' +description = "This R/Bioconductor package provides an interface between HDF5 and R." + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + 'http://bioconductor.org/packages/release/bioc/src/contrib/', + 'http://bioconductor.org/packages/3.3/bioc/src/contrib/', +] +sources = ['rhdf5_%(version)s.tar.gz'] + +dependencies = [ + ('R', '3.2.3'), + ('zlibbioc', '1.18.0', versionsuffix), + ('HDF5', '1.8.16'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb b/easybuild/easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..28ef2c7ef618fabc019df802f07457730ee98cd9 --- /dev/null +++ b/easybuild/easyconfigs/s/S.A.G.E./S.A.G.E.-6.3.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'S.A.G.E.' +version = '6.3' + +homepage = 'https://code.google.com/archive/p/opensage/' +description = """ S.A.G.E. (Statistical Analysis for Genetic +Epidemiology) is free software package containing programs for +use in the genetic analysis of family, pedigree and individual data.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/opensage/'] +sources = ['%(name)sv%(version)s_Linux_x86_64.tar.gz'] + +sanity_check_paths = { + 'files': ["bin/freq", "bin/ageon", "bin/segreg"], + 'dirs': ["data_files", "documentaion"] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2016a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..94699dd9a051375bd94921317a8243eb62090935 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2016a.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': '2016a'} +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-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/SAMtools/SAMtools-1.3.1-intel-2016b.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..068f81d41af5ae9c447fb52545faf43087db8178 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.3.1-intel-2016b.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:: Robert Schmidt , Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# Modified by: Adam Huffman +# The Francis Crick Institute +## +name = 'SAMtools' +version = '1.3.1' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] + +# Patch Makefile to link against zlib provided by EB +patches = ['SAMtools-%(version)s_Makefile.patch'] + +dependencies = [ + ('ncurses', '6.0'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..b9287e35c21c7a68bbdb1f05ed8c80e7f7d7aeb6 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOOP/SCOOP-0.6.2-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'SCOOP' +version = '0.6.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://pyscoop.org' +description = """SCOOP (Scalable COncurrent Operations in Python) is a distributed task module + allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/soravux/scoop/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.12'), # python with builtin argparse + ('Greenlet', '0.4.11', versionsuffix), + ('PyZMQ', '16.0.2', versionsuffix + '-zmq4'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' 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-GCC-4.9.3-2.25.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCC-4.9.3-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..212dfd1d759aa2babb6fef13c6dc9a71626c4fc5 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-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 = '3.13.0' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCC', 'version': '4.9.3-2.25'} + +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-3.13.0-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..c8632b48d572c276b996aba0b56456a7b0c36ec9 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-GCC-5.4.0-2.26.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': 'GCC', 'version': '5.4.0-2.26'} + +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-3.13.0-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-3.13.0-foss-2016a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..ec5703f27d295215cc4c2feabe8bbc54f2fc6861 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016a.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': '2016a'} + +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-3.13.0-foss-2016b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..1c9912537cd18e464e190ab516d13458d1f91a72 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-foss-2016b.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: 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': '2016b'} + +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-3.13.0-intel-2016b.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e6b03228911fc5aded438146b45172caa9daa78c --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.13.0-intel-2016b.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: 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': 'intel', 'version': '2016b'} + +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-3.14.1-GCCcore-4.9.3.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..d38cf611011d8eaaaed9f20aee025c8ad36f397e --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.14.1-GCCcore-4.9.3.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.14.1' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +# eg. http://www.sqlite.org/2014/sqlite-autoconf-3080600.tar.gz +source_urls = ['http://www.sqlite.org/2016/'] +version_str = '%%(version_major)s%s00' % ''.join('%02d' % int(x) for x in version.split('.')[1:]) +sources = ['sqlite-autoconf-%s.tar.gz' % version_str] + +builddependencies = [ + ('binutils', '2.25'), +] + +dependencies = [ + ('libreadline', '6.3'), + ('Tcl', '8.6.6'), +] + +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-3.8.8.1-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-CrayGNU-2015.11.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..429cfc37d81766ab26d3097b26b8591d0f7c5baf --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2015.11.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': 'CrayGNU', 'version': '2015.11'} + +# 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-CrayGNU-2016.03.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..51941069b6bf227a4229e958a20022bc753645f1 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.9.2-CrayGNU-2016.03.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': 'CrayGNU', 'version': '2016.03'} + +# 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-2016.07.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 new file mode 100644 index 0000000000000000000000000000000000000000..f3009cafcc3dcecf3dd7c29b72f93d4f6b4fc386 --- /dev/null +++ b/easybuild/easyconfigs/s/STAMP/STAMP-1.2-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'CmdCp' + +name = 'STAMP' +version = '1.2' + +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', '2.1')] + +start_dir = 'src' + +cmds_map = [('.*', "$CXX $CXXFLAGS -o stamp *.cpp $LDFLAGS -lm -lgsl -lgslcblas")] + +files_to_copy = [(['stamp'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/stamp'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016a.eb b/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4eb03dff0151993df6eef1c7149c03c7f61f97d9 --- /dev/null +++ b/easybuild/easyconfigs/s/STAMP/STAMP-1.3-intel-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'CmdCp' + +name = 'STAMP' +version = '1.3' + +homepage = 'http://www.benoslab.pitt.edu/stamp/' +description = """STAMP is a tool for characterizing similarities between transcription factor binding motifs""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/seqcode/stamp/archive/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [('GSL', '2.2.1')] + +start_dir = 'src' + +cmds_map = [('.*', "$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 $LDFLAGS -lm -lgsl -lgslcblas")] + +files_to_copy = [(['stamp'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/stamp'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..769bc0a35c7132d8fb88b49f83bd890e4f13e743 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.5.2a-foss-2016a.eb @@ -0,0 +1,49 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.5.2a' + +homepage = 'https://github.com/alexdobin/STAR' +description = """ STAR aligns RNA-seq reads to a reference genome using + uncompressed suffix arrays. """ + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/alexdobin/STAR/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('zlib', '1.2.8'), +] + +start_dir = 'source' + +buildopts = ' STAR && make STARlong' + +parallel = 1 + +files_to_copy = [ + (["source/STAR", "source/STARlong"], "bin"), + "CHANGES.md", + "doc", + "extras", + "LICENSE", + "README.md", + "RELEASEnotes.md" +] + +sanity_check_paths = { + 'files': ["bin/STAR", "bin/STARlong"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb index 79841574824ac44256ab1cc50406beface9a6f6a..44cf8f84ff4a407078896fbbcee923a88ec5bc8f 100644 --- a/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb +++ b/easybuild/easyconfigs/s/STREAM/STREAM-5.10-intel-2015a.eb @@ -22,13 +22,15 @@ cmds_str = "$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/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb b/easybuild/easyconfigs/s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..15d674493593396e9eade81b57bdac12757acf40 --- /dev/null +++ b/easybuild/easyconfigs/s/SUMACLUST/SUMACLUST-1.0.20-foss-2016a.eb @@ -0,0 +1,27 @@ +# Author: Pablo Escobar Lopez; Wiktor Jurkowski +# Swiss Institute of Bioinformatics (SIB), Biozentrum - University of Basel +# Babraham Institute, UK + +easyblock = 'MakeCp' + +name = 'SUMACLUST' +version = '1.0.20' + +homepage = "http://metabarcoding.org/sumatra" +description = """SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://git.metabarcoding.org/obitools/sumaclust/uploads/69f757c42f2cd45212c587e87c75a00f/'] +sources=['%(namelower)s_v%(version)s.tar.gz'] + +prebuildopts = 'make clean &&' + +files_to_copy = [(['sumaclust'],'bin'),'sumaclust_user_manual.pdf'] + +sanity_check_paths = { + 'files': ['bin/sumaclust', 'sumaclust_user_manual.pdf'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb b/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6ad5e46d49ceaf0caa6a5983a4906de00ca2cc96 --- /dev/null +++ b/easybuild/easyconfigs/s/SUMATRA/SUMATRA-1.0.20-foss-2016a.eb @@ -0,0 +1,27 @@ +# Author: Pablo Escobar Lopez; Wiktor Jurkowski +# Swiss Institute of Bioinformatics (SIB), Biozentrum - University of Basel +# Babraham Institute, UK + +easyblock = 'MakeCp' + +name = 'SUMATRA' +version = '1.0.20' + +homepage = "http://metabarcoding.org/sumatra" +description = """SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://git.metabarcoding.org/obitools/sumatra/uploads/251020bbbd6c6595cb9fce6077e29952/'] +sources=['%(namelower)s_v%(version)s.tar.gz'] + +prebuildopts = 'make clean &&' + +files_to_copy = [(['sumatra'],'bin'),'sumatra_user_manual.pdf'] + +sanity_check_paths = { + 'files': ['bin/sumatra', 'sumatra_user_manual.pdf'], + 'dirs': [], +} + +moduleclass = 'bio' 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-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.10-foss-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..1c14fe070d3ba67dbd53a57cc204ab19908f24ff --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.10-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,20 @@ +name = 'SWIG' +version = '3.0.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('PCRE', '8.39'), +] + +moduleclass = 'devel' 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/SWIG/SWIG-3.0.10-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.10-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..fed2dcb3c3e8e192be41e49543029de9a363fdb2 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.10-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,20 @@ +name = 'SWIG' +version = '3.0.10' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '2.7.12'), + ('PCRE', '8.38'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..c200cf4e19081cdbd7f7c248640df3b5986fce98 --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.8-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,20 @@ +name = 'SWIG' +version = '3.0.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.swig.org/' +description = """SWIG is a software development tool that connects programs written in C and C++ with + a variety of high-level programming languages.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), + ('PCRE', '8.38'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.06-OpenBLAS-0.2.18-LAPACK-3.6.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.06-OpenBLAS-0.2.18-LAPACK-3.6.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..ba5f361de58731008e6f3fd03db1aaf46d5209f9 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.06-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': 'gompi', 'version': '2016.06'} +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', '5.4.0-2.26'))] + +# parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016.07-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-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016b-OpenBLAS-0.2.18-LAPACK-3.6.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..114c917ec84adc5f079dc862b8f2e1fab99b0e6b --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2016b-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': '2016b'} +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, ('GCC', '5.4.0-2.26'))] + +# 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/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb index 267282ee9720e542c2a63de23041e8c7d863ad3e..3fb71e8f46ba5bd4fa042dec341be9fd0b09fae2 100644 --- a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-foss-2016a-Python-2.7.11.eb @@ -11,7 +11,7 @@ description = """ScientificPython is a collection of Python modules for scientif toolchain = {'name': 'foss', 'version': '2016a'} -source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] sources = [SOURCE_TAR_GZ] dependencies = [ diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..90ba25242907d6c1261e81fdcdc8c18adee07e94 --- /dev/null +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'ScientificPython' +version = '2.9.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://sourcesup.cru.fr/projects/scientific-py/' +description = """ScientificPython is a collection of Python modules for scientific computing. + It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, + and parallelization.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://sourcesup.cru.fr/frs/download.php/file/4570'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + # older version of numpy than the one included in Python module required + # cfr. https://bitbucket.org/khinsen/scientificpython/issue/13/numpy-19-has-dropped-support-for + ('numpy', '1.8.2', versionsuffix), +] + +options = {'modulename': 'Scientific'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Scientific'], +} + +moduleclass = 'math' 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..1b943d40629f80f642a5024e671bc59bf09951cd --- /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/Seqmagick/Seqmagick-0.6.1-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.6.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..ae2145d3dff09f4d8df0f69c9f8fcbbe50029026 --- /dev/null +++ b/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.6.1-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2016 University of Geneva Switzerland +# Authors:: Yann Sagon +# License:: MIT/GPL +# +## +easyblock = "PythonPackage" + +name = 'Seqmagick' +version = '0.6.1' + +python = 'Python' +pyver = '2.7.11' +versionsuffix = '-%s-%s' % (python, pyver) + +homepage = 'https://fhcrc.github.io/seqmagick/' +description = """We often have to convert between sequence formats and do little tasks on them, and it's not worth + writing scripts for that. Seqmagick is a kickass little utility built in the spirit of imagemagick to expose the + file format conversion in Biopython in a convenient way. Instead of having a big mess of scripts, there is one that + takes arguments. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://files.pythonhosted.org/packages/source/s/seqmagick/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +dependencies = [ + ('Biopython', '1.65', versionsuffix) +] + +sanity_check_paths = { + 'files': ['bin/seqmagick'], + 'dirs': [] +} + +options = {'modulename': 'Bio'} + +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/SortMeRNA/SortMeRNA-2.1-foss-2016a.eb b/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f15b6559acfcb79fd47bd0c55b0a5a2981cea879 --- /dev/null +++ b/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1-foss-2016a.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +easyblock = 'ConfigureMake' + +name = 'SortMeRNA' +version = '2.1' + +homepage = 'http://bioinfo.lifl.fr/RNA/sortmerna/' +description = """ +SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://github.com/biocore/sortmerna/archive/'] +sources = ['%(version)s.tar.gz'] + +# Patch for double includes of header files in Makefile.in +patches=['SortMeRNA-%(version)s_Makefile.in.patch'] + +sanity_check_paths={ + 'files': ['bin/indexdb_rna','bin/sortmerna'], + 'dirs': ['include','sortmerna'] + +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1_Makefile.in.patch b/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1_Makefile.in.patch new file mode 100644 index 0000000000000000000000000000000000000000..14b80c8523dd7da3debefde957681ae8120cc9a1 --- /dev/null +++ b/easybuild/easyconfigs/s/SortMeRNA/SortMeRNA-2.1_Makefile.in.patch @@ -0,0 +1,13 @@ +# Remove double includes of header files in Makefile.in +# Author: Fokke Dijkstra - University of Groningen +--- Makefile.in 2014-10-30 23:24:56.000000000 +0100 ++++ Makefile.in 2015-03-09 15:42:14.213220762 +0100 +@@ -340,7 +340,7 @@ + top_builddir = @top_builddir@ + top_srcdir = @top_srcdir@ + include_HEADERS = ./alp/gumbel_params.hpp ./alp/njn_dynprogprob.hpp ./alp/njn_dynprogproblim.hpp ./alp/njn_dynprogprobproto.hpp ./alp/njn_ioutil.hpp ./alp/njn_localmaxstat.hpp ./alp/njn_localmaxstatmatrix.hpp ./alp/njn_localmaxstatutil.hpp ./alp/njn_random.hpp ./alp/sls_alp.hpp ./alp/sls_alp_data.hpp ./alp/sls_alp_regression.hpp ./alp/sls_alp_sim.hpp ./alp/sls_pvalues.hpp \ +- ./alp/gumbel_params.hpp ./alp/njn_approx.hpp ./alp/njn_doubletype.hpp ./alp/njn_dynprogprob.hpp ./alp/njn_dynprogproblim.hpp ./alp/njn_dynprogprobproto.hpp ./alp/njn_function.hpp ./alp/njn_integer.hpp ./alp/njn_ioutil.hpp ./alp/njn_localmaxstat.hpp ./alp/njn_localmaxstatmatrix.hpp ./alp/njn_localmaxstatutil.hpp ./alp/njn_matrix.hpp ./alp/njn_memutil.hpp ./alp/njn_random.hpp ./alp/njn_root.hpp ./alp/njn_stringutil.hpp ./alp/njn_uniform.hpp ./alp/njn_vector.hpp ./alp/sls_alp.hpp ./alp/sls_alp_data.hpp ./alp/sls_alp_regression.hpp ./alp/sls_alp_sim.hpp ./alp/sls_normal_distr_array.hpp ./alp/sls_pvalues.hpp \ ++ ./alp/njn_approx.hpp ./alp/njn_doubletype.hpp ./alp/njn_function.hpp ./alp/njn_integer.hpp ./alp/njn_matrix.hpp ./alp/njn_memutil.hpp ./alp/njn_root.hpp ./alp/njn_stringutil.hpp ./alp/njn_uniform.hpp ./alp/njn_vector.hpp ./alp/sls_normal_distr_array.hpp \ + ./cmph/bdz.h ./cmph/bdz_ph.h ./cmph/bdz_structs.h ./cmph/bdz_structs_ph.h ./cmph/bitbool.h ./cmph/bmz.h ./cmph/bmz8.h ./cmph/bmz8_structs.h ./cmph/bmz_structs.h ./cmph/brz.h ./cmph/brz_structs.h ./cmph/buffer_entry.h ./cmph/buffer_manager.h ./cmph/chd.h ./cmph/chd_ph.h ./cmph/chd_structs.h ./cmph/chd_structs_ph.h ./cmph/chm.h ./cmph/chm_structs.h ./cmph/cmph.h ./cmph/cmph_structs.h ./cmph/cmph_time.h ./cmph/cmph_types.h ./cmph/compressed_rank.h ./cmph/compressed_seq.h ./cmph/debug.h ./cmph/fch.h ./cmph/fch_buckets.h ./cmph/fch_structs.h ./cmph/graph.h ./cmph/hash.h ./cmph/hash_state.h ./cmph/jenkins_hash.h ./cmph/miller_rabin.h ./cmph/select.h ./cmph/select_lookup_tables.h ./cmph/vqueue.h ./cmph/vstack.h \ + ./include/bitvector.hpp ./include/common.hpp ./include/indexdb.hpp ./include/loadgenome.hpp ./include/paralleltraversal.hpp ./include/ssw.h ./include/outputformats.hpp + diff --git a/easybuild/easyconfigs/s/Spark/Spark-2.0.0.eb b/easybuild/easyconfigs/s/Spark/Spark-2.0.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..6ca9cd502bcd4f4a10a552d1221e793d2446ae49 --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-2.0.0.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'Spark' +version = '2.0.0' + +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/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..e8b9b26666b35fc1eeb190dfb46f1b3d93e09ef5 --- /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..a58b6b19e0b507ef2072cc8abc64fdd5fc52034a --- /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/Stacks/Stacks-1.40-foss-2016a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.40-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..189d7f6db0caae13bbc990311e8eff217fe923f6 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.40-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '1.40' + +homepage = 'http://creskolab.uoregon.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose + of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('SAMtools', '1.3.1'), + ('sparsehash', '2.0.2'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%s' % binfile for binfile in [ + 'clone_filter', 'denovo_map.pl', 'exec_velvet.pl', 'genotypes', 'index_radtags.pl', 'load_radtags.pl', + 'populations', 'process_shortreads', 'ref_map.pl', 'sstacks', 'ustacks', 'cstacks', 'estacks', + 'export_sql.pl', 'hstacks', 'kmer_filter', 'load_sequences.pl', 'process_radtags', 'pstacks', + 'sort_read_pairs.pl', 'stacks_export_notify.pl', + ] + ], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6d5d6358c842bdfc156a56a5761834999be5bf02 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.42-foss-2016a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Stacks' +version = '1.42' + +homepage = 'http://creskolab.uoregon.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on + the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose + of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['http://catchenlab.life.illinois.edu/stacks/source/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('zlib', '1.2.8'), + ('SAMtools', '1.3.1'), + ('sparsehash', '2.0.2'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%s' % binfile for binfile in [ + 'clone_filter', 'denovo_map.pl', 'exec_velvet.pl', 'genotypes', 'index_radtags.pl', 'load_radtags.pl', + 'populations', 'process_shortreads', 'ref_map.pl', 'sstacks', 'ustacks', 'cstacks', 'estacks', + 'export_sql.pl', 'hstacks', 'kmer_filter', 'load_sequences.pl', 'process_radtags', 'pstacks', + 'sort_read_pairs.pl', 'stacks_export_notify.pl', + ] + ], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/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/Subread/Subread-1.5.0-p1-foss-2016b.eb b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ecdac2f7d2a7fdca54c47212898ab53d673253df --- /dev/null +++ b/easybuild/easyconfigs/s/Subread/Subread-1.5.0-p1-foss-2016b.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Adam Huffman +# The Francis Crick Institute +easyblock = 'MakeCp' + +name = 'Subread' +version = '1.5.0-p1' + +homepage = 'http://subread.sourceforge.net/' +description = """High performance read alignment, quantification and mutation discovery""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +source_urls = [('https://sourceforge.net/projects/%(namelower)s/files/%(namelower)s-%(version)s', 'download')] + +start_dir = 'src' +buildopts = '-f Makefile.Linux' + +files_to_copy = ['bin', 'annotation', 'doc', 'LICENSE', 'README.txt', 'src', 'test'] + +sanity_check_paths = { + 'files': ['LICENSE', 'README.txt'], + 'dirs': ['bin', 'annotation', 'doc', 'src', 'test'] +} + +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-4.5.2-foss-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..526438ac190e992d4624ff1e33728b8efce25b05 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.2-foss-2016a-METIS-5.1.0.eb @@ -0,0 +1,20 @@ +name = 'SuiteSparse' +version = '4.5.2' + +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-foss-2016a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.3-foss-2016a-METIS-5.1.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..85cd57732ede72d8cfecd0afe92f9d5ecf1243c0 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.3-foss-2016a-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': '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-foss-2016a-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.3-foss-2016a-ParMETIS-4.0.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..3b604c9d6d563f66ed11358e1bd9eb1e764d2bb5 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.3-foss-2016a-ParMETIS-4.0.3.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': 'foss', 'version': '2016a'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +parmetis = 'ParMETIS' +parmetis_ver = '4.0.3' +versionsuffix = '-%s-%s' % (parmetis, parmetis_ver) +dependencies = [(parmetis, parmetis_ver)] + +maxparallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.3-intel-2016a-ParMETIS-4.0.3.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.3-intel-2016a-ParMETIS-4.0.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..e0c73b3419703785fbeeaf53d9f9ca296013105d --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-4.5.3-intel-2016a-ParMETIS-4.0.3.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': '2016a'} +toolchainopts = {'opt': True, 'unroll': True, 'pic': True} + +source_urls = ['http://faculty.cse.tamu.edu/davis/SuiteSparse/'] +sources = [SOURCE_TAR_GZ] + +parmetis = 'ParMETIS' +parmetis_ver = '4.0.3' +versionsuffix = '-%s-%s' % (parmetis, parmetis_ver) +dependencies = [(parmetis, parmetis_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/SuperLU/SuperLU-5.1.1-intel-2016a.eb b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6adf4c050f9884a13e2caa70b74949eba6cd54ca --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU/SuperLU-5.1.1-intel-2016a.eb @@ -0,0 +1,19 @@ +name = 'SuperLU' +version = '5.1.1' + +homepage = 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'opt': True, 'pic': True} + +source_urls = ['http://crd-legacy.lbl.gov/~xiaoye/SuperLU/'] +sources = ["superlu_%(version)s.tar.gz"] + +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['260a3cd90b2100122abff38587a8290a'] + +builddependencies = [('CMake', '3.4.3')] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2016b.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..93decc8ff1714321b56a39536400ac479ed5765a --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2016b.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': 'foss', 'version': '2016b'} +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-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-intel-2016b.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..8317e70e0b4795cbfde8436df2087ca12d4e09cd --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2016b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic" + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2017.01.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2017.01.eb new file mode 100644 index 0000000000000000000000000000000000000000..73468933aa94ba25c6488ee800e87185f87afcc0 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-intel-2017.01.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1' + +homepage = 'http://www.hdfgroup.org/doc_resource/SZIP/' +description = "Szip compression software, providing lossless compression of scientific data" + +toolchain = {'name': 'intel', 'version': '2017.01'} +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-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..7a34f126ed0c616a70bccb2a4aec4032bb198fe1 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-2.7.11.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': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), + ('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-0.17.1-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..9c2111d9465b0fe4686dea9d4016545c7b311fec --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.17.1-foss-2016a-Python-3.5.1.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': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), + ('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-0.17.1-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/scipy/scipy-0.16.0-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/s/scipy/scipy-0.16.0-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..a6ab83c9a798f8f2b22848575281a2fc1fb043e9 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.16.0-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,33 @@ +name = 'scipy' +version = '0.16.0' +versionsuffix = '-Python-2.7.12' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +patches = ['scipy-%(version)s_fix-failing-tests-mkl.patch'] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +# recompile patch Cython source file +prebuildopts = "cython scipy/linalg/_decomp_update.pyx && " + +# need to use pip rather than regular 'setup.py install,' +# to ensure that this scipy wins over the one in the Python installation; +# using easy_install does not work... +use_pip = True + +# install as zipped egg to get a .pth file in lib/python*/site-packages; +# this enables shadowing of the scipy that is part of the Python installation +zipped_egg = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.16.0_fix-failing-tests-mkl.patch b/easybuild/easyconfigs/s/scipy/scipy-0.16.0_fix-failing-tests-mkl.patch new file mode 100644 index 0000000000000000000000000000000000000000..9284ae921c4b0b46b41904c6e6deab270540ae9d --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.16.0_fix-failing-tests-mkl.patch @@ -0,0 +1,76 @@ +backported fix from https://github.com/scipy/scipy/pull/6135, +requires recompiling scipy/linalg/_decomp_update.pyx using 'cython scipy/linalg/_decomp_update.pyx' +see also https://github.com/scipy/scipy/issues/6132 +author: Kenneth Hoste (HPC-UGent) +--- scipy/linalg/_decomp_update.pyx.in.orig 2015-06-26 08:28:59.000000000 +0200 ++++ scipy/linalg/_decomp_update.pyx.in 2016-12-07 09:44:34.757075909 +0100 +@@ -47,7 +47,6 @@ + cimport libc.float + from libc.math cimport sqrt, fabs, hypot + from libc.string cimport memset +-cimport libc.stdio + + cimport numpy as cnp + +@@ -715,9 +714,15 @@ + # First zero the lower part of the new columns using a qr. + + # query the workspace, ++ # set tau to point at something to keep new MKL working. ++ tau = &c + info = geqrf(m-n+p, p, index2(r, rs, n-p, k), m, tau, &c, -1) ++ if info < 0: ++ return libc.stdlib.abs(info) + info = ormqr(side, trans, m, m-(n-p), p, index2(r, rs, n-p, k), m, + tau, index2(q, qs, 0, n-p), m, &s, -1) ++ if info < 0: ++ return info + + # we're only doing one allocation, so use the larger + lwork = to_lwork(c, s) +@@ -887,6 +892,8 @@ + # query the workspace + # below p_subdiag_qr will need workspace of size m, which is the + # minimum, ormqr will also require. ++ # set tau to point at something, to keep new MKL working. ++ tau = &c + info = geqrf(m-n, p, index2(u, us, n, 0), m, tau, &c, -1) + if info < 0: + return libc.stdlib.abs(info) +--- scipy/linalg/tests/test_decomp_update.py.orig 2016-12-07 09:40:24.369816052 +0100 ++++ scipy/linalg/tests/test_decomp_update.py 2016-12-07 09:46:41.725683380 +0100 +@@ -876,7 +876,7 @@ + check_qr(q1, r1, a1, self.rtol, self.atol, False) + + def test_Mx1_economic_p_col(self): +- a, q, r, u = self.generate('Mx1', 'full', 'col', 3) ++ a, q, r, u = self.generate('Mx1', 'economic', 'col', 3) + for col in range(r.shape[1]): + q1, r1 = qr_insert(q, r, u, col, 'col', overwrite_qru=False) + a1 = np.insert(a, col*np.ones(3, np.intp), u, 1) +--- ./scipy/linalg/_decomp_update.pyx.orig 2016-12-07 10:32:54.264284722 +0100 ++++ ./scipy/linalg/_decomp_update.pyx 2016-12-07 10:34:47.153042590 +0100 +@@ -759,9 +759,15 @@ + # First zero the lower part of the new columns using a qr. + + # query the workspace, ++ # set tau to point at something to keep new MKL working. ++ tau = &c + info = geqrf(m-n+p, p, index2(r, rs, n-p, k), m, tau, &c, -1) ++ if info < 0: ++ return libc.stdlib.abs(info) + info = ormqr(side, trans, m, m-(n-p), p, index2(r, rs, n-p, k), m, + tau, index2(q, qs, 0, n-p), m, &s, -1) ++ if info < 0: ++ return info + + # we're only doing one allocation, so use the larger + lwork = to_lwork(c, s) +@@ -931,6 +937,7 @@ + # query the workspace + # below p_subdiag_qr will need workspace of size m, which is the + # minimum, ormqr will also require. ++ tau = &c + info = geqrf(m-n, p, index2(u, us, n, 0), m, tau, &c, -1) + if info < 0: + return libc.stdlib.abs(info) diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.16.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/s/scipy/scipy-0.16.1-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..6126cbe4898b6d6a8f7df60bbc4242c1feab095b --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.16.1-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.16.1' +versionsuffix = '-Python-2.7.10' + +homepage = 'http://www.scipy.org' +description = """SciPy is a collection of mathematical algorithms and convenience + functions built on the Numpy extension for Python.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.10.4', versionsuffix), +] + +moduleclass = 'math' 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/s/splitRef/splitRef-0.0.2.eb b/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..e2411ef3f5963afd41e6a3696fb7c836d5ecacf2 --- /dev/null +++ b/easybuild/easyconfigs/s/splitRef/splitRef-0.0.2.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "Tarball" + +name = 'splitRef' +version = '0.0.2' + +homepage = 'http://www.sph.umich.edu/csg/yli/splitRef/index.html' +description = """ splitRef splits a reference haplotype file into smaller files + with subsets of markers. The current version is a pre-release. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.sph.umich.edu/csg/yli/splitRef/download/'] +sources = ['%s.V%s.tgz' % (name, version.replace(".", ""))] + +altver = version.replace('.', '') + +sanity_check_paths = { + 'files': ["splitRef_V%s/splitRef.pl" % altver], + 'dirs': ["examples"] +} + +# add folder splitRef_V002 to PATH +modextrapaths = { + 'PATH': '%s_V%s' % (name, altver) +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..09140f6d09e00224c5e33da0f635477dd2b84052 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.0-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'sympy' +version = '1.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +#Patch to fix tests +patches = ['sympy-1.0_tests-unicode.patch'] + +dependencies = [ + ('Python', '2.7.11'), + ('mpmath', '0.19', '-Python-%(pyver)s'), +] + +runtest = 'python setup.py test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s-py%(pyshortver)s.egg/%(name)s'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/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/TRF/TRF-4.09-linux64.eb b/easybuild/easyconfigs/t/TRF/TRF-4.09-linux64.eb new file mode 100644 index 0000000000000000000000000000000000000000..ea29356e919f40c6c6e3a480e93ac8dfec3e1f70 --- /dev/null +++ b/easybuild/easyconfigs/t/TRF/TRF-4.09-linux64.eb @@ -0,0 +1,23 @@ +easyblock = 'Binary' + +name = 'TRF' +version = '4.09' +versionsuffix = '-linux64' + +homepage = 'https://tandem.bu.edu/trf/trf.html' +description = """Tandem repeats finder: a program to analyze DNA sequences. Legacy version.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://tandem.bu.edu/trf/downloads'] +sources = ['trf%(version_major)s%(version_minor)s.legacylinux64'] +checksums = [('md5', 'f97b6d1fc06adbd1484b384d5481916a')] + +postinstallcmds = ["mv %(installdir)s/trf%(version_major)s%(version_minor)s.legacylinux64 %(installdir)s/trf"] + +sanity_check_paths = { + 'files': ['trf'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TVB-deps/TVB-deps-20160618-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/TVB-deps/TVB-deps-20160618-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..7095cc94e00ae93f5e134af67fc58ce388cbf1b0 --- /dev/null +++ b/easybuild/easyconfigs/t/TVB-deps/TVB-deps-20160618-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,89 @@ +easyblock = 'Bundle' + +name = 'TVB-deps' +version = '20160618' # date of most recent updated package included in this bundle (psutil) +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://thevirtualbrain.org' +description = """Bundle of dependency Python packages for TVB (The Virtual Brain)""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +freetype_ver = '2.6.3' +dependencies = [ + ('Python', '2.7.11'), + ('matplotlib', '1.5.1', versionsuffix + '-freetype-%s' % freetype_ver), + ('NiBabel', '2.0.2', versionsuffix + '-freetype-%s' % freetype_ver), + ('scikit-learn', '0.17.1', versionsuffix + '-freetype-%s' % freetype_ver), + ('Pillow', '3.2.0', versionsuffix + '-freetype-%s' % freetype_ver), + ('h5py', '2.6.0', versionsuffix), + ('lxml', '3.6.0', versionsuffix), + ('numba', '0.26.0', versionsuffix), +] + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +exts_list = [ + ('APScheduler', '3.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/APScheduler/'], + }), + ('BeautifulSoup', '3.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/B/BeautifulSoup/'], + 'modulename': 'BeautifulSoup', + }), + ('CherryPy', '6.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/C/CherryPy/'], + }), + ('Genshi', '0.7', { + 'source_urls': ['https://pypi.python.org/packages/source/G/Genshi/'], + }), + ('cfflib', '2.0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cfflib/'], + }), + ('FormEncode', '1.3.0a1', { + 'source_urls': ['https://pypi.python.org/packages/source/F/FormEncode/'], + }), + ('minixsv', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/minixsv/'], + 'source_tmpl': 'minixsv-%(version)s.zip', + }), + ('mod_pywebsocket', '0.7.9', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mod_pywebsocket/'], + }), + ('networkx', '1.11', { + 'source_urls': ['https://pypi.python.org/packages/source/n/networkx/'], + }), + ('numexpr', '2.6.0', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numexpr/'], + }), + ('psutil', '4.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/psutil/'], + }), + ('simplejson', '3.8.2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # versions of SQLAlchemy & sqlalchemy-migrate are fixed to old versions by TVB, probably with good reason + ('SQLAlchemy', '0.7.8', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('sqlalchemy-migrate', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sqlalchemy-migrate/'], + 'modulename': 'migrate', + }), + ('gdist', '1.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/g/gdist/'], + }), +] + +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 = 'tools' diff --git a/easybuild/easyconfigs/t/TVB/TVB-1.4.1-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/TVB/TVB-1.4.1-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..8247c99973a048284886e3b393c5fda38d5780ca --- /dev/null +++ b/easybuild/easyconfigs/t/TVB/TVB-1.4.1-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'TVB' +version = '1.4.1' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://thevirtualbrain.org' +description = """The Virtual Brain will deliver the first open simulation of the human brain + based on individual large-scale connectivity.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +dependencies = [ + ('tvb-data', '20150915', versionsuffix), + ('tvb-framework', '20150921', versionsuffix), + ('tvb-library', '20150922', versionsuffix), +] + +# SVN revision 7595 corresponds to TVB Distribution v1.4.1 +modextravars = {'SVN_REVISION': '7595'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TVB/TVB-1.5-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/TVB/TVB-1.5-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..cf4af9a0e2ea701fee00638b53473eea270e6fb9 --- /dev/null +++ b/easybuild/easyconfigs/t/TVB/TVB-1.5-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,22 @@ +easyblock = 'Bundle' + +name = 'TVB' +version = '1.5' +versionsuffix = '-Python-2.7.11' + +homepage = 'http://thevirtualbrain.org' +description = """The Virtual Brain will deliver the first open simulation of the human brain + based on individual large-scale connectivity.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +dependencies = [ + ('tvb-data', '1.5', versionsuffix), + ('tvb-framework', '1.5', versionsuffix), + ('tvb-library', '1.5', versionsuffix), +] + +# SVN revision 8027 corresponds to TVB Distribution v1.5 +modextravars = {'SVN_REVISION': '8027'} + +moduleclass = 'bio' 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 new file mode 100644 index 0000000000000000000000000000000000000000..37cac05971ca295976e12935cd875ef7022dd5d7 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2015.11.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': 'CrayGNU', 'version': '2015.11'} + +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-CrayGNU-2016.03.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..8211069c61bf6ba656017c07b84aa789834df14e --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-CrayGNU-2016.03.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': 'CrayGNU', 'version': '2016.03'} + +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-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 new file mode 100644 index 0000000000000000000000000000000000000000..3f4c4832f3b5f24ec33651b94acaf45c96b66873 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCC-4.9.3-2.25.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': 'GCC', 'version': '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-5.4.0-2.26.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..0c3128d6576615a262bcd6722bd87428f0e8b1e2 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-GCC-5.4.0-2.26.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': 'GCC', 'version': '5.4.0-2.26'} + +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-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 new file mode 100644 index 0000000000000000000000000000000000000000..f15e62a824cc9a2101144dea4dd964881b16ba20 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-foss-2016a.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': '2016a'} + +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-2016b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..ee88524e1eef501c160fa443c532d8f565b8f978 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-foss-2016b.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': '2016b'} + +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-intel-2016b.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..b9bb3175fadac1ea38ec2217e8974bccbc04961b --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.5-intel-2016b.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': 'intel', 'version': '2016b'} + +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-8.6.6-GCCcore-4.9.3.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..d71a52e8c4a3ff2f98da6afbdd8854d06c2f61e3 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.6-GCCcore-4.9.3.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.6' + +homepage = 'http://www.tcl.tk/' +description = """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, +suitable for a very wide range of uses, including web and desktop applications, networking, administration, +testing and many more.""" + +toolchain = {'name': 'GCCcore', 'version': '4.9.3'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +builddependencies = [ + ('binutils', '2.25'), +] + +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/Text-CSV/Text-CSV-1.33-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/t/Text-CSV/Text-CSV-1.33-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..3b019db7fc65cb09345195a72be16dbbb7c150db --- /dev/null +++ b/easybuild/easyconfigs/t/Text-CSV/Text-CSV-1.33-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,26 @@ +easyblock = 'PerlModule' + +name = 'Text-CSV' +version = '1.33' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'https://metacpan.org/pod/Text::CSV' +description = """Text-CSV parser""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://cpan.metacpan.org/authors/id/M/MA/MAKAMAKA/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Perl', '5.22.1') +] + +options = {'modulename': 'Text::CSV'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/Text/CSV.pm'], + 'dirs': ['man/man3'], +} + +moduleclass = 'data' 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..c127bf926194aaa23e27a6a2792e30045616dc9b --- /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' 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..bb0c6b10ffd7fe07ea33390d77ef4a76a0930c90 --- /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..ce6dc2f2056c16853d8ef5e226a1b1984b9df35b --- /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/TiCCutils/TiCCutils-0.11-foss-2016a.eb b/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.11-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..88604444ed83a65134cd509371291d8a7d8aee44 --- /dev/null +++ b/easybuild/easyconfigs/t/TiCCutils/TiCCutils-0.11-foss-2016a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'TiCCutils' +version = '0.11' + +homepage = 'http://ilk.uvt.nl/ticcutils/' +description = """TiCC utils is a collection of generic C++ software which is used in a lot of programs produced at + Tilburg centre for Cognition and Communication (TiCC) at Tilburg University and + Centre for Dutch Language and Speech at University of Antwerp.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True, 'opt': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://software.ticc.uvt.nl/'] + +configopts = '--with-pic' + +sanity_check_paths = { + 'files': ['lib/libticcutils.so', 'lib/libticcutils.a'], + 'dirs': ['include/ticcutils'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.7-foss-2016a.eb b/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.7-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b4b56f19e0b912facf56b87f45692d2ee9c33505 --- /dev/null +++ b/easybuild/easyconfigs/t/TiMBL/TiMBL-6.4.7-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'TiMBL' +version = '6.4.7' + +homepage = 'http://ilk.uvt.nl/timbl/' +description = """TiMBL (Tilburg Memory Based Learner) + is an open source software package implementing several memory-based learning algorithms, + among which IB1-IG, an implementation of k-nearest neighbor classification with feature weighting suitable for + symbolic feature spaces, and IGTree, a decision-tree approximation of IB1-IG. All implemented algorithms have in + common that they store some representation of the training set explicitly in memory. During testing, new cases are + classified by extrapolation from the most similar stored cases.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'optarch': True, 'pic': True, 'opt': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://software.ticc.uvt.nl/'] + +dependencies = [ + ('TiCCutils', '0.11'), + ('libxml2', '2.9.3'), +] + +configopts = '--with-ticcutils=$EBROOTTICCUTILS' + +sanity_check_paths = { + 'files': ['bin/timbl', 'lib/libtimbl.%s' % SHLIB_EXT, 'lib/libtimbl.a'], + 'dirs': ['include/timbl'] +} + +moduleclass = 'data' 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 new file mode 100644 index 0000000000000000000000000000000000000000..02c810f4e3a3606b5b7ed58257e4cf71ad42c47f --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2015.11-no-X11.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +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': 'CrayGNU', 'version': '2015.11'} + +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), +] + +# 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-8.6.4-CrayGNU-2016.03-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2016.03-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..f156bb1a1bfb7ed620ac2e3a11a6d239794add9d --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-CrayGNU-2016.03-no-X11.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.4' +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': 'CrayGNU', 'version': '2016.03'} + +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), +] + +# 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-8.6.4-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$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.5-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..f2a063069a2d9beb04f9a028e04fe7684e4008c3 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-GCC-5.4.0-2.26.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.5' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCC', 'version': '5.4.0-2.26'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] + +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.5-foss-2016.04.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-foss-2016.04.eb new file mode 100644 index 0000000000000000000000000000000000000000..5587e8e8dc2b6f3a9e831c8ede461977f23cd820 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-foss-2016.04.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.5' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'foss', 'version': '2016.04'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] + +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.5-foss-2016a.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..42bbe165173a9a89c654b5bf7b67ea291edb75e7 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-foss-2016a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.5' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] + +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.5-foss-2016b.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..6a31ea52f49e99fa018bb3d727a35735ec477c52 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-foss-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.5' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] + +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.5-intel-2016b.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..cc0f1220b7e09ddf29d9c4123a913da4511613f1 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.5-intel-2016b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.5' + +homepage = 'http://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] + +dependencies = [ + ('Tcl', version), + ('zlib', '1.2.8'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2016a.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..bf3b1885b25cc80841cba85486c562439ad257f3 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.1.1-foss-2016a.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'TopHat' +version = '2.1.1' + +homepage = 'http://ccb.jhu.edu/software/tophat/' +description = """TopHat is a fast splice junction mapper for RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] + +patches = [ + 'tophat-2.0.13-zlib.patch', +] + +dependencies = [ + ('Boost', '1.61.0'), + ('zlib', '1.2.8'), +] + +configopts = '--with-boost=$EBROOTBOOST' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/tophat'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-0-linux-x86-64.eb b/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-0-linux-x86-64.eb index 132fdbeeb9f91e30ee08e5c42204bbfcba561433..edea937fc8bc36a5ab34068f5c8d5b45c2216ca3 100644 --- a/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-0-linux-x86-64.eb +++ b/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-0-linux-x86-64.eb @@ -30,8 +30,6 @@ sources = [ '%(namelower)s.%(version)s-doc.tar', ] -# licensepath -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "roguewave", "license.lic") +license_file = HOME + '/licenses/roguewave/license.lic' moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-2-linux-x86-64.eb b/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-2-linux-x86-64.eb index c3d83422cba4168281462a2f0aa3245b91a67e0d..7af5c3b6cd9baee3dc8cf220e85841009c9c2dd7 100644 --- a/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-2-linux-x86-64.eb +++ b/easybuild/easyconfigs/t/TotalView/TotalView-8.11.0-2-linux-x86-64.eb @@ -30,8 +30,6 @@ sources = [ '%(namelower)s.%(version)s-doc.tar', ] -# licensepath -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "roguewave", "license.lic") +license_file = HOME + '/licenses/roguewave/license.lic' moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/t/TotalView/TotalView-8.12.0-0-linux-x86-64.eb b/easybuild/easyconfigs/t/TotalView/TotalView-8.12.0-0-linux-x86-64.eb index 6144d45261eb68d4c6916c37d0c8ed858c81e4ed..69f8803b05b01c73d16eed75a020e6ae1fd8ea04 100644 --- a/easybuild/easyconfigs/t/TotalView/TotalView-8.12.0-0-linux-x86-64.eb +++ b/easybuild/easyconfigs/t/TotalView/TotalView-8.12.0-0-linux-x86-64.eb @@ -30,8 +30,6 @@ sources = [ '%(namelower)s.%(version)s-doc.tar', ] -# licensepath -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "roguewave", "license.lic") +license_file = HOME + '/licenses/roguewave/license.lic' moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/t/Triangle/Triangle-1.6-foss-2016a.eb b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c29bcc0a882cdb2eba99eb59d7dfd58b47bc95bc --- /dev/null +++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6-foss-2016a.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'Triangle' +version = '1.6' + +homepage = 'http://www.cs.cmu.edu/~quake/triangle.html' +description = """Triangle generates exact Delaunay triangulations, constrained Delaunay triangulations, + conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes. + The latter can be generated with no small or large angles, + and are thus suitable for finite element analysis.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.netlib.org/voronoi/'] +sources = ['%(namelower)s.zip'] +checksums = [('md5', '10aff8d7950f5e0e2fb6dd2e340be2c9')] + +patches = ['%(name)s-%(version)s_makefile.patch'] + +buildopts = 'triangle trilibrary' + +files_to_copy = [ + (['triangle', 'tricall'], 'bin'), + (['triangle.h'], 'include'), + (['libtriangle.a'], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/triangle', 'bin/tricall', 'include/triangle.h', 'lib/libtriangle.a'], + 'dirs': [] +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/t/Triangle/Triangle-1.6_makefile.patch b/easybuild/easyconfigs/t/Triangle/Triangle-1.6_makefile.patch new file mode 100644 index 0000000000000000000000000000000000000000..01806e267ea03e120a4fb0cca4a3880f324e9e13 --- /dev/null +++ b/easybuild/easyconfigs/t/Triangle/Triangle-1.6_makefile.patch @@ -0,0 +1,41 @@ +#Pick compiler and flags from environmental variables and make libtriangle.a from triangle.o +# Aug 04th 2016 by B. Hajgato (Free Univeristy Brussels - VUB) +--- makefile.orig 2005-07-28 02:22:01.000000000 +0200 ++++ makefile 2016-08-04 14:29:37.360139408 +0200 +@@ -18,7 +18,7 @@ + + # CC should be set to the name of your favorite C compiler. + +-CC = cc ++CC ?= cc + + # CSWITCHES is a list of all switches passed to the C compiler. I strongly + # recommend using the best level of optimization. I also strongly +@@ -73,7 +73,7 @@ + # + # CSWITCHES = -O -DNO_TIMER -DLINUX -I/usr/X11R6/include -L/usr/X11R6/lib + +-CSWITCHES = -O -DLINUX -I/usr/X11R6/include -L/usr/X11R6/lib ++CSWITCHES = $(CFLAGS) -DLINUX + + # TRILIBDEFS is a list of definitions used to compile an object code version + # of Triangle (triangle.o) to be called by another program. The file +@@ -96,7 +96,7 @@ + + all: $(BIN)triangle $(BIN)showme + +-trilibrary: $(BIN)triangle.o $(BIN)tricall ++trilibrary: $(BIN)libtriangle.a $(BIN)tricall + + $(BIN)triangle: $(SRC)triangle.c + $(CC) $(CSWITCHES) -o $(BIN)triangle $(SRC)triangle.c -lm +@@ -109,6 +109,9 @@ + $(CC) $(CSWITCHES) $(TRILIBDEFS) -c -o $(BIN)triangle.o \ + $(SRC)triangle.c + ++$(BIN)libtriangle.a: $(SRC)triangle.o ++ $(AR) cqs $(BIN)libtriangle.a triangle.o ++ + $(BIN)showme: $(SRC)showme.c + $(CC) $(CSWITCHES) -o $(BIN)showme $(SRC)showme.c -lX11 + 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/Trinity/Trinity-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..58018d93350fd5ff63bec5cba9c884c7d02fb328 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0-foss-2016a.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 + +name = 'Trinity' +version = '2.2.0' + +homepage = 'http://trinityrnaseq.github.io/' +description = """Trinity represents a novel method for the efficient and robust de novo reconstruction + of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, + Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = [ + 'chrysalis_commandline_noconsts_2012-10-05.patch', + 'Trinity-2.2.0_jellyfish-Makefile.patch', +] + +builddependencies = [ + ('Autotools', '20150215'), +] + +dependencies = [ + ('Java', '1.8.0_92', '', True), + ('ant', '1.9.7', '-Java-%(javaver)s', True), + ('Bowtie', '1.1.2'), + ('Bowtie2', '2.2.8'), + ('ncurses', '6.0',), + ('zlib', '1.2.8'), + ('Perl', '5.22.1'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0_jellyfish-Makefile.patch b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0_jellyfish-Makefile.patch new file mode 100644 index 0000000000000000000000000000000000000000..33fecc091177170c20bffec01e28b695b5e11f83 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.2.0_jellyfish-Makefile.patch @@ -0,0 +1,30 @@ +use EasyBuild-provided zlib, don't hardcode gcc/g++ for jellyfish plugin +authors: B. Hajgato (Vrije Universiteit Brussel), Kenneth Hoste (HPC-UGent) +--- trinityrnaseq-2.2.0/trinity-plugins/Makefile.orig 2016-07-07 11:42:18.000000000 +0200 ++++ trinityrnaseq-2.2.0/trinity-plugins/Makefile 2016-07-07 11:44:04.000000000 +0200 +@@ -2,6 +2,9 @@ + JELLYFISH_CODE="jellyfish-2.1.4" + HTSLIB_CODE="htslib.github.Aug182015.tar.gz" + ++CC?=gcc ++CXX?=g++ ++ + ####################### + ### Required by Trinity + ####################### +@@ -26,12 +29,13 @@ + + samtools: + tar xvf samtools-0.1.19.tar.bz2 +- cd samtools-0.1.19 && $(MAKE) ${LTINFO} ++ sed -e 's/ -lz/ -L\$$\{EBROOTZLIB\}\/lib -lz/' -i samtools-0.1.19/misc/Makefile ++ cd samtools-0.1.19 && $(MAKE) LIBPATH=-L${EBROOTZLIB}/lib + mv samtools-0.1.19/samtools ./BIN/. + + jellyfish: + tar -zxvf ${JELLYFISH_CODE}.tar.gz && ln -sf ${JELLYFISH_CODE} tmp.jellyfish +- cd ./tmp.jellyfish/ && ./configure CC=gcc CXX=g++ --enable-static --disable-shared --prefix=`pwd` && $(MAKE) LDFLAGS="-lpthread -all-static" AM_CPPFLAGS="-Wall -Wnon-virtual-dtor -I"`pwd`"/include" ++ cd ./tmp.jellyfish/ && ./configure CC=$(CC) CXX=$(CXX) --enable-static --disable-shared --prefix=`pwd` && $(MAKE) LDFLAGS="-lpthread -all-static" AM_CPPFLAGS="-Wall -Wnon-virtual-dtor -I"`pwd`"/include" + mv tmp.jellyfish jellyfish + + htslib_target: diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb index e966db8b0a5d5c323daec5a9d338a62d7b24ba65..dcb9ea5cadbd7db87fd330cd1b704c97439eb226 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2012-10-05-goolf-1.4.10.eb @@ -34,7 +34,6 @@ bwapluginver = "0.5.7" RSEMmod = True # required for GCC v4.7, see http://forums.bannister.org/ubbthreads.php?ubb=showflat&Number=79791&page=2 -import os -os.putenv('CPPONLYFLAGS', '-Wno-narrowing') +prebuildopts = "export CPPONLYFLAGS='-Wno-narrowing' && " moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2016a.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..30c58df38b902b14e598e61cfbe82269c3a354a5 --- /dev/null +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-foss-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'tabix' +version = '0.2.6' + +homepage = 'http://samtools.sourceforge.net' +description = """ Generic indexer for TAB-delimited genome position files """ + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [('http://sourceforge.net/projects/samtools/files/', 'download')] +sources = [SOURCE_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +buildopts = 'CC="$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/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/tbb/tbb-4.0.0.233.eb b/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb index a157686a4a744d0ac6a524d584ffc418f6862532..276beb485d9639a3b211705143b3947dcc6da661 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.0.0.233.eb @@ -19,8 +19,6 @@ patches = ['tbb-4.0_productsdb.patch'] dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb b/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb index 150aaf30f9922c5e4f0dcfb2e2fc92d3f6ad6f92..88a0f193971e1466e3d32642829a8d7ce89eaa76 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.0.5.339.eb @@ -19,8 +19,6 @@ patches = ['tbb-4.0_productsdb.patch'] dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb b/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb index 27609d139ffd72804cb514bf9f6cc71325d57223..bf885c9389faba90db08eccc33e375048a363eaf 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.3.6.211.eb @@ -17,8 +17,6 @@ sources = ['l_%(name)s_%(version)s.tgz'] dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb b/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb index a09fc4527004ea2b2fd9da680cfe469d9868fb60..c5d8deaf1fc5a357d6c8e76740298f73298a8051 100644 --- a/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb +++ b/easybuild/easyconfigs/t/tbb/tbb-4.4.2.152.eb @@ -17,8 +17,6 @@ sources = ['l_%(name)s_%(version)s.tgz'] dontcreateinstalldir = 'True' -# license file -import os -license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") +license_file = HOME + '/licenses/intel/license.lic' moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb index 40607b696078338253ed8b22aea8d9883ced9f7a..da50b02fdfbbcf27e926a228e6988f025e43b5c2 100644 --- a/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb +++ b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb @@ -4,10 +4,8 @@ name = 'tecplot360ex' version = 'linux64' homepage = 'http://www.tecplot.com/products/tecplot-360/' -description = """ - Quickly plot and animate your CFD results exactly the way you want. Analyze complex solutions, arrange multiple layouts, - and communicate your results with professional images and animations. -""" +description = """Quickly plot and animate your CFD results exactly the way you want. Analyze complex solutions, +arrange multiple layouts, and communicate your results with professional images and animations.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/t/testpath/testpath-0.3-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/testpath/testpath-0.3-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..fdca3b5b455ffcf7364591ee38e3d7e99396d007 --- /dev/null +++ b/easybuild/easyconfigs/t/testpath/testpath-0.3-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'testpath' +version = '0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jupyter/testpath' +description = """Test utilities for code working with files and commands""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://pypi.python.org/packages/py2.py3/t/testpath/'] +sources = ['testpath-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '2.7.11'), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/testpath'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/testpath/testpath-0.3-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/t/testpath/testpath-0.3-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..4f5329cde6b5e279c7e07ee366236167114ebfbc --- /dev/null +++ b/easybuild/easyconfigs/t/testpath/testpath-0.3-foss-2016a-Python-3.5.1.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': 'foss', 'version': '2016a'} + +source_urls = ['https://pypi.python.org/packages/py2.py3/t/testpath/'] +sources = ['testpath-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '3.5.1'), +] + +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/testpath/testpath-0.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/t/testpath/testpath-0.3-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..d1f78192c930a8a017cc80e9daf3d35efd1b00da --- /dev/null +++ b/easybuild/easyconfigs/t/testpath/testpath-0.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'testpath' +version = '0.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jupyter/testpath' +description = """Test utilities for code working with files and commands""" + +toolchain = {'name': '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', '2.7.12'), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/testpath'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/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/t/tmux/tmux-1.9a-GCC-4.9.2.eb b/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb index b34529fe922c37209f866e1007779dd376c0d659..8b0f6b51a85ab79229a735fd626bd347401af5b4 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-1.9a-GCC-4.9.2.eb @@ -4,8 +4,8 @@ name = 'tmux' version = '1.9a' homepage = 'http://tmux.sourceforge.net/' -description = """tmux is a terminal multiplexer. It lets you switch easily -between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.""" +description = """tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, +detach them (they keep running in the background) and reattach them to a different terminal.""" toolchain = {'name': 'GCC', 'version': '4.9.2'} toolchainopts = {'optarch': True} diff --git a/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb b/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb index a8b6500ba32d8509115fae3a9fca9e86385b0efb..391b43238fd170e9c1b173c66ec2491500faf1d1 100644 --- a/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb +++ b/easybuild/easyconfigs/t/tmux/tmux-2.2-GCCcore-4.9.3.eb @@ -4,8 +4,8 @@ name = 'tmux' version = '2.2' homepage = 'http://tmux.sourceforge.net/' -description = """tmux is a terminal multiplexer. It lets you switch easily -between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.""" +description = """tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, +detach them (they keep running in the background) and reattach them to a different terminal.""" toolchain = {'name': 'GCCcore', 'version': '4.9.3'} toolchainopts = {'optarch': True} diff --git a/easybuild/easyconfigs/t/travis/travis-1.8.4-Ruby-2.3.3.eb b/easybuild/easyconfigs/t/travis/travis-1.8.4-Ruby-2.3.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..6327f1f42effe0ffcd5625af6ffd1dbcbee39b06 --- /dev/null +++ b/easybuild/easyconfigs/t/travis/travis-1.8.4-Ruby-2.3.3.eb @@ -0,0 +1,24 @@ +easyblock = 'RubyGem' + +name = 'travis' +version = '1.8.4' + +rubyver = '2.3.3' +versionsuffix = '-Ruby-%s' % rubyver + +homepage = 'https://github.com/travis-ci/travis.rb' +description = """Travis CI Client (CLI and Ruby library)""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://rubygems.org/downloads/'] +sources = ['%(namelower)s-%(version)s.gem'] + +dependencies = [('Ruby', rubyver)] + +sanity_check_paths = { + 'files': ['bin/travis'], + 'dirs': ['gems/travis-%(version)s/lib/travis'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tvb-data/tvb-data-1.5-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/tvb-data/tvb-data-1.5-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..c2d5dc9c0dc1ae88f6dba92a2608a2188391b8ad --- /dev/null +++ b/easybuild/easyconfigs/t/tvb-data/tvb-data-1.5-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'tvb-data' +version = '1.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.thevirtualbrain.org/' +description = """The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the + Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains. + Various demonstration data for use with TVB.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/the-virtual-brain/tvb-data/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.11'), + ('TVB-deps', '20160618', versionsuffix), +] + +buildininstalldir = True +use_setup_py_develop = True + +options = {'modulename': 'tvb_data'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tvb-data/tvb-data-20150915-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/tvb-data/tvb-data-20150915-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..975a960c4d420f98834fd0a4026c83de8be3637a --- /dev/null +++ b/easybuild/easyconfigs/t/tvb-data/tvb-data-20150915-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'tvb-data' +version = '20150915' +commit = '212e60b' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.thevirtualbrain.org/' +description = """The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the + Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains. + Various demonstration data for use with TVB.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/the-virtual-brain/tvb-data/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('Python', '2.7.11'), + ('TVB-deps', '20160618', versionsuffix), +] + +buildininstalldir = True +use_setup_py_develop = True + +options = {'modulename': 'tvb_data'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tvb-framework/tvb-framework-1.5-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/tvb-framework/tvb-framework-1.5-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..1197e6d9025f4cd8652d7405945943d9beb83fc7 --- /dev/null +++ b/easybuild/easyconfigs/t/tvb-framework/tvb-framework-1.5-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'tvb-framework' +version = '1.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.thevirtualbrain.org/' +description = """The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the + Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains. + TVB Scientific Library is the most important scientific contribution of TVB Project.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/the-virtual-brain/tvb-framework/archive/'] +sources = ['%(version)s.tar.gz'] + +patches = ['tvb-framework-%(version)s_unfix-pypkg-versions.patch'] + +dependencies = [ + ('Python', '2.7.11'), + ('TVB-deps', '20160618', versionsuffix), +] + +buildininstalldir = True +use_setup_py_develop = True + +options = {'modulename': 'tvb.core'} + +sanity_check_paths = { + 'files': ['tvb-framework-%(version)s/tvb/config/logger/logger_config.conf'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tvb-framework/tvb-framework-1.5_unfix-pypkg-versions.patch b/easybuild/easyconfigs/t/tvb-framework/tvb-framework-1.5_unfix-pypkg-versions.patch new file mode 100644 index 0000000000000000000000000000000000000000..c3f43af73b2f66b069c2d3056a96174caf377254 --- /dev/null +++ b/easybuild/easyconfigs/t/tvb-framework/tvb-framework-1.5_unfix-pypkg-versions.patch @@ -0,0 +1,16 @@ +don't fix versions of h5py and matplotlib Python packages +author: Kenneth Hoste (HPC-UGent) +--- tvb-framework-1.5/setup.py.orig 2016-06-18 00:18:13.000000000 +0200 ++++ tvb-framework-1.5/setup.py 2016-06-23 10:45:57.454497000 +0200 +@@ -47,9 +47,9 @@ + TVB_TEAM += "Stuart Knock, Marmaduke Woodman, Paula Sansz Leon, " + + TVB_INSTALL_REQUIREMENTS = ["apscheduler", "beautifulsoup", "cherrypy", "genshi", "cfflib", "formencode==1.3.0a1", +- "h5py==2.3.0", "lxml", "minixsv", "mod_pywebsocket", "networkx", "nibabel", "numpy", ++ "h5py", "lxml", "minixsv", "mod_pywebsocket", "networkx", "nibabel", "numpy", + "numexpr", "psutil", "scikit-learn", "scipy", "simplejson", "Pillow", +- "sqlalchemy==0.7.8", "sqlalchemy-migrate==0.7.2", "matplotlib==1.5.1"] ++ "sqlalchemy==0.7.8", "sqlalchemy-migrate==0.7.2", "matplotlib"] + + EXCLUDE_INTROSPECT_FOLDERS = [folder for folder in os.listdir(".") + if os.path.isdir(os.path.join(".", folder)) and folder != "tvb"] diff --git a/easybuild/easyconfigs/t/tvb-framework/tvb-framework-20150921-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/tvb-framework/tvb-framework-20150921-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..0d6f908984d40f39c33d81064c41609bb8438924 --- /dev/null +++ b/easybuild/easyconfigs/t/tvb-framework/tvb-framework-20150921-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'tvb-framework' +version = '20150921' +commit = '7e49b604aed41bb7525547cc4b54ebe744a80716' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.thevirtualbrain.org/' +description = """The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the + Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains. + TVB Scientific Library is the most important scientific contribution of TVB Project.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/the-virtual-brain/tvb-framework/archive/'] +sources = ['%s.tar.gz' % commit] + +patches = ['tvb-framework-%(version)s_unfix-pypkg-versions.patch'] + +dependencies = [ + ('Python', '2.7.11'), + ('TVB-deps', '20160618', versionsuffix), +] + +buildininstalldir = True +use_setup_py_develop = True + +options = {'modulename': 'tvb.core'} + +sanity_check_paths = { + 'files': ['tvb-framework-%s/tvb/config/logger/logger_config.conf' % commit], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tvb-framework/tvb-framework-20150921_unfix-pypkg-versions.patch b/easybuild/easyconfigs/t/tvb-framework/tvb-framework-20150921_unfix-pypkg-versions.patch new file mode 100644 index 0000000000000000000000000000000000000000..279e5a3e2b41d343b1621f0eeafb4478bddd1f3b --- /dev/null +++ b/easybuild/easyconfigs/t/tvb-framework/tvb-framework-20150921_unfix-pypkg-versions.patch @@ -0,0 +1,16 @@ +don't fix versions of h5py and matplotlib Python packages +author: Kenneth Hoste (HPC-UGent) +--- setup.py.orig 2016-03-29 08:34:20.000000000 +0200 ++++ setup.py 2016-04-28 15:27:35.764121169 +0200 +@@ -47,9 +47,9 @@ + TVB_TEAM += "Stuart Knock, Marmaduke Woodman, Paula Sansz Leon, " + + TVB_INSTALL_REQUIREMENTS = ["apscheduler", "beautifulsoup", "cherrypy", "genshi", "cfflib", "formencode==1.3.0a1", +- "h5py==2.3.0", "lxml", "minixsv", "mod_pywebsocket", "networkx", "nibabel", "numpy", ++ "h5py", "lxml", "minixsv", "mod_pywebsocket", "networkx", "nibabel", "numpy", + "numexpr", "psutil", "scikit-learn", "scipy", "simplejson", "Pillow", +- "sqlalchemy==0.7.8", "sqlalchemy-migrate==0.7.2", "matplotlib==1.2.1"] ++ "sqlalchemy==0.7.8", "sqlalchemy-migrate==0.7.2", "matplotlib"] + + EXCLUDE_INTROSPECT_FOLDERS = [folder for folder in os.listdir(".") + if os.path.isdir(os.path.join(".", folder)) and folder != "tvb"] diff --git a/easybuild/easyconfigs/t/tvb-library/tvb-library-1.5-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/tvb-library/tvb-library-1.5-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..e8dc51bfc398bd6adfb296cc18ea7a915547bb50 --- /dev/null +++ b/easybuild/easyconfigs/t/tvb-library/tvb-library-1.5-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'tvb-library' +version = '1.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.thevirtualbrain.org/' +description = """The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the + Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains. + TVB Scientific Library is the most important scientific contribution of TVB Project.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/the-virtual-brain/tvb-library/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Python', '2.7.11'), + ('TVB-deps', '20160618', versionsuffix), +] + +buildininstalldir = True +use_setup_py_develop = True + +options = {'modulename': 'tvb.simulator'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tvb-library/tvb-library-20150922-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/t/tvb-library/tvb-library-20150922-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..c31bf9f004c23d063d64246637dd64bfefbde84d --- /dev/null +++ b/easybuild/easyconfigs/t/tvb-library/tvb-library-20150922-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'tvb-library' +version = '20150922' +commit = '924a22f' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.thevirtualbrain.org/' +description = """The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the + Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains. + TVB Scientific Library is the most important scientific contribution of TVB Project.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = ['https://github.com/the-virtual-brain/tvb-library/archive/'] +sources = ['%s.tar.gz' % commit] + +dependencies = [ + ('Python', '2.7.11'), + ('TVB-deps', '20160618', versionsuffix), +] + +buildininstalldir = True +use_setup_py_develop = True + +options = {'modulename': 'tvb.simulator'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCLUST/UCLUST-1.2.22q-i86linux64.eb b/easybuild/easyconfigs/u/UCLUST/UCLUST-1.2.22q-i86linux64.eb new file mode 100644 index 0000000000000000000000000000000000000000..9defd28727f0a6432e27d47bd2476ff6676c0346 --- /dev/null +++ b/easybuild/easyconfigs/u/UCLUST/UCLUST-1.2.22q-i86linux64.eb @@ -0,0 +1,22 @@ +easyblock = 'Binary' + +name = 'UCLUST' +version = '1.2.22q' +versionsuffix = '-i86linux64' + +homepage = 'http://www.drive5.com/usearch/index.html' +description = """UCLUST: Extreme high-speed sequence clustering, alignment and database search.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# licensed for use with PyNAST and QIIME, see http://www.drive5.com/uclust/downloads1_2_22q.html +source_urls = ['http://www.drive5.com/uclust/'] +uclust_bin = 'uclust%s%s_%s' % (version[-1], version[:-1], versionsuffix[1:]) +sources = [uclust_bin] + +install_cmd = "mkdir -p %%(installdir)s/bin && mv %s %%(installdir)s/bin/%%(namelower)s" % uclust_bin + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.20-foss-2016a.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.20-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a1f9ee01f434a8fb89a1206d5b14d2d818e7a37c --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.20-foss-2016a.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': 'foss', 'version': '2016a'} +toolchainopts = {'opt': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['ftp://ftp.unidata.ucar.edu/pub/udunits'] + +dependencies = [('expat', '2.1.1')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/u/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/u/UFL/UFL-1.0.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/u/UFL/UFL-1.0.0-goolf-1.4.10-Python-2.7.3.eb index 44bbfb4a0628f7bb69af1e4643049c047ca68e4c..5ef4a81e2da5bf5ce4c3fef45ce2daac89543a9e 100644 --- a/easybuild/easyconfigs/u/UFL/UFL-1.0.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/u/UFL/UFL-1.0.0-goolf-1.4.10-Python-2.7.3.eb @@ -4,9 +4,9 @@ name = 'UFL' version = '1.0.0' homepage = 'https://launchpad.net/ufl' -description = """The Unified Form Language (UFL) is a domain specific language for declaration of finite element discretizations -of variational forms. More precisely, it defines a flexible interface for choosing finite element spaces and defining expressions -for weak forms in a notation close to mathematical notation.""" +description = """The Unified Form Language (UFL) is a domain specific language for declaration of finite element +discretizations of variational forms. More precisely, it defines a flexible interface for choosing finite element +spaces and defining expressions for weak forms in a notation close to mathematical notation.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/u/UFL/UFL-1.0.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/u/UFL/UFL-1.0.0-ictce-5.3.0-Python-2.7.3.eb index 30a212235a062a7378a7d4a0bac5d575b6cdc233..325975ad7c1ae8ada99331e648f24ecaf7960449 100644 --- a/easybuild/easyconfigs/u/UFL/UFL-1.0.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/u/UFL/UFL-1.0.0-ictce-5.3.0-Python-2.7.3.eb @@ -4,10 +4,9 @@ name = 'UFL' version = '1.0.0' homepage = 'https://launchpad.net/ufl' -description = """The Unified Form Language (UFL) is a domain specific language for declaration of finite element discretizations - of variational forms. More precisely, it defines a flexible interface for choosing finite element spaces and defining expressions - for weak forms in a notation close to mathematical notation.""" - +description = """The Unified Form Language (UFL) is a domain specific language for declaration of finite element +discretizations of variational forms. More precisely, it defines a flexible interface for choosing finite element +spaces and defining expressions for weak forms in a notation close to mathematical notation.""" toolchain = {'name': 'ictce', 'version': '5.3.0'} diff --git a/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-6.1.544-i86linux32.eb b/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-6.1.544-i86linux32.eb new file mode 100644 index 0000000000000000000000000000000000000000..52e94958738237964c1195c827a6471e9ddc876f --- /dev/null +++ b/easybuild/easyconfigs/u/USEARCH/USEARCH-5.2.236-6.1.544-i86linux32.eb @@ -0,0 +1,37 @@ +easyblock = 'Binary' + +name = 'USEARCH' +ver1 = '5.2.236' +ver2 = '6.1.544' +version = '%s-%s' % (ver1, ver2) +versionsuffix = '-i86linux32' + +homepage = 'http://www.drive5.com/usearch/index.html' +description = """USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are + often orders of magnitude faster than BLAST.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# download via http://www.drive5.com/usearch/download.html +usearch5_bin = 'usearch%s_%s' % (ver1, versionsuffix[1:]) +usearch6_bin = 'usearch%s_%s' % (ver2, versionsuffix[1:]) +sources = [ + usearch5_bin, + usearch6_bin, +] + +install_cmd = "mkdir -p %(installdir)s/bin && " +install_cmd += "cp %s %%(installdir)s/bin/%%(namelower)s && " % usearch5_bin +install_cmd += "cp %s %%(installdir)s/bin/%%(namelower)s61 && " % usearch6_bin +install_cmd += "chmod a+rx %(installdir)s/bin/*" + +modloadmsg = """USEARCH (32-bit) is licensed software but + can be used for free by individuals when registered. A 64-bit version is + also available. For more information see http://www.drive5.com/usearch .""" + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/%(namelower)s61'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/u/USPEX/USPEX-9.4.4-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/u/USPEX/USPEX-9.4.4-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..ae04827ae1a568d80bb05ec99f00afd6ee8b7ca2 --- /dev/null +++ b/easybuild/easyconfigs/u/USPEX/USPEX-9.4.4-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,49 @@ +easyblock = 'PackedBinary' + +name = 'USPEX' +version = '9.4.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://uspex-team.org/uspex/overview' +description = """USPEX (Universal Structure Predictor: Evolutionary Xtallography... + and in Russian "uspekh" means "success" - owing to the high success rate and many + useful results produced by this method) is a method developed by the Oganov + laboratory since 2004. The problem of crystal structure prediction is very old and + does, in fact, constitute the central problem of theoretical crystal chemistry. + +USPEX can also be used for finding low-energy metastable phases, as well as stable + structures of nanoparticles, surface reconstructions, molecular packings in organic + crystals, and for searching for materials with desired physical (mechanical, + electronic) properties. The USPEX code is based on an efficient evolutionary + algorithm developed by A.R. Oganov's group, but also has options for using + alternative methods (random sampling, metadynamics, corrected particle swarm + optimization algorithms). USPEX is interfaced with many ab initio codes, such as + VASP, SIESTA, GULP, Quantum Espresso, CP2K, CASTEP, LAMMPS, and so on. """ + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = ['%(name)s-%(version)s.tar.gz'] +#You have to register before download +#source_urls = ['http://uspex-team.org/uspex/downloads'] + +dependencies = [ + ('Python', '2.7.12'), + ('Octave', '4.0.3'), +] + +postinstallcmds = [ + 'echo $EBROOTOCTAVE/bin/octave > %(installdir)s/CODEPATH', + 'chmod +x %(installdir)s/src/FunctionFolder/Tool/*', + 'rm %(installdir)s/INSTALL', + 'rm %(installdir)s/install.sh', + 'rm %(installdir)s/job', +] + +sanity_check_paths = { + 'files': ['USPEX'], + 'dirs': ['doc', 'examples', 'lib', 'src', 'tests'] +} + +modextravars = {'USPEXPATH': '%(installdir)s/src'} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb index dec0e334cae810c3e1c313d15505e4738c8c880b..395c68df0e6971329f4d56d499fadbb531930a5c 100644 --- a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-goolf-1.4.10.eb @@ -26,7 +26,7 @@ configopts += "--without-python " dependencies = [('ncurses', '5.9')] sanity_check_paths = { - 'files': ['lib/lib%s.a' % x for x in ['blkid' , 'mount', 'uuid']], + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], 'dirs': ['include', 'bin', 'share', 'sbin'], } diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.28-foss-2016a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.28-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8c21c443e70c2e86c7a1185b8e648c7e3b59e0c9 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.28-foss-2016a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.28' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.28.1-intel-2016b.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.28.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..d02d397e2393d7203faf091d133e14169179cd37 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.28.1-intel-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.28.1' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.29-foss-2016b.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.29-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..27b08c5298d2607d1f5c5b6ef7380d7a2c608e6b --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.29-foss-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.29' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.29-intel-2016b.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.29-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..b5ac58a535cb6d5b633fe048a0a84f3d29d46889 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.29-intel-2016b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.29' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] + +# disable account related utilities (they need OS dependant pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +dependencies = [('ncurses', '6.0')] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/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..c9841ec8b60b98f51f9dc4e86a4bcda645551901 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/VCFtools/VCFtools-0.1.11-ictce-5.5.0-Perl-5.16.3.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-ictce-5.5.0-Perl-5.16.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..1350a7b674dbb8883cbcfbf71b2067cf135e2888 --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.11-ictce-5.5.0-Perl-5.16.3.eb @@ -0,0 +1,39 @@ +# 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 + +name = 'VCFtools' +version = '0.1.11' + +easyblock = 'MakeCp' + +homepage = "http://vcftools.sourceforge.net/" +description = """The aim of VCFtools is to provide + methods for working with VCF files: validating, + merging, comparing and calculate some basic population + genetic statistics. """ + +toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s_%(version)s.tar.gz'] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) +dependencies = [ + (perl, perlver), +] + +files_to_copy = ["bin", "lib"] + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['vcftools', 'vcf-sort', 'vcf-stats']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb index cbdd6fa4ebb4a8bf47935077c87408f03dd42fd5..c4c82d2f79a5258fff6f6ad774b8fa4e7e8738ed 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.4.10-Perl-5.16.3.eb @@ -18,7 +18,7 @@ source_urls = ['https://github.com/vcftools/vcftools/releases/download/v%(versio sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('Perl' , '5.16.3'), + ('Perl', '5.16.3'), ] sanity_check_paths = { @@ -28,7 +28,7 @@ sanity_check_paths = { } modextrapaths = { - 'PERL5LIB': 'lib/perl5/site_perl/', + 'PERL5LIB': 'lib/perl5/site_perl/', } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.7.20-Perl-5.22.2.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.7.20-Perl-5.22.2.eb index c98bd7490496c6cec84f30f9ea7f2d6bdda2a50b..6a770e5ef19f4745b801575e3675d91bac66ce7e 100644 --- a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.7.20-Perl-5.22.2.eb +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.14-goolf-1.7.20-Perl-5.22.2.eb @@ -18,7 +18,7 @@ source_urls = ['https://github.com/vcftools/vcftools/releases/download/v%(versio sources = [SOURCELOWER_TAR_GZ] dependencies = [ - ('Perl' , '5.22.2'), + ('Perl', '5.22.2'), ] sanity_check_paths = { @@ -28,7 +28,7 @@ sanity_check_paths = { } modextrapaths = { - 'PERL5LIB': 'lib/perl5/site_perl/', + 'PERL5LIB': 'lib/perl5/site_perl/', } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb b/easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb new file mode 100644 index 0000000000000000000000000000000000000000..367fff56961428c99a2b009a51c0e81a65da05f7 --- /dev/null +++ b/easybuild/easyconfigs/v/VEGAS/VEGAS-0.8.27.eb @@ -0,0 +1,29 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Ravi Tripathi +# Email: ravi89@uab.edu + +easyblock = "Tarball" + +name = 'VEGAS' +version = '0.8.27' + +homepage = 'http://gump.qimr.edu.au/VEGAS/' +description = """ VEGAS (Versatile Gene-based Association Study) is +a free program for performing gene-based tests for association using +the results from genetic association studies """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://gump.qimr.edu.au/VEGAS/'] +sources = ['vegas-%(version)s-hapmapCEU.tar.gz'] + +checksums = ['87ca985fec0c64820bfd202f15fb31de'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ["vegas", "glist-hg18", "VEGAS-readme.pdf"], + 'dirs': ["hapmapCEU"] +} + +moduleclass = 'bio' 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-2013_update10.eb b/easybuild/easyconfigs/v/VTune/VTune-2013_update10.eb index 109b1823e3d0a427ad76cc8aa34d4f860cf4b45e..2c12506de30ff18deb2ff9f83a2f8e88dd80bb09 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2013_update10.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2013_update10.eb @@ -2,7 +2,8 @@ name = 'VTune' version = '2013_update10' homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' -description = "Intel VTune Amplifier XE 2013 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java." +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/v/VTune/VTune-2013_update6.eb b/easybuild/easyconfigs/v/VTune/VTune-2013_update6.eb index 52589402c4f48fc1524ab6f84605e8a2a362b511..3a689d534753a237b17a569a6cd2d34464ab9a16 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2013_update6.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2013_update6.eb @@ -2,7 +2,8 @@ name = 'VTune' version = '2013_update6' homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' -description = "Intel VTune Amplifier XE 2013 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java." +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/v/VTune/VTune-2013_update8.eb b/easybuild/easyconfigs/v/VTune/VTune-2013_update8.eb index de9aeec90dc3798abd61fca1cd0e9dab9d648a68..210397b41a50c74609b04c550c6de3d637715b6e 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2013_update8.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2013_update8.eb @@ -2,7 +2,8 @@ name = 'VTune' version = '2013_update8' homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' -description = "Intel VTune Amplifier XE 2013 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java." +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" toolchain = {'name': 'dummy', 'version': 'dummy'} diff --git a/easybuild/easyconfigs/v/VTune/VTune-2013_update9.eb b/easybuild/easyconfigs/v/VTune/VTune-2013_update9.eb index f40578b690df1af7d499a173affccf661527b364..c56eb2232523890f6e88e2f9730b266cabe5fcbc 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2013_update9.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2013_update9.eb @@ -2,7 +2,8 @@ name = 'VTune' version = '2013_update9' homepage = 'http://software.intel.com/en-us/intel-vtune-amplifier-xe' -description = "Intel VTune Amplifier XE 2013 is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java." +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" toolchain = {'name': 'dummy', 'version': 'dummy'} 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/VTune/VTune-2017_update1.eb b/easybuild/easyconfigs/v/VTune/VTune-2017_update1.eb new file mode 100644 index 0000000000000000000000000000000000000000..7c95b0c1d73a4e81b442db1d5a0051958842a83d --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2017_update1.eb @@ -0,0 +1,16 @@ +name = 'VTune' +version = '2017_update1' + +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.""" + +checksums = ['c3524d972072780023c3839b1188baaa'] + +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/Valgrind/Valgrind-3.11.0-foss-2016a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..1582b5a179778423338e592f4ef1f8dc06d61986 --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.11.0-foss-2016a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.11.0' + +homepage = 'http://valgrind.org/downloads/' +description = "Valgrind: Debugging and profiling tools" + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://valgrind.org/downloads/'] + +toolchain = {'name': 'foss', 'version': '2016a'} + +configopts = ' --with-mpicc="$MPICC"' + +binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binaries] + + ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-goolf-1.5.14.eb b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..8c1fc2104fe1a6349c9b0b53ba535f5db9a0ed66 --- /dev/null +++ b/easybuild/easyconfigs/v/VampirTrace/VampirTrace-5.14.4-goolf-1.5.14.eb @@ -0,0 +1,50 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: New BSD +# +# This work is based from experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## +easyblock = 'ConfigureMake' + +name = 'VampirTrace' +version = '5.14.4' + +homepage = 'http:/www.tu-dresden.de/zih/vampirtrace/' +description = """VampirTrace is an open source library that allows detailed logging of program + execution for parallel applications using message passing (MPI) and threads (OpenMP), Pthreads).""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=vampirtrace&get='] + +dependencies = [ + ('OTF', '1.12.4'), + ('PAPI', '5.2.0'), + ('PDT', '3.19'), +] + +configopts = 'MPIFC="$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/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb index 1e20cf23ec2d0441a40525d67e6245c2310b41db..759ecb7840e83e1ba0c439c5bb2ec7a88c6bd477 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-goolf-1.4.10.eb @@ -29,7 +29,7 @@ source_urls = ['http://www.tbi.univie.ac.at/~ronny/RNA'] configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory # Code NOT yet tested, therefor left here for future recycling -#preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' +# preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb index a66be3332b645b7eca8cf323a57e2552eff304b8..f0b402025371329db9087c9c188aa613cd950eb7 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.0.7-ictce-5.3.0.eb @@ -32,7 +32,7 @@ patches = ['ViennaRNA_ictce-pragma.patch'] configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory # Code NOT yet tested, therefor left here for future recycling -#preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' +# preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', diff --git a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb index 664ec56172f9d0ac0b9b23e61ddebb43dc8f9299..106d2f71e31e8705848bfcfcf29914429fc8a6fb 100644 --- a/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/v/ViennaRNA/ViennaRNA-2.1.6-ictce-5.5.0.eb @@ -31,7 +31,7 @@ patches = ['ViennaRNA-2.1.6_ictce.patch'] configopts = '--without-perl' # Alternatively, you may want to use the following to copy the perl-module to a "local" directory # Code NOT yet tested, therefor left here for future recycling -#preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' +# preconfigopts = 'env PERLPREFIX="/path/where/the/perl/module/shoud/go"' sanity_check_paths = { 'files': ['bin/RNA%s' % x for x in ['fold', 'eval', 'heat', 'pdist', 'distance', diff --git a/easybuild/easyconfigs/v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb b/easybuild/easyconfigs/v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..daa2ad6b9362039aee4182a5964584129415c959 --- /dev/null +++ b/easybuild/easyconfigs/v/VirSorter/VirSorter-20160601-foss-2016a-Perl-5.22.1.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'VirSorter' +version = '20160601' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'https://github.com/simroux/VirSorter' +description = """VirSorter: mining viral signal from microbial genomic data.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/simroux/%(name)s/archive/'] +sources = ['master.zip'] + +dependencies = [ + ('Perl', '5.22.1'), + ('BioPerl', '1.6.924', '-Perl-%(perlver)s'), + ('HMMER', '3.1b2'), + ('MCL', '14.137'), + ('MetaGeneAnnotator', '20080819', '-x86-64', True), + ('MUSCLE', '3.8.31'), + ('BLAST', '2.2.26', '-Linux_x86_64', True), +] + +sanity_check_paths = { + 'files': ['wrapper_phage_contigs_sorter_iPlant.pl'], + 'dirs': ['Scripts'], +} + +modextrapaths = {'PATH': ['', 'Scripts']} +modaliases = {'%(namelower)s': 'wrapper_phage_contigs_sorter_iPlant.pl'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-foss-2016a.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7020ae2236abdc1a2ac45935189852db0ff8be0e --- /dev/null +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-foss-2016a.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Voro++' +version = '0.4.6' + +homepage = 'http://math.lbl.gov/voro++/' +description = """Voro++ is a software library for carrying out three-dimensional computations of the Voronoi +tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, +computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that +rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used +to analyze a system of particles.""" + +toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://math.lbl.gov/voro++/download/dir/'] + +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['2338b824c3b7b25590e18e8df5d68af9'] + +# No configure +skipsteps = ['configure'] + +# Override CXX and CFLAGS variables from Makefile +buildopts = 'CXX="$CXX" CFLAGS="$CXXFLAGS"' + +# Override PREFIX variable from Makefile +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/voro++', 'lib/libvoro++.a', 'include/voro++/voro++.hh'], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/voro++'} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-intel-2016a.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d7bac431f70fec49ad6d8ccabe520fc8924e546e --- /dev/null +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-intel-2016a.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'Voro++' +version = '0.4.6' + +homepage = 'http://math.lbl.gov/voro++/' +description = """Voro++ is a software library for carrying out three-dimensional computations of the Voronoi +tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, +computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that +rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used +to analyze a system of particles.""" + +toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://math.lbl.gov/voro++/download/dir/'] + +# Let's store the checksum in order to be sure it doesn't suddenly change +checksums = ['2338b824c3b7b25590e18e8df5d68af9'] + +# No configure +skipsteps = ['configure'] + +# Override CXX and CFLAGS variables from Makefile +buildopts = 'CXX="$CXX" CFLAGS="$CXXFLAGS"' + +# Override PREFIX variable from Makefile +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/voro++', 'lib/libvoro++.a', 'include/voro++/voro++.hh'], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/voro++'} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.3-foss-2016a.eb b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.3-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d08f6ddb122edca18046c54af57db35eceeb6291 --- /dev/null +++ b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.3-foss-2016a.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'verifyBamID' +version = '1.1.3' + +homepage = "http://csg.sph.umich.edu/kang/verifyBamID/index.html" +description = """verifyBamID is a software that verifies whether the reads in particular file match previously known + genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of + two samples. verifyBamID can detect sample contamination and swaps when external genotypes are available. When + external genotypes are not available, verifyBamID still robustly detects sample swaps. +""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://github.com/statgen/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)sLibStatGen.%(version)s.tgz'] + +checksums = ['9b3d4c73c8f72e6b8f1e014702bc5bec'] + +buildopts = 'CXX="$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/v/vsc-base/vsc-base-2.5.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..4663f7299c918b4be99ac582105b0762fb46be98 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.5.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'vsc-base' +version = '2.5.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/vsc-base' +description = """Base library for Python tools developed by UGent's HPC group, including generaloption (option parser) +and fancylogger (logging functionality).""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +builddependencies = [('vsc-install', '0.10.11', versionsuffix)] +dependencies = [ + ('Python', '2.7.12'), +] + +options = {'modulename': 'vsc.utils.fancylogger'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.11-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.11-intel-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..a3bd950894cb5bff2b0b21079ade3f99d5b39465 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.11-intel-2016a-Python-2.7.11.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'vsc-install' +version = '0.10.11' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/vsc-install' +description = """vsc-install provides shared setuptools functions and classes for Python libraries + developed by UGent's HPC group""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +dependencies = [ + ('Python', '2.7.11'), +] + +options = {'modulename': 'vsc.install'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.11-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.11-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..cac40f2de54f3574afbbefce13e9da57ef18db1c --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-install/vsc-install-0.10.11-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'vsc-install' +version = '0.10.11' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/vsc-install' +description = """vsc-install provides shared setuptools functions and classes for Python libraries + developed by UGent's HPC group""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +dependencies = [ + ('Python', '2.7.12'), +] + +options = {'modulename': 'vsc.install'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..fa730a6cadd4f01115c36011ffd94cf1b6412ec1 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun-scoop/vsc-mympirun-scoop-3.4.1-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,29 @@ +easyblock = 'VSCPythonPackage' + +name = 'vsc-mympirun-scoop' +version = '3.4.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://hpcugent.github.com/vsc-mympirun/' +description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/hpcugent/vsc-mympirun-scoop/archive/'] + +dependencies = [ + ('vsc-processcontrol', '1.0', '-vsc-base-2.1.2', True), + ('vsc-mympirun', '3.4.2', '', True), + ('Python', '2.7.12'), + ('SCOOP', '0.6.2', versionsuffix), +] + +options = {'modulename': 'vsc.mympirun.scoop'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/vsc/mympirun/scoop'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.3-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.3-intel-2016b-Python-2.7.12.eb new file mode 100755 index 0000000000000000000000000000000000000000..78647ea88ee3b71e6c34417ba1fe0f1ac9d3d320 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.3-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'vsc-mympirun' +version = '3.4.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] + +dependencies = [ + ('Python', '2.7.12'), + ('vsc-base', '2.5.1', versionsuffix), +] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +options = {'modulename': 'vsc.mympirun'} + +sanity_check_paths = { + 'files': ['bin/mympirun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vt/vt-0.577-goolf-1.7.20.eb b/easybuild/easyconfigs/v/vt/vt-0.577-goolf-1.7.20.eb index 8a87b5f90807eb396ab165d5ac61ab8e07b08773..f8de4a4721538b577e478163e8ecf78973959932 100644 --- a/easybuild/easyconfigs/v/vt/vt-0.577-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/v/vt/vt-0.577-goolf-1.7.20.eb @@ -6,7 +6,7 @@ easyblock = 'MakeCp' name = 'vt' -version = '0.577' +version = '0.577' homepage = 'http://genome.sph.umich.edu/wiki/Vt' description = """A tool set for short variant discovery in genetic sequence data.""" @@ -17,13 +17,13 @@ source_urls = ['https://github.com/atks/vt/archive/'] sources = ['%(version)s.tar.gz'] dependencies = [ - ('zlib', '1.2.8'), + ('zlib', '1.2.8'), ] runtest = 'test' files_to_copy = [(["vt"], "bin"), "README.md", "LICENSE"] - + sanity_check_paths = { 'files': ["bin/vt"], 'dirs': [], 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/Whoosh/Whoosh-2.7.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/w/Whoosh/Whoosh-2.7.0-goolf-1.4.10-Python-2.7.3.eb index db2dcb5741aaf597f38771ff617087bd0502702e..428e7a9607b33e49fbf4eddb92cec831377400ad 100644 --- a/easybuild/easyconfigs/w/Whoosh/Whoosh-2.7.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/w/Whoosh/Whoosh-2.7.0-goolf-1.4.10-Python-2.7.3.eb @@ -19,9 +19,9 @@ pyshortver = ".".join(pyver.split(".")[:-1]) versionsuffix = "-%s-%s" % (python, pyver) dependencies = [ - (python, pyver), - ('numpy','1.6.2', versionsuffix), - ('scipy', '0.11.0', versionsuffix), + (python, pyver), + ('numpy', '1.6.2', versionsuffix), + ('scipy', '0.11.0', versionsuffix), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/w/wcwidth/wcwidth-0.1.7-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/w/wcwidth/wcwidth-0.1.7-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..e5cebd1105a8a2e9eeeb590295ab291ff03a36e9 --- /dev/null +++ b/easybuild/easyconfigs/w/wcwidth/wcwidth-0.1.7-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'wcwidth' +version = '0.1.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jquast/wcwidth' +description = """wcwidth is a low-level Python library to simplify Terminal emulation.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = ['https://pypi.python.org/packages/7e/9f/526a6947247599b084ee5232e4f9190a38f398d7300d866af3ab571a5bfe/'] +sources = ['%(name)s-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '2.7.11'), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/wcwidth'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/wcwidth/wcwidth-0.1.7-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/w/wcwidth/wcwidth-0.1.7-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..0f9bbee11b4bfb9a54424fcadedaadd7852c65c4 --- /dev/null +++ b/easybuild/easyconfigs/w/wcwidth/wcwidth-0.1.7-foss-2016a-Python-3.5.1.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': 'foss', 'version': '2016a'} + +source_urls = ['https://pypi.python.org/packages/7e/9f/526a6947247599b084ee5232e4f9190a38f398d7300d866af3ab571a5bfe/'] +sources = ['%(name)s-%(version)s-py2.py3-none-any.whl'] + +dependencies = [ + ('Python', '3.5.1'), +] + +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/wcwidth/wcwidth-0.1.7-intel-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/w/wcwidth/wcwidth-0.1.7-intel-2016b-Python-2.7.12.eb new file mode 100644 index 0000000000000000000000000000000000000000..3ba469ef19985ac2b14b13ffc11935236c7da4e6 --- /dev/null +++ b/easybuild/easyconfigs/w/wcwidth/wcwidth-0.1.7-intel-2016b-Python-2.7.12.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'wcwidth' +version = '0.1.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jquast/wcwidth' +description = """wcwidth is a low-level Python library to simplify Terminal emulation.""" + +toolchain = {'name': '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', '2.7.12'), +] +builddependencies = [ + ('pip', '8.1.2', versionsuffix), +] + +use_pip = True +unpack_sources = False + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/wcwidth'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/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/wget/wget-1.17.1-foss-2016a.eb b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb index bbebd9aa833c3ac3dc702be5aaa288cb0db19de1..05a38bee324174ba5a109023ee96b154b3c458ea 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.17.1-foss-2016a.eb @@ -14,13 +14,15 @@ source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_XZ] dependencies = [ - #('gnutls', '3.4.11'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date gnutls for security reasons ('PCRE', '8.38'), ('libidn', '1.32'), ('zlib', '1.2.8'), - #('OpenSSL', '1.0.1s'), # OS dependency should be preferred if the os version is more recent then this version, it's - # nice to have an up to date openssl for security reasons + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1s'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date gnutls for security reasons + # ('GnuTLS', '3.4.11'), ] configopts = '--with-ssl=openssl ' @@ -28,7 +30,7 @@ configopts = '--with-ssl=openssl ' osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # Optionally, you can use gnutls (default) instead of OpenSSL. # Do not forget to comment out configopts in that case. -#osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] +# osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] sanity_check_paths = { 'files': ['bin/wget'], diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.29.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/w/wheel/wheel-0.29.0-foss-2016a-Python-2.7.11.eb new file mode 100644 index 0000000000000000000000000000000000000000..c66afc64449e3b97e6a08efd55cdc5440ba4f2e7 --- /dev/null +++ b/easybuild/easyconfigs/w/wheel/wheel-0.29.0-foss-2016a-Python-2.7.11.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'wheel' +version = '0.29.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/wheel' +description = """A built-package format for Python.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '2.7.11'), +] + +sanity_check_paths = { + 'files': ['bin/wheel'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/wheel/wheel-0.29.0-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/w/wheel/wheel-0.29.0-foss-2016a-Python-3.5.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..765f814390648797dfc9d8f6a936b8c822707ec7 --- /dev/null +++ b/easybuild/easyconfigs/w/wheel/wheel-0.29.0-foss-2016a-Python-3.5.1.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'wheel' +version = '0.29.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/wheel' +description = """A built-package format for Python.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.5.1'), +] + +sanity_check_paths = { + 'files': ['bin/wheel'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/wkhtmltopdf/wkhtmltopdf-0.12.3-Linux-x86_64.eb b/easybuild/easyconfigs/w/wkhtmltopdf/wkhtmltopdf-0.12.3-Linux-x86_64.eb index ee433ddeae637f3e89a324dae90196542ce71461..daaefceb38c23cd18bc62ef580a8a6d899123b7c 100644 --- a/easybuild/easyconfigs/w/wkhtmltopdf/wkhtmltopdf-0.12.3-Linux-x86_64.eb +++ b/easybuild/easyconfigs/w/wkhtmltopdf/wkhtmltopdf-0.12.3-Linux-x86_64.eb @@ -20,12 +20,12 @@ source_urls = ['http://download.gna.org/wkhtmltopdf/%(version_major_minor)s/%(ve sources = ['wkhtmltox-%(version)s_linux-generic-amd64.tar.xz'] osdependencies = [ - ('zlib', 'zlib1g'), - 'fontconfig', - ('freetype', 'libfreetype6'), - ('libX11', 'libx11-6'), - ('libXext', 'libxext6'), - ('libXrender', 'libxrender1') + ('zlib', 'zlib1g'), + 'fontconfig', + ('freetype', 'libfreetype6'), + ('libX11', 'libx11-6'), + ('libXext', 'libxext6'), + ('libXrender', 'libxrender1') ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.5-intel-2016a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.5-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..cd2ac131f0aad5143ea24fa8685839a48de0a667 --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.6.5-intel-2016a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'worker' +version = '1.6.5' + +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': 'intel', 'version': '2016a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/gjbex/worker/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Perl', '5.22.2') +] + +# 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 = intel/2016a@g" %(installdir)s/conf/worker.conf', + '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/worker/worker-1.6.6-intel-2016b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.6-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..dd9436b448a298b7f33329f2ddaff59f3351fe67 --- /dev/null +++ b/easybuild/easyconfigs/w/worker/worker-1.6.6-intel-2016b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'worker' +version = '1.6.6' + +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': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/gjbex/worker/archive/'] +sources = ['%(version)s.tar.gz'] + +dependencies = [ + ('Perl', '5.24.0') +] + +# 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 = intel/2016b@g" %(installdir)s/conf/worker.conf', + '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/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..3ba6c18a9ae63cbc3f5ad9bbf2dda76c1cef6d23 --- /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/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..93c328cff66a60c43d290f73289af8b542a0130a --- /dev/null +++ b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.7.3.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 = 'wxPropertyGrid' +version = '1.4.15' + +homepage = 'http://wxpropgrid.sourceforge.net/' +description = """wxPropertyGrid is a property sheet control for wxWidgets. In other words, it is + a specialized two-column grid for editing properties such as strings, numbers, flagsets, string arrays, and colours.""" + +toolchain = {'name': 'GCC', 'version': '4.7.3'} + +osdependencies = [('wxGTK-devel', 'libwxgtk2.8-dev', 'wxWidgets-ansi-devel')] + +# http://prdownloads.sourceforge.net/wxpropgrid/wxpropgrid-1.4.15-src.tar.gz?download +sources = ['wxpropgrid' + '-%(version)s-src.tar.gz'] +source_urls = ['http://prdownloads.sourceforge.net/wxpropgrid/'] + +sanity_check_paths = { + 'files': ['include/wx/propgrid/propgrid.h', + ('lib/libwxcode_gtk2u_propgrid-2.8.so', 'lib64/libwxcode_gtk2u_propgrid-2.8.so')], + 'dirs': [] +} + +parallel = 1 + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.9.2.eb b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..ccad95cd1da0eaf0423054d1327e29f359506573 --- /dev/null +++ b/easybuild/easyconfigs/w/wxPropertyGrid/wxPropertyGrid-1.4.15-GCC-4.9.2.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 = 'wxPropertyGrid' +version = '1.4.15' + +homepage = 'http://wxpropgrid.sourceforge.net/' +description = """wxPropertyGrid is a property sheet control for wxWidgets. In other words, it is + a specialized two-column grid for editing properties such as strings, numbers, flagsets, string arrays, and colours.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +osdependencies = [('wxGTK-devel', 'libwxgtk2.8-dev', 'wxWidgets-ansi-devel')] + +# http://prdownloads.sourceforge.net/wxpropgrid/wxpropgrid-1.4.15-src.tar.gz?download +sources = ['wxpropgrid' + '-%(version)s-src.tar.gz'] +source_urls = ['http://prdownloads.sourceforge.net/wxpropgrid/'] + +sanity_check_paths = { + 'files': ['include/wx/propgrid/propgrid.h', + ('lib/libwxcode_gtk2u_propgrid-2.8.so', 'lib64/libwxcode_gtk2u_propgrid-2.8.so')], + 'dirs': [] +} + +parallel = 1 + +moduleclass = 'devel' 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..f64e8d14e9150c8f22495877ab6e351614be9fdb --- /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-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016a-Python-2.7.11.eb index 803388b88a7ba8f2620721c14fccdb34863b7765..dbd0b2a2506bfb9563ad30d640fea51f894e32a1 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-3.0.2.0-intel-2016a-Python-2.7.11.eb @@ -1,6 +1,6 @@ name = 'wxPython' version = '3.0.2.0' -versionsuffix = "-Python-%(pyver)s" +versionsuffix = '-Python-%(pyver)s' homepage = 'http://www.wxpython.org' description = """wxPython is a GUI toolkit for the Python programming language. 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..181aa9aaf1280087f15b9ebbfb01b31e72cc1d0a --- /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 new file mode 100644 index 0000000000000000000000000000000000000000..556bda9f6eb6ed8d8e21799201a95af3ac63ddd5 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20160819-intel-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': 'intel', '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/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/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb index 10d7fbd3ea43ed149f1d8d61350be558ecb96e3e..1c770debd8ea180b0aa0a2c2828c662383442453 100644 --- a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb +++ b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-foss-2016a.eb @@ -19,6 +19,13 @@ builddependencies = [ ('libxslt', '1.1.28'), ('gettext', '0.19.7'), ('intltool', '0.51.0', '-Perl-5.22.1'), + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('kbproto', '1.0.7'), + ('xtrans', '1.3.5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb index e72178d939c41cebfff1949873493db93b0dc90b..ce56b41359e41b0ae2f32fc7a69d956c4eb6cea5 100644 --- a/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb +++ b/easybuild/easyconfigs/x/XKeyboardConfig/XKeyboardConfig-2.17-intel-2016a.eb @@ -19,6 +19,13 @@ builddependencies = [ ('libxslt', '1.1.28'), ('gettext', '0.19.7'), ('intltool', '0.51.0', '-Perl-5.22.1'), + ('xextproto', '7.3.0'), + ('xcb-proto', '1.11', '', True), + ('inputproto', '2.3.1'), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('kbproto', '1.0.7'), + ('xtrans', '1.3.5'), ] dependencies = [ diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44_01-GCCcore-4.9.3-Perl-5.24.0.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44_01-GCCcore-4.9.3-Perl-5.24.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..9234f034719e5ab49cced4e165263ffeaf4a041b --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.44_01-GCCcore-4.9.3-Perl-5.24.0.eb @@ -0,0 +1,31 @@ +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': 'GCCcore', 'version': '4.9.3'} + +source_urls = ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [ + ('binutils', '2.25') +] + +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/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..afbf05b28716efce81bae453ad7af9b85a0ad06a --- /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..0fe5f964f003bec6cbee5eae779eed924e0a55dc --- /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/XQilla/XQilla-2.3.0-foss-2015a.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a.eb index aa79e514746830b44cd355279f2736a5d9ba9eae..d587fbd42c91d37e1836ec70ede367d53a2a6590 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-foss-2015a.eb @@ -4,7 +4,8 @@ name = 'XQilla' version = '2.3.0' homepage = 'http://xqilla.sourceforge.net/HomePage' -description = """XQilla is an XQuery and XPath 2 library and command line utility written in C++, implemented on top of the Xerces-C∞ library.""" +description = """XQilla is an XQuery and XPath 2 library and command line utility written in C++, +implemented on top of the Xerces-C∞ library.""" toolchain = {'name': 'foss', 'version': '2015a'} diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a.eb index b169cb58403cd41d80c00233610837d82d7c7ed8..d8f0b44347431dae23c6c286ea952d07382c207c 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.0-intel-2015a.eb @@ -4,7 +4,8 @@ name = 'XQilla' version = '2.3.0' homepage = 'http://xqilla.sourceforge.net/HomePage' -description = """XQilla is an XQuery and XPath 2 library and command line utility written in C++, implemented on top of the Xerces-C∞ library.""" +description = """XQilla is an XQuery and XPath 2 library and command line utility written in C++, +implemented on top of the Xerces-C++ library.""" toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb index d7fbf9539451b6d046b38936e7edda3aa57110af..75b45c2966c780f08d1074deb0073a37577f5b8e 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-foss-2015a.eb @@ -5,8 +5,8 @@ version = '2.3.2' homepage = 'http://xqilla.sourceforge.net/HomePage' -description = """XQilla is an XQuery and XPath 2 library and command line -utility written in C++, implemented on top of the Xerces-C++ library.""" +description = """XQilla is an XQuery and XPath 2 library and command line utility written in C++, +implemented on top of the Xerces-C++ library.""" toolchain = {'name': 'foss', 'version': '2015a'} diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb index c6db3af286f8f7d64ac0f915f9950397eaf998d9..4d539658839aa676107ce30a586a56b29b941267 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-goolf-1.7.20.eb @@ -5,8 +5,8 @@ version = '2.3.2' homepage = 'http://xqilla.sourceforge.net/HomePage' -description = """XQilla is an XQuery and XPath 2 library and command line -utility written in C++, implemented on top of the Xerces-C++ library.""" +description = """XQilla is an XQuery and XPath 2 library and command line utility written in C++, +implemented on top of the Xerces-C++ library.""" toolchain = {'name': 'goolf', 'version': '1.7.20'} diff --git a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb index 1fe033551cbd732240c8abe22d636b90773a8682..df53082bddc3c146d7dc56157e6b9a48ae217ba5 100644 --- a/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb +++ b/easybuild/easyconfigs/x/XQilla/XQilla-2.3.2-intel-2015a.eb @@ -5,8 +5,8 @@ version = '2.3.2' homepage = 'http://xqilla.sourceforge.net/HomePage' -description = """XQilla is an XQuery and XPath 2 library and command line -utility written in C++, implemented on top of the Xerces-C++ library.""" +description = """XQilla is an XQuery and XPath 2 library and command line utility written in C++, +implemented on top of the Xerces-C++ library.""" toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-GCC-4.8.2.eb b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-GCC-4.8.2.eb index 3d54b29efd3f8e5025a8ca701c921aab5ee0d7c7..652e4ccaae022e507afa9c6b497b80e090567d7c 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-GCC-4.8.2.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] # may become useful in non-x86 archs -#configopts = ' --disable-assembler ' +# configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb index e60568da6efb51ea8badca0ae8d6b0148b95214d..134222d629fe7258f2ff48004c086624e3ba3e67 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-goolf-1.4.10.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] # may become useful in non-x86 archs -#configopts = ' --disable-assembler ' +# configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb index 6f7148a406a89fecde26a47a660497697bbbbf78..da40fe12f88e05f9a565ea49676d31cbd131eee3 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.0.5-ictce-5.3.0.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] # may become useful in non-x86 archs -#configopts = ' --disable-assembler ' +# configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb index 99b4d29f28dcda07be4ea7b3f1a039383fdb5c4c..544734e689676d32cc744a829185f94353687311 100644 --- a/easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.0-GCC-4.9.2.eb @@ -12,7 +12,7 @@ sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] # may become useful in non-x86 archs -#configopts = ' --disable-assembler ' +# configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], 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..96695c9d5cb9eb2bba5805f6c4cc13cf76982823 --- /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..f08ddf7da4a28196e65d2c12dd3256ed5cfdf1f2 --- /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..d4f3584da4bbfb5ed53d5c39421925bcd707a00a 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 @@ -13,14 +13,11 @@ 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 -#configopts = ' --disable-assembler ' +# configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], 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..90393732b9c2a2c07caef233f465c51fa291bd2c --- /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 new file mode 100644 index 0000000000000000000000000000000000000000..52273a7c6b698923b372b19f8dfa783914c2e10f --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a-gettext-0.19.7.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +gettext_ver = '0.19.7' +versionsuffix = '-gettext-%s' % gettext_ver + +builddependencies = [ + ('Autotools', '20150215'), + ('gettext', gettext_ver, '', 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.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016a.eb index 2a89ca6af63efcce64d992e231e493b084028ad7..8985ebbf18886d1967f9684951a071428b8ca5bc 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 @@ -13,14 +13,11 @@ 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 -#configopts = ' --disable-assembler ' +# configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], 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 new file mode 100644 index 0000000000000000000000000000000000000000..aaea1f659f17154fa8f0bfee51ccef7a12f39ef9 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-foss-2016b.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': '2016b'} + +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-goolf-1.4.10.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-goolf-1.4.10.eb index f9a06be7327fdd83b568218cf5f373b55f036b03..1b63e653414033c230bdf4ef69399761b79d2ebc 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 @@ -13,14 +13,11 @@ 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 -#configopts = ' --disable-assembler ' +# configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], 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..2cb7040caf5d6caae85f8256aedd5873ebe71f17 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 @@ -13,14 +13,11 @@ 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 -#configopts = ' --disable-assembler ' +# configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], 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 new file mode 100644 index 0000000000000000000000000000000000000000..98229490710a6428e519ddb066ef776cbb774986 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a-gettext-0.19.7.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://tukaani.org/xz/'] + +gettext_ver = '0.19.7' +versionsuffix = '-gettext-%s' % gettext_ver + +builddependencies = [ + ('Autotools', '20150215'), + ('gettext', gettext_ver, '', 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-intel-2016a.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016a.eb index b717af018aaf06fa298f64daca32824917cf202c..bcd46743d29b779fdf30a48946c41f6ed2e36530 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 @@ -13,14 +13,11 @@ 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 -#configopts = ' --disable-assembler ' +# configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], 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 new file mode 100644 index 0000000000000000000000000000000000000000..95304a848da78fc16f1e2f1650b59ac862fa9f17 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.2-intel-2016b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.2' + +homepage = 'http://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'intel', 'version': '2016b'} + +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/Xerces-C++/Xerces-C++-3.1.1-foss-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-foss-2015a.eb index 031a0f54b942355c4f8b80d818c71014362b41c4..5d61dee01a0dc664b748ef723bd7011ee494ba55 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-foss-2015a.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-foss-2015a.eb @@ -4,7 +4,11 @@ name = 'Xerces-C++' version = '3.1.1' homepage = 'http://xerces.apache.org/xerces-c/' -description = """Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.""" +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" toolchain = {'name': 'foss', 'version': '2015a'} diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb index 2dd8450711f0d840dc213a8c65579d0c121224f4..d8c4aa7381fb3c75dc877472bff9dd6012c0dca5 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.1-intel-2015a.eb @@ -4,7 +4,11 @@ name = 'Xerces-C++' version = '3.1.1' homepage = 'http://xerces.apache.org/xerces-c/' -description = """Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.""" +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" toolchain = {'name': 'intel', 'version': '2015a'} diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb index b0abf7e5ebafe66d71e2f45c848a115e21c7f8ad..878febbbdf867c73bd28374066f1b0c6527e31b2 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-foss-2015a.eb @@ -4,7 +4,6 @@ name = 'Xerces-C++' version = '3.1.2' homepage = 'http://xerces.apache.org/xerces-c/' - description = """Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb index 64c371a561fe171d500828a37d9af061e50624e3..54a281fc04bc59ef888eb68f6832487b766d57e4 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-goolf-1.7.20.eb @@ -4,7 +4,6 @@ name = 'Xerces-C++' version = '3.1.2' homepage = 'http://xerces.apache.org/xerces-c/' - description = """Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb index 1ddefd9f9655c8423a02f6c83dae4447f5ff523f..9f7deab432109b14f2519a362baf5315333ef40c 100644 --- a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.1.2-intel-2015a.eb @@ -4,7 +4,6 @@ name = 'Xerces-C++' version = '3.1.2' homepage = 'http://xerces.apache.org/xerces-c/' - description = """Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb index fc928c6c5783657b8fd914d7e699b5a76da73e86..63e623f082d503c05bd31a98f92ca6130d404d6a 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb @@ -2,7 +2,8 @@ name = 'Xmipp' version = '3.1' homepage = 'http://xmipp.cnb.csic.es/' -description = "Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy." +description = """Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron + microscopy.""" source_urls = ['http://xmipp.cnb.csic.es/Downloads/'] sources = ['Xmipp-%(version)s-src.tar.gz'] diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb index ec08bd48fa2909fcf3d677c2092420df96f2b746..18d8b11833b5724f4d446ded08d79eb0dc07df94 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb @@ -3,7 +3,8 @@ version = '3.1' versionsuffix = '-with-incl-deps' homepage = 'http://xmipp.cnb.csic.es/' -description = "Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy." +description = """Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron + microscopy.""" source_urls = ['http://xmipp.cnb.csic.es/Downloads/'] sources = ['Xmipp-%(version)s-src.tar.gz'] diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb index 82d76eef0e88122546444a7d5e09fae201a18931..d6d8c64ef43b210e08cfbbd18ae8eac1ee9660e4 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb @@ -2,7 +2,8 @@ name = 'Xmipp' version = '3.1' homepage = 'http://xmipp.cnb.csic.es/' -description = "Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy." +description = """Xmipp is a suite of image processing programs, primarily aimed at single-particle 3D electron + microscopy.""" source_urls = ['http://xmipp.cnb.csic.es/Downloads/'] sources = ['Xmipp-%(version)s-src.tar.gz'] 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/x264/x264-20160614-intel-2016b.eb b/easybuild/easyconfigs/x/x264/x264-20160614-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..d348640a5d2700c444694be71ca516dd0343b621 --- /dev/null +++ b/easybuild/easyconfigs/x/x264/x264-20160614-intel-2016b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'x264' +version = '20160614' + +homepage = 'http://www.videolan.org/developers/x264.html' +description = """x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 + AVC compression format, and is released under the terms of the GNU GPL.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = [ + 'https://download.videolan.org/pub/videolan/x264/snapshots/', + 'ftp://ftp.videolan.org/pub/videolan/x264/snapshots/', +] +sources = ['x264-snapshot-%(version)s-2245-stable.tar.bz2'] + +dependencies = [('Yasm', '1.3.0')] + +configopts = " --enable-shared --enable-static " + +sanity_check_paths = { + 'files': ['bin/x264', 'include/x264_config.h', 'include/x264.h', 'lib/libx264.a', 'lib/libx264.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/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..bf1fda81a1dab827913a04aa8a501972acfd1627 --- /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/xbitmaps/xbitmaps-1.1.1-foss-2016a.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..16ab637e45b8fa6ad79708299d2d4617febf3c6a --- /dev/null +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'xbitmaps' +version = '1.1.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """provides bitmaps for x""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_DATA_SOURCE] + +sanity_check_paths = { + 'files': ['include/X11/bitmaps/gray'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb index bb023fe4176faf55776022880c5ff0d6523294bd..43b7d9e5a5455a28606dec6b1be1d738966ddec4 100644 --- a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-foss-2016a.eb @@ -11,6 +11,13 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] +builddependencies = [ + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), +] + dependencies = [ ('xcb-util', '0.4.0'), ] diff --git a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb index a0cf9f13dda2aec1bfb91177760d078a2ea58ce8..599b3a7ea3e51ff89ce6864f47e9cb2403d65085 100644 --- a/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-image/xcb-util-image-0.4.0-intel-2016a.eb @@ -11,6 +11,13 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] +builddependencies = [ + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), +] + dependencies = [ ('xcb-util', '0.4.0'), ] diff --git a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb index 000b28f3095131a0fa9bf394e22debbf1d46ddea..6694d3c8d1a9afa977b34a2c6c3b95e6ddc1ce31 100644 --- a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-foss-2016a.eb @@ -12,6 +12,13 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] +builddependencies = [ + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), +] + dependencies = [ ('libxcb', '1.11.1'), ] diff --git a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb index ab965a9d36541a3f1a70764754bbc95307353742..6d95a13dc4907ecd599cc6efbc9857678cabd823 100644 --- a/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-keysyms/xcb-util-keysyms-0.4.0-intel-2016a.eb @@ -12,6 +12,13 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] +builddependencies = [ + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), +] + dependencies = [ ('libxcb', '1.11.1'), ] diff --git a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb index fd3484fb387b5f48281be8f7b89ee818d2760728..20b75e6be453db434be9a82b1f5d952587814894 100644 --- a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-foss-2016a.eb @@ -11,6 +11,13 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] +builddependencies = [ + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), +] + dependencies = [ ('libxcb', '1.11.1'), ] diff --git a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb index c926c17dd18263be4bbb6221c7085a18795db220..2470683fb8a9dd5b68594d246425ce6e0e8d8130 100644 --- a/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-renderutil/xcb-util-renderutil-0.3.9-intel-2016a.eb @@ -11,6 +11,13 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] +builddependencies = [ + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), +] + dependencies = [ ('libxcb', '1.11.1'), ] diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb index d412a4babfe83127c5102c3ac850609247e0b777..1c0793e3c1aea49f37905c1adea5ae1f97155898 100644 --- a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-foss-2016a.eb @@ -4,13 +4,21 @@ name = 'xcb-util-wm' version = '0.4.1' homepage = 'http://xcb.freedesktop.org/' -description = """The xcb-util-wm package contains libraries which provide client and window-manager helpers for EWMH and ICCCM.""" +description = """The xcb-util-wm package contains libraries which provide client and window-manager helpers + for EWMH and ICCCM.""" toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] +builddependencies = [ + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), +] + dependencies = [ ('libxcb', '1.11.1'), ] diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2015b-Python-2.7.11.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2015b-Python-2.7.11.eb index 39589444102cec3cfbedf74607e3c333892bc86a..b4ccaeddaac27f1073b86ead793510c41f9968ec 100644 --- a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2015b-Python-2.7.11.eb +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2015b-Python-2.7.11.eb @@ -5,7 +5,8 @@ version = '0.4.1' versionsuffix = '-Python-2.7.11' homepage = 'http://xcb.freedesktop.org/' -description = """The xcb-util-wm package contains libraries which provide client and window-manager helpers for EWMH and ICCCM.""" +description = """The xcb-util-wm package contains libraries which provide client and window-manager helpers + for EWMH and ICCCM.""" toolchain = {'name': 'intel', 'version': '2015b'} diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2015b.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2015b.eb index 147e33bc0cd18eccbaec8bb76be0d1c6f746373c..a789c945cbcda38784dc8c751154a8ec255be8e6 100644 --- a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2015b.eb @@ -4,7 +4,8 @@ name = 'xcb-util-wm' version = '0.4.1' homepage = 'http://xcb.freedesktop.org/' -description = """The xcb-util-wm package contains libraries which provide client and window-manager helpers for EWMH and ICCCM.""" +description = """The xcb-util-wm package contains libraries which provide client and window-manager helpers + for EWMH and ICCCM.""" toolchain = {'name': 'intel', 'version': '2015b'} diff --git a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb index 5d58f2a9b27528d832d3a3eddca6b479027ebce1..c5509644a13d52e8af5ff983376c5bdee83a0ccc 100644 --- a/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util-wm/xcb-util-wm-0.4.1-intel-2016a.eb @@ -4,13 +4,21 @@ name = 'xcb-util-wm' version = '0.4.1' homepage = 'http://xcb.freedesktop.org/' -description = """The xcb-util-wm package contains libraries which provide client and window-manager helpers for EWMH and ICCCM.""" +description = """The xcb-util-wm package contains libraries which provide client and window-manager helpers + for EWMH and ICCCM.""" toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] +builddependencies = [ + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), + ('xorg-macros', '1.19.0'), +] + dependencies = [ ('libxcb', '1.11.1'), ] diff --git a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb index 78a0c3a9b799ca5542f24f4c44e5562196a3a7a2..42b8d1faf079a6edbb6367ef0d737809ef3d0e11 100644 --- a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-foss-2016a.eb @@ -12,6 +12,12 @@ toolchain = {'name': 'foss', 'version': '2016a'} source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] +builddependencies = [ + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), +] + dependencies = [ ('libxcb', '1.11.1'), ] diff --git a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb index 18a587a56e970c79626c525c0525ed09f23772d1..f862af46cb90b0cd6bc2d6c667dd3da24cc8d3a1 100644 --- a/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xcb-util/xcb-util-0.4.0-intel-2016a.eb @@ -12,6 +12,12 @@ toolchain = {'name': 'intel', 'version': '2016a'} source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] +builddependencies = [ + ('xcb-proto', '1.11', '', True), + ('xproto', '7.0.28'), + ('libpthread-stubs', '0.3'), +] + dependencies = [ ('libxcb', '1.11.1'), ] diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb index 53735a84e4e81edd0a77cae71c05f55ab08724ab..617061c73dc16a3358268a13dd1950dfa3c4c64c 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-foss-2016a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] +builddependencies = [('xorg-macros', '1.19.0')] + sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', diff --git a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb index 08ca1e412b26911602694c56cab2b9c41abf7288..9c12013fe4d329018bebc0ea7574b43681541f90 100644 --- a/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xextproto/xextproto-7.3.0-intel-2016a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] +builddependencies = [('xorg-macros', '1.19.0')] + sanity_check_paths = { 'files': ['include/X11/extensions/%s' % x for x in [ 'agproto.h', 'cupproto.h', 'dbeproto.h', 'dpmsproto.h', 'EVIproto.h', 'geproto.h', 'lbxproto.h', diff --git a/easybuild/easyconfigs/x/xf86vidmodeproto/xf86vidmodeproto-2.3.1-foss-2016a.eb b/easybuild/easyconfigs/x/xf86vidmodeproto/xf86vidmodeproto-2.3.1-foss-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..db5ad9e13045fc485cc13007786e8cab963f0c5f --- /dev/null +++ b/easybuild/easyconfigs/x/xf86vidmodeproto/xf86vidmodeproto-2.3.1-foss-2016a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'xf86vidmodeproto' +version = '2.3.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 XFree86 video mode extension protocol headers.""" + +toolchain = {'name': 'foss', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xf86vm%s.h' % x for x in ['', 'proto', 'str']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb index fdbb9a1f7d26287c7d0ceb7c4c86ee88531103d7..8e6955597a3441d7da097104df5f67b6b180dc4b 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-foss-2016a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] +builddependencies = [('xorg-macros', '1.19.0')] + sanity_check_paths = { 'files': ['include/X11/extensions/panoramiXproto.h'], 'dirs': [] diff --git a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb index 892ed9f5bd720e5daeb669184af0556285023c39..e2714568f69851a1afff3d3c6869bbe8615d06ff 100644 --- a/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xineramaproto/xineramaproto-1.2.1-intel-2016a.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] +builddependencies = [('xorg-macros', '1.19.0')] + sanity_check_paths = { 'files': ['include/X11/extensions/panoramiXproto.h'], 'dirs': [] diff --git a/easybuild/easyconfigs/x/xonsh/xonsh-0.3.2-intel-2016a.eb b/easybuild/easyconfigs/x/xonsh/xonsh-0.3.2-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a881582db32701faa8844c46e43ed671c981845e --- /dev/null +++ b/easybuild/easyconfigs/x/xonsh/xonsh-0.3.2-intel-2016a.eb @@ -0,0 +1,46 @@ +easyblock = 'Bundle' + +name = 'xonsh' +version = '0.3.2' + +homepage = 'http://xon.sh/' +description = """Xonsh is a Python-ish, BASHwards-looking shell language and command prompt.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' + +dependencies = [('Python', '3.5.1')] + +exts_list = [ + ('ply', '3.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/ply/'], + }), + ('wcwidth', '0.1.6', { + 'source_urls': ['https://pypi.python.org/packages/source/w/wcwidth/'], + }), + ('prompt-toolkit', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/prompt-toolkit/'], + 'source_tmpl': 'prompt_toolkit-%(version)s.tar.gz', + 'modulename': 'prompt_toolkit', + }), + ('Pygments', '2.1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/Pygments/'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/x/xonsh/'], + }), +] + +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': ['bin/xonsh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' 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/x/xproto/xproto-7.0.23-goolf-1.4.10.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb index 6eb06bc7d4044f60d154ca4cd62fd7e776376c86..4bddac5b2c0466cf903211184e48472c62e73640 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.4.10.eb @@ -13,11 +13,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { - 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb index 5054d70df3ef0db5072919e92f4caa664fc6c774..07bf42b5f5eb4e5dbafddcca7fd550b664a9c99e 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-goolf-1.5.14.eb @@ -13,11 +13,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { - 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb index 7d12c7f86a82fcda66fe7ef818c0effee05fc7bf..483afe06f30ee6a6da7f644e5d795e8285584dac 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.23-ictce-5.3.0.eb @@ -14,11 +14,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { - 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb index 76cc9f4a7a2dfe3570d118a9db3d994f4c869406..e908c62705ecea311026da15873b2b806e78ecd9 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-foss-2014b.eb @@ -13,11 +13,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { - 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb index 1caa382ace1bf12e41e4c39ef099211abf3bd5f9..2b1221a5079ceecb7af4e3389b3424f54e348ee5 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.26-intel-2014b.eb @@ -13,11 +13,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { - 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb index 4d66b00ecbd20e265786c8a3c42d6b92c9f459a5..634833a4a6452f5611a49feea77138b3c2ebc7e4 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-goolf-1.5.14.eb @@ -13,11 +13,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { - 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb index a0292fbf8eff131391bdf3f5fe34dbbc43facfc6..361e38a9326703ce1b1319bd7334d7a82e74440d 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.27-intel-2015a.eb @@ -13,11 +13,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { - 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb index 2a47f2490bb2ad7b194de2c0f1786d67c5046dfe..7de030149302c17824c72878167df4508a2cd740 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-foss-2016a.eb @@ -11,12 +11,14 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] +builddependencies = [('xorg-macros', '1.19.0')] + sanity_check_paths = { - 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb index 8dab7213fbd304548df8d00f21192b260a137180..4a16c78f1b1538c098b842bb1e4c2601cf1d1c2b 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-gimkl-2.11.5.eb @@ -12,11 +12,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { - 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015a.eb index 532a92d31513aab4adba9f9074dcfb8ee88b3cfa..30b6582acd21c4de512fcae9d36ba41f16d76d8a 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015a.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015a.eb @@ -13,11 +13,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { - 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb index 6722798efb176a1e5ac704dc195beaabbcf199e5..1c8cddb38f2199de24465d4e5368e2773528698e 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2015b.eb @@ -13,11 +13,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] sanity_check_paths = { - 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb index 9de353786c0931661b85db26c015bf08f01c870e..f6d63bc3d97089f88d1139f0469f3637cb7a20f3 100644 --- a/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.28-intel-2016a.eb @@ -11,12 +11,14 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_PROTO_SOURCE] +builddependencies = [('xorg-macros', '1.19.0')] + sanity_check_paths = { - 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', - 'Xatom.h', 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', - 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', 'Xarch.h', - 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', 'Xproto.h', 'Xthreads.h', - 'XWDFile.h', 'Xwinsock.h']], + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], 'dirs': [] } diff --git a/easybuild/easyconfigs/x/xproto/xproto-7.0.29-intel-2016a.eb b/easybuild/easyconfigs/x/xproto/xproto-7.0.29-intel-2016a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3fb339cba12390afb25e4c2db53559a78aa96d6c --- /dev/null +++ b/easybuild/easyconfigs/x/xproto/xproto-7.0.29-intel-2016a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'xproto' +version = '7.0.29' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "X protocol and ancillary headers" + +toolchain = {'name': 'intel', 'version': '2016a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_PROTO_SOURCE] + +builddependencies = [('xorg-macros', '1.19.0')] + +sanity_check_paths = { + 'files': ['include/X11/%s' % x for x in ['ap_keysym.h', 'HPkeysym.h', 'keysym.h', 'Xalloca.h', 'Xatom.h', + 'XF86keysym.h', 'Xfuncs.h', 'Xmd.h', 'Xos.h', 'Xpoll.h', 'Xprotostr.h', + 'Xw32defs.h', 'Xwindows.h', 'DECkeysym.h', 'keysymdef.h', 'Sunkeysym.h', + 'Xarch.h', 'Xdefs.h', 'Xfuncproto.h', 'X.h', 'Xosdefs.h', 'Xos_r.h', + 'Xproto.h', 'Xthreads.h', 'XWDFile.h', 'Xwinsock.h']], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb index 1d32cb1ae6538682288102a3353c4cbf23399c19..0f0a3295c34e580466b5dbf1fe4ea0f5ce562412 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-foss-2016a.eb @@ -13,8 +13,10 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] +builddependencies = [('xorg-macros', '1.19.0')] + sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c']], 'dirs': [], } diff --git a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb index bb8657a96c50ba70998f2054343e1ed92a68eab3..f8d039234efd2e3c92f602efd195b6559fbf39b4 100644 --- a/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb +++ b/easybuild/easyconfigs/x/xtrans/xtrans-1.3.5-intel-2016a.eb @@ -13,8 +13,10 @@ toolchain = {'name': 'intel', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] +builddependencies = [('xorg-macros', '1.19.0')] + sanity_check_paths = { - 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', + 'files': ['include/X11/Xtrans/%s' % x for x in ['transport.c', 'Xtrans.c', 'Xtrans.h', 'Xtransint.h', 'Xtranslcl.c', 'Xtranssock.c', 'Xtransutil.c']], 'dirs': [], } 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-0.4.4-foss-2015a.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.4.4-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c754d53b2757d696340830bdc1a518a34cf36be3 --- /dev/null +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.4.4-foss-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'YAXT' +version = '0.4.4' + +homepage = 'https://www.dkrz.de/redmine/projects/yaxt' +description = "Yet Another eXchange Tool" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.dkrz.de/redmine/attachments/download/464/'] +sources = [SOURCELOWER_TAR_GZ] + +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="$F90FLAGS -cpp"' + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.5.1-intel-2016b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.5.1-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e2e871aa138cc75be19684e1e63d021a8b86091d --- /dev/null +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.5.1-intel-2016b.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'YAXT' +version = '0.5.1' + +homepage = 'https://www.dkrz.de/redmine/projects/yaxt' +description = "Yet Another eXchange Tool" + +toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://www.dkrz.de/redmine/attachments/download/473/'] +checksums = [('md5', '2176c5b1096146e58163656b9d83c0b3')] + +sanity_check_paths = { + 'files': ["include/yaxt.h", "include/yaxt.mod", "lib/libyaxt.a", "lib/libyaxt.%s" % SHLIB_EXT], + 'dirs': ["include/xt"], +} + +configopts = 'FC="$F90" FCFLAGS="$F90FLAGS -cpp"' + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb index f94f281e774fdfc7461860c99bc80f2bec3d650e..a6e0dada54a528d3e8af62dff6eb94e2e940af95 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-foss-2016a-Python-2.7.11.eb @@ -53,7 +53,7 @@ modextrapaths = { 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)], + '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')], } diff --git a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb index cecf209b8ad018a4c7a93d1b2ea1d44457c7f009..4d7005749aa29b183c07b8f413d55cb0da6d86cd 100644 --- a/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb +++ b/easybuild/easyconfigs/y/Yade/Yade-1.20.0-intel-2016a-Python-2.7.11.eb @@ -53,7 +53,7 @@ modextrapaths = { 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)], + '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')], } 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..1c86ea984c5350f7ca61a8ccf6acbe329e57509c --- /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/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb index d3ce57aec017ec02954e064649dfe322c4672880..81c441670608a11c809fe5fd4c61d28b1bcb27f3 100644 --- a/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb +++ b/easybuild/easyconfigs/y/Yambo/Yambo-3.4.2-intel-2016.02-GCC-4.9.eb @@ -30,7 +30,7 @@ parallel = 1 files_to_copy = [(['bin/*'], 'bin')] sanity_check_paths = { - 'files': ['bin/'+prog for prog in ['a2y', 'iotk', 'iotk.x', 'p2y', 'yambo', + 'files': ['bin/' + prog for prog in ['a2y', 'iotk', 'iotk.x', 'p2y', 'yambo', 'yambo_kerr', 'yambo_ph', 'yambo_surf', 'ypp', 'ypp_ph', 'ypp_surf']], 'dirs': [] } diff --git a/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb b/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..0c99f457cb4b54ff780c9baa40b114643bfbb6b9 --- /dev/null +++ b/easybuild/easyconfigs/y/Yambo/Yambo-4.0.2-rev.90-intel-2015b-QuantumESPRESSO-5.2.1.eb @@ -0,0 +1,53 @@ +easyblock = 'MakeCp' + +name = 'Yambo' +version = '4.0.2-rev.90' +qe = 'QuantumESPRESSO' +qever = '5.2.1' +versionsuffix = '-%s-%s' % (qe, qever) + +homepage = 'http://www.yambo-code.org' +description = """Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. + Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf.""" + +toolchain = {'name': 'intel', 'version': '2015b'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://qe-forge.org/gf/download/frsrelease/201/870/'] +checksums = ['03d5ffc655eb4c03db4e264606117c86'] + +dependencies = [ + ('netCDF-Fortran', '4.4.2'), + (qe, qever), +] + +with_configure = 'True' + +configopts = 'CPPFLAGS="" FCFLAGS="-nofor_main" ' +configopts += '--with-blas-libs="$LIBBLAS" ' +configopts += '--with-lapack-libs="$LIBLAPACK" ' +configopts += '--with-fft-libs="$LIBFFT" ' +configopts += '--with-iotk-path="$EBROOTQUANTUMESPRESSO/espresso-%s/S3DE/iotk" ' % qever +configopts += '--enable-netcdf-hdf5 ' +configopts += '--with-netcdf-includedir="$EBROOTNETCDFMINFORTRAN/include" ' +configopts += '--with-netcdf-libdir="$EBROOTNETCDFMINFORTRAN/lib" ' + +buildopts = 'yambo interfaces ypp' + +parallel = 1 + +files_to_copy = [(['bin/*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/' + prog for prog in ['a2y', 'p2y', 'yambo', 'ypp']], + 'dirs': [] +} + +# Yambo is installed with QuantumESPRESSO. I do not like if the same program (with different versions) +# is twice in the PATH. Withouth removing the QuantumESPRESSO one, this version of Yambo would be used, +# because it is earlier in the PATH +modtclfooter = "remove-path PATH $::env(EBROOTQUANTUMESPRESSO)/espresso-%s/YAMBO/bin" % qever +modluafooter = 'remove_path("PATH", os.getenv("EBROOTQUANTUMESPRESSO") .. "/espresso-%s/YAMBO/bin")' % qever + +moduleclass = 'phys' 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/y/Yasm/Yasm-1.3.0-intel-2016b.eb b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..bd4bc5d66f8301218b2425b424e00ec6ddbe4e6f --- /dev/null +++ b/easybuild/easyconfigs/y/Yasm/Yasm-1.3.0-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 +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'Yasm' +version = '1.3.0' + +homepage = 'http://www.tortall.net/projects/yasm/' +description = """Yasm: Complete rewrite of the NASM assembler with BSD license""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.tortall.net/projects/yasm/releases/'] + +sanity_check_paths = { + 'files': ['bin/yasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.5-intel-2016b.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.5-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..dec76702b25c793a674703bbcc9ceff8db9a7da0 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.1.5-intel-2016b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.1.5' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/zeromq/zeromq%(version_major)s-%(version_minor)s/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.28.1'), + ('libsodium', '1.0.11'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-foss-2016b.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..2e2077d5990de7ab2045762249a73e6e59ce53c0 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-foss-2016b.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.2.0' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums=['1fb2595d2a905a9e820c976a1d8348bc'] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.29'), + ('libsodium', '1.0.11'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-intel-2016b.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..b5d9aa81e3f91d3d5fd7524252f2599247ba8e28 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.2.0-intel-2016b.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.2.0' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'intel', 'version': '2016b'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums=['1fb2595d2a905a9e820c976a1d8348bc'] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.29'), + ('libsodium', '1.0.11'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2016.03.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2016.03.eb new file mode 100644 index 0000000000000000000000000000000000000000..20e9ee0821fecae65ebde227727300591748be3d --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-2016.03.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': 'CrayGNU', 'version': '2016.03'} +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-GCC-4.7.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..1192872c10316dd3162a345a2deafeccbff72486 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.7.3.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': '4.7.3'} +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-GCC-4.8.3.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..93106f89eeee1d21888b3099ab1a469a82dfe486 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.8.3.eb @@ -0,0 +1,21 @@ +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': '4.8.3'} + +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-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-GCC-5.4.0-2.26.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.4.0-2.26.eb new file mode 100644 index 0000000000000000000000000000000000000000..2155a965c083701439ac6d2fb545b0964408135a --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.4.0-2.26.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': '5.4.0-2.26'} +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-4.9.4.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..1b44bb978029b484c3237d906bece9811c0e7b25 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-4.9.4.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': '4.9.4'} +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', '2.25', '', 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-GCCcore-5.4.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..36dc3d169871913bae67041f70d796d06780e995 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-5.4.0.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': '5.4.0'} +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', '2.26', '', True)] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-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-GCCcore-6.2.0.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..ecd6eff1be1c48d22b79ba4b5aa6a8c1fa8cddea --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCCcore-6.2.0.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': '6.2.0'} +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-foss-2016b.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..175fa4f97e793df9938dd0dd9ea508c0f45f6793 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2016b.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': '2016b'} +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-intel-2016b.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..0427d92cc1ec09f0bbb2ebd779b085ff54a0dd26 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2016b.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': 'intel', 'version': '2016b'} +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-intel-2017.01.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2017.01.eb new file mode 100644 index 0000000000000000000000000000000000000000..a722d48768c0ad2b1a84c9d50507e19598b0a7be --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2017.01.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': 'intel', 'version': '2017.01'} +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..b192852da80fa3e5c3f776dce46b9d6b9119a585 --- /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..dacfba135a5b6d174d0005156743613a3f015c9d --- /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/easybuild/easyconfigs/z/zlibbioc/zlibbioc-1.18.0-intel-2016a-R-3.2.3.eb b/easybuild/easyconfigs/z/zlibbioc/zlibbioc-1.18.0-intel-2016a-R-3.2.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..9ebe413224904383313e11aebf0cefb778909460 --- /dev/null +++ b/easybuild/easyconfigs/z/zlibbioc/zlibbioc-1.18.0-intel-2016a-R-3.2.3.eb @@ -0,0 +1,26 @@ +easyblock = 'RPackage' + +name = 'zlibbioc' +version = '1.18.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://bioconductor.org/packages/release/bioc/html/zlibbioc.html' +description = """This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have + these available via other means.""" + +toolchain = {'name': 'intel', 'version': '2016a'} + +source_urls = [ + 'http://bioconductor.org/packages/release/bioc/src/contrib/', + 'http://bioconductor.org/packages/3.3/bioc/src/contrib/', +] +sources = ['zlibbioc_%(version)s.tar.gz'] + +dependencies = [('R', '3.2.3')] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zsh/zsh-5.2-foss-2016b.eb b/easybuild/easyconfigs/z/zsh/zsh-5.2-foss-2016b.eb new file mode 100644 index 0000000000000000000000000000000000000000..635c04bd7447209f7a4118d03098c57227144735 --- /dev/null +++ b/easybuild/easyconfigs/z/zsh/zsh-5.2-foss-2016b.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'zsh' +version = '5.2' + +homepage = 'http://www.zsh.org/' +description = "Zsh is a shell designed for interactive use, although it is also a powerful scripting language." + +toolchain = {'name': 'foss', 'version': '2016b'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [ + ('ncurses', '6.0'), +] + +moduleclass = 'tools' diff --git a/setup.py b/setup.py index 9065cef46bcc6f794cb14214d5f9ad83bd53a452..3979a91f642d0618632b821bd48ed2d69f660a81 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 = '2.8.1' +VERSION = '3.0.2' 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 c92b7c5d9365a07064948566373f84ee7a0e6262..551695c2591a5e250d6a7af1067548de16e10314 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -44,9 +44,11 @@ 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.format.format import DEPENDENCY_PARAMETERS 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 @@ -55,7 +57,7 @@ from easybuild.tools.module_naming_scheme import GENERAL_CLASS from easybuild.tools.module_naming_scheme.easybuild_mns import EasyBuildMNS from easybuild.tools.module_naming_scheme.utilities import det_full_ec_version from easybuild.tools.modules import modules_tool -from easybuild.tools.robot import resolve_dependencies +from easybuild.tools.robot import check_conflicts, resolve_dependencies from easybuild.tools.options import set_tmpdir @@ -146,57 +148,8 @@ class EasyConfigTest(TestCase): if self.ordered_specs is None: self.process_all_easyconfigs() - def mk_dep_mod_name(spec): - return tuple(EasyBuildMNS().det_full_module_name(spec).split(os.path.sep)) - - # construct a dictionary: (name, installver) tuple to (build) dependencies - depmap = {} - for spec in self.ordered_specs: - # exclude external modules, since we can't check conflicts on them (we don't even know the software name) - build_deps = [mk_dep_mod_name(d) for d in spec['builddependencies'] if not d.get('external_module', False)] - deps = [mk_dep_mod_name(d) for d in spec['ec'].all_dependencies if not d.get('external_module', False)] - - # separate runtime deps from build deps - runtime_deps = [d for d in deps if d not in build_deps] - key = tuple(spec['full_mod_name'].split(os.path.sep)) - depmap.update({key: [build_deps, runtime_deps]}) - - # iteratively expand list of dependencies - depmap_last = None - while depmap != depmap_last: - depmap_last = copy.deepcopy(depmap) - for (spec, (build_deps, runtime_deps)) in depmap_last.items(): - # extend runtime dependencies with non-build dependencies of own runtime dependencies - for dep in runtime_deps: - depmap[spec][1].extend([d for d in depmap[dep][1] if d not in depmap[dep][0]]) - depmap[spec][1] = sorted(nub(depmap[spec][1])) - # extend build dependencies with non-build dependencies of own build dependencies - for dep in build_deps: - depmap[spec][0].extend([d for d in depmap[dep][1] if d not in depmap[dep][0]]) - depmap[spec][0] = sorted(nub(depmap[spec][0])) - - def check_conflict((name, installver), (name1, installver1), (name2, installver2)): - """Check whether dependencies with given name/(install) version conflict with each other.""" - # dependencies with the same name should have the exact same install version - # if not => CONFLICT! - if name1 == name2 and installver1 != installver2: - specname = '%s-%s' % (name, installver) - vs_msg = "%s-%s vs %s-%s" % (name1, installver1, name2, installver2) - print "Conflict found for dependencies of %s: %s" % (specname, vs_msg) - return True - else: - return False - - # for each of the easyconfigs, check whether the dependencies (incl. build deps) contain any conflicts - conflicts = False - for ((name, installver), (build_deps, runtime_deps)) in depmap.items(): - # also check whether module itself clashes with any of its dependencies - for i, dep1 in enumerate(build_deps + runtime_deps + [(name, installver)]): - for dep2 in (build_deps + runtime_deps)[i+1:]: - # don't worry about conflicts between module itself and any of its build deps - if dep1 != (name, installver) or dep2 not in build_deps: - conflicts |= check_conflict((name, installver), dep1, dep2) - self.assertFalse(conflicts, "No conflicts detected") + self.assertFalse(check_conflicts(self.ordered_specs, modules_tool(), check_inter_ec_conflicts=False), + "No conflicts detected") def test_sanity_check_paths(self): """Make sure specified sanity check paths adher to the requirements.""" @@ -217,11 +170,11 @@ 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')] @@ -259,7 +212,7 @@ 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) @@ -307,7 +260,8 @@ 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() @@ -318,7 +272,7 @@ 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 @@ -327,10 +281,51 @@ 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() + orig_toolchain = ec_dict['toolchain'] + 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 + + orig_val = resolve_template(ec_dict[key], ec.template_values) + dumped_val = resolve_template(dumped_ec[key], ec.template_values) + + # take into account that dumped value for *dependencies may include hard-coded subtoolchains + # if no easyconfig was found for the dependency with the 'parent' toolchain, + # if may get resolved using a subtoolchain, which is then hardcoded in the dumped easyconfig + if key in DEPENDENCY_PARAMETERS: + # number of dependencies should remain the same + self.assertEqual(len(orig_val), len(dumped_val)) + for orig_dep, dumped_dep in zip(orig_val, dumped_val): + # name/version should always match + self.assertEqual(orig_dep[:2], dumped_dep[:2]) + + # 3rd value is versionsuffix; + if len(dumped_dep) >= 3: + # if no versionsuffix was specified in original dep spec, then dumped value should be empty string + if len(orig_dep) >= 3: + self.assertEqual(dumped_dep[2], orig_dep[2]) + else: + self.assertEqual(dumped_dep[2], '') + + # 4th value is toolchain spec + if len(dumped_dep) >= 4: + if len(orig_dep) >= 4: + self.assertEqual(dumped_dep[3], orig_dep[3]) + else: + # if a subtoolchain is specifed (only) in the dumped easyconfig, + # it should *not* be the same as the parent toolchain + self.assertNotEqual(dumped_dep[3], (orig_toolchain['name'], orig_toolchain['version'])) + + else: + self.assertEqual(orig_val, dumped_val) # cache the parsed easyconfig, to avoid that it is parsed again self.parsed_easyconfigs.append(ecs[0]) @@ -338,6 +333,7 @@ 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 @@ -345,6 +341,11 @@ 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