diff --git a/RELEASE_NOTES b/RELEASE_NOTES index b504cb01ce1542e7af64d1124d31634632951bb4..7d3ae9ed16239959de1d3946a444a11d3fb2f3f3 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,18 +3,133 @@ 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 3,344 easyconfig files, for 581 different software packages, -32 different (compiler) toolchains and 6 software bundles. +The latest version of easybuild-easyconfig provides 4,061 easyconfig files, for 673 different software packages, +34 different (compiler) toolchains, 12 software bundles and 1 meta-package. +v2.2.0 (July 15th 2015) +----------------------- + +feature + bugfix release +- added example easyconfig files for 62 new software packages: + ADF (#899), AutoDock_Vina (#808), bibtexparser (#1726), Biggus (#1770), Bismark (#990), blasr (#1662), BSMAP (#1171), + Check (#811), Circuitscape (#1222), CONTRAfold (#689), cramtools (#1741), DBD-Pg (#1066), DendroPy (#995), + EMAN2 (#1737), ETSF_IO (#727), eudev (#1578), fastqc (#1636), FDS (#814, #1617, #1625), FPM (#1440), + frealign (#1619), g2log (#1035), GC3Pie (#1692, #1756, #1768), GenotypeHarmonizer (#1672), gensim (#1762), + GraphViz (#1658), hisat (#1674), IDBA-UD (#1045), IMa2 (#828), IMPUTE2 (#824), JUBE (#1396), LAMARC (#760), + libXScrnSaver (#1653), MATIO (#1004), MuTect (#1483), ncdf (#617), NEMO (#1640), ngspice (#1116), + ordereddict (#1774), OSU Micro-Benchmarks (#1777), Parallel-ForkManager (#847), pBWA (#1009), PeakSeq (#1412), + Pillow (#1702), Pindel (#1126), PLUMED (#1596, #1665), PostgreSQL (#1066), PROJ (#1006), PyAMG (#1222), Pyke (#1776), + rpy2 (#1775), Sailfish (#1035), SCANMS (#1386), Seaborn (#1763), snpEff (#1680), SOBAcl (#1658), + SPIDER (#1624, #1723), STAR (#1043, #1676), system GCC (#1778), tabix (#1059), tecplot360ex (#1100), Vampir (#512), + VampirServer (#512), verifyBamID (#1675) +- added easyconfigs for 4 new software bundles: + R-bundle-Bioconductor (#1573, #1795), R-bundle-devtools (#1621, #1759), R-bundle-extra (#1387, #1759), + R-bundle-pbd (#1659) +- added easyconfigs for new GNU toolchain (#1346, #1669) +- added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06 +- added example easyconfig for generating buildenv module (#1503) +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + including BLAST 2.2.31+, Clang 3.6.1, CUDA 6.x, GCC 4.9.3, GROMACS 5.0.5, HDF5 1.8.15 + 1.8.15-patch1, + Python 2.7.10, R 3.2.0 + 3.2.1, WRF 3.6.1 +- various other enhancements, including: + - update all ncurses easyconfigs to enable ncursesw and use ConfigureMake easyblock (#1337) + - update PDT easyconfigs to use PDT easyblock (#1687) + - add custom sanity_check_paths in libxml2 easyconfigs (#1690) + - enhance unit tests to also cover EasyConfig.dump() method on all easyconfigs (#1761) + - include snappy as dependency in Hadoop easyconfigs (#1758, #1773) + - enable SSL support in CMake v3.2.3 easyconfigs (#1784) + - add additional extensions in R easyconfigs (#1637) +- various bug fixes, including: + - add patch file required for correct CUDA-aware OpenMPI v1.7.3 build (#631) + - fix issue with OpenMPI dependency in ECore easyconfigs (#777) + - don't run the Bloom tests for Jellyfish, they can randomly fail (#1016) + - fix source URLs in BioPerl easyconfigs (#1075) + - patch out svnversion command in Python 2.5.6 to fix build on recent systems (#1576) + - consistently use https for PyPI URLs in homepage/source_urls (#1616, #1722) + - include Tcl and Tk as dependencies in R easyconfig (#1623) + - add patch for installing paycheck as Py3 extension (#1629) + - add Perl dependency in git 2.x easyconfigs (#1631) + - fix easyconfig for GMP 6.0.0, don't use 6.0.0a sources (#1635) + - fix source_urls in QuantumESPRESSO 5.0.2 easyconfigs (#1652) + - include Tk as dependency in Python 2.7.9 easyconfigs (#1654) + - include tk-devel is list of OS deps for Python 2.7.9 Cray easyconfigs, make sure 'import Tkinter' works (#1655) + - drop gpfs versionsuffix and stop using no longer existing --enable-gpfs configopt for recent HDF5 versions (#1657) + - include missing libxml2 dep in GLib easyconfigs (#1666) + - fix source URLs in Qt easyconfigs (#1673) + - fix source URLs for argparse Python extension (#1697) + - fix source URLs for deap Python extension (#1699) + - fix easyconfigs unit tests after making ModulesTool a non-singleton class (#1708) + - fix names for Xmipp easyconfigs and patches (#1719) + - add patch for Qt 4.8.6 to fix build issue on RHEL6 with intel/2015a (#1734) + - add M4 as build dep for GCC 5.1.0 (#1735) + - fix Bioconductor extension versions in R 3.1.3 easyconfigs (#1748) + - remove custom exts_filter definition from Python 3.4.3 easyconfig (#1765) + - fix source_urls in netCDF easyconfigs (#1766) + - fix source_urls in netCDF-C++ and netCDF-Fortran easyconfigs (#1767) + +v2.1.1 (May 18th 2015) +---------------------- + +bugfix release +- added example easyconfig files for 3 new software packages: + networkx (#1592), Platanus (#1597), SaguaroGW (#1600) +- added new easyconfigs for existing toolchains: ictce/7.3.5, CrayCCE/5.2.40, CrayGNU/5.2.40, CrayIntel/5.2.40 +- added easyconfigs using CrayGNU/5.2.25 and CrayGNU/5.2.40 toolchains (#1610, #1611) +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + including Boost 1.58.0, GROMACS 5.0.4, Python 3.4.3 +- various bug fixes, including: + - enable usempi in GROMACS easyconfig using CrayGNU toolchain (as required by GROMACS easyblock) (#1590) + - use system-provided tcsh when building WRF on Cray systems, to avoid hanging build (#1595) + - only use 'dynamic' toolchain option, not 'shared', in easyconfigs using Cray toolchain (#1609) + +v2.1.0 (April 30th 2015) +------------------------ + +feature + bugfix release +- added example easyconfig files for 27 new software packages: + AFNI (#1322, #1521), BCFtools (#1492), getdp (#1518), gmsh (#1518), gtest (#1244), hanythingondemand (#1530), + mawk (#1369), Minimac (#815), Minimac3 (#1502), monty (#1548), Octave (#1563), pbs_python (#1530), pigz (#1036), + Pygments (#1536), pyhull (#1539), pymatgen (#1549), PyQt (#1322, #1521), Ray (#1494), requests (#1536), + seqtk (#1524), SIP (#1322, #1521), S-Lang (#1369), Spark (#1554), spglib (#1549), TINKER (#1465), tmux (#1369), + Xmipp (#1489) +- added easyconfigs for new (Cray-specific) toolchains (#1538): CrayGNU, CrayIntel, CrayCCE + - initially supported software (using CrayGNU toolchains): CP2K, GROMACS, HPL, Python + numpy/scipy, WRF (#1558) + - see also https://github.com/hpcugent/easybuild/wiki/EasyBuild-on-Cray +- added new easyconfigs for existing toolchains: goolf/1.5.16, intel/2014.06 +- added additional easyconfigs for various supported software packages: version updates, different toolchains, ... + including GCC v5.1.0, OpenFOAM v2.3.1, R v3.1.3 and v3.2.0, PETSc/SLEPc v3.5.3, WIEN2k v14.1 +- various other enhancements, including: + - include 'pbr' dependency for 'lockfile' Python extension in Python v2.7.9 easyconfigs + mock/pytz/pandas (#1462, #1540) + - include SQLite as dependency in Python v2.7.9 easyconfigs (#1468) + - set $LD_PRELOAD for Hoard and jemalloc (#1470) + - fix homepage in SCOTCH easyconfigs (#1485) + - adding missing six/ecdsa dependencies for dateutil/paramiko Python packages in Python easyconfigs (#1504, #1505, #1506, #1507, #1508, #1509, #1510) + - enable pic toolchain option in expat easyconfigs (#1562) + - extend list of source URLs for Bioconductor packages in R easyconfigs to include 'release' source URLs (#1568) +- various bug fixes, including: + - adding missing zlib dependency in all Tcl easyconfig files (#1344) + - fix homepage in FLUENT easyconfigs (#1472) + - use --with-verbs rather than deprecated --with-openib in OpenMPI configure options (#1511) + - stop relying on OS_NAME constant to specify OS dependencies in OpenMPI easyconfigs (#1512) + - replace use of $root with %(installdir)s to ensure compatibility with module files in Lua syntax (#1532) + - stop relying on $MKLROOT in ROOT easyconfigs (#1537) + - use proper Bundle easyblock for biodeps/PRACE (#1566) + - make source_urls in Cube and Scalasca easyconfigs compatible with --try-software-version (#1574) + - add patch for Cube to fix configure script w.r.t. Qt dependency, add --without-java-reader configure option (#1574) v2.0.0 (March 6th 2015) ----------------------- feature + bugfix release - added example easyconfig files for 29 new software packages: - bsoft (#1353), Coot (#1400), Cuby (#1258), DSRC (#1242), Exonerate (#568), fastqz (#1242), FSA (#568), fqzcomp (#1242), GAMESS-US (#1153, #1406), Grep (#1308), Hadoop (#1418), Hoard (#1415), IMB (#1284), ISL (#1389), jemalloc (#1416), libdwarf (#1283), libelf (#1283), MPC (#1310), multitail (#1327), Pmw (#1403), Quip (#1242), rCUDA (#720), SCALCE (#1242), SMALT (#568), STREAM (#1332), worker (#1307), Xerces-C++ (#1370), XQilla (#1370), ZPAQ (#1242) + bsoft (#1353), Coot (#1400), Cuby (#1258), DSRC (#1242), Exonerate (#568), fastqz (#1242), FSA (#568), + fqzcomp (#1242), GAMESS-US (#1153, #1406), Grep (#1308), Hadoop (#1418), Hoard (#1415), IMB (#1284), ISL (#1389), + jemalloc (#1416), libdwarf (#1283), libelf (#1283), MPC (#1310), multitail (#1327), Pmw (#1403), Quip (#1242), + rCUDA (#720), SCALCE (#1242), SMALT (#568), STREAM (#1332), worker (#1307), Xerces-C++ (#1370), XQilla (#1370), + ZPAQ (#1242) - added easyconfigs for new (common) toolchains - foss/2015a (#1239), gompi/1.5.16 (#1380), gmvolf/1.7.20 (#1397), goolf/1.7.20 (#1294), intel/2015a (#1238), intel/2015.02 (#1393), iomkl/2015.01 (#1325), iomkl/2015.02 (#1401) + foss/2015a (#1239), gompi/1.5.16 (#1380), gmvolf/1.7.20 (#1397), goolf/1.7.20 (#1294), intel/2015a (#1238), + intel/2015.02 (#1393), iomkl/2015.01 (#1325), iomkl/2015.02 (#1401) - added new software bundle: Autotools (#1385) - various other enhancements, including: - don't define $LDSHARED in zlib easyconfigs (#1350) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a-incl-deps.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a-incl-deps.eb new file mode 100644 index 0000000000000000000000000000000000000000..a8aa4213454f04b7d0ecb32328d04ab22b0b9afb --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a-incl-deps.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '7.10.4' +versionsuffix = '-incl-deps' + +homepage = 'http://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, charge density and + electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional + Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bfc76a5f93c3f148c049f57541864e76'] + +configopts = "--with-mpi-prefix=$EBROOTIMPI/intel64 --with-trio-flavor='etsf_io+netcdf' " +configopts += "--with-dft-flavor='atompaw+bigdft+libxc+wannier90' " +configopts += '--with-linalg-flavor=mkl --with-linalg-libs="-L$LAPACK_LIB_DIR $LIBLAPACK" ' +configopts += '--enable-mpi=yes --with-mpi-level=2 --enable-mpi-io=yes ' +configopts += '--with-fft-flavor=fftw3-mkl --with-fft-libs="-L$FFT_LIB_DIR $LIBFFT" ' +configopts += '--with-fft-incs=-I$FFT_INC_DIR/fftw ' +configopts += '--enable-gw-dpc="yes" --enable-64bit-flags="yes" ' + +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-7.10.4-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7561f6f45cc051b43e53ace2de02af23b41a794f --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.10.4-intel-2015a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '7.10.4' + +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': '2015a'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bfc76a5f93c3f148c049f57541864e76'] + +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$EBROOTLIBXC/lib -lxc" ' + +dependencies = [ + ('libxc', '2.2.2'), + ('netCDF', '4.3.2'), + ('netCDF-Fortran', '4.4.0'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..97bc886c26c88a54f6f93bb0ae7597a9de37b389 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.11.6-intel-2015a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '7.11.6' + +homepage = 'http://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, charge density and + electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional + Theory (DFT), using pseudopotentials and a planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c8b166ec8e65ad1d795d42b889fd772b'] + +configopts = "--with-mpi-prefix=$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', '2.2.2'), + ('netCDF', '4.3.2'), + ('netCDF-Fortran', '4.4.0'), +] + +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-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..4d319523acef9584081e14f56c2b426f7d692824 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-7.4.3-goolf-1.4.10-ETSF_IO-1.0.4.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = "ConfigureMake" + +name = 'ABINIT' +version = '7.4.3' +versionsuffix = '-ETSF_IO-1.0.4' + +homepage = 'http://www.abinit.org/' +description = """Abinit is a plane wave pseudopotential code for doing + condensed phase electronic structure calculations using DFT.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://ftp.abinit.org/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '--enable-mpi --enable-mpi-io --with-mpi-prefix=$EBROOTOPENMPI --enable-fallbacks ' +configopts += '--with-netcdf-incs="-I$EBROOTNETCDF/include" ' +configopts += '--with-netcdf-libs="-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff" ' +configopts += '--with-fft-libs="-L$EBROOTFFTW/lib -lfftw3 -lfftw3f" --with-fft-flavor=fftw3 ' +configopts += '--with-trio-flavor="netcdf+etsf_io" --enable-gw-dpc' + +dependencies = [ + ('netCDF', '4.1.3'), + ('ETSF_IO', '1.0.4'), +] + +sanity_check_paths = { + 'files': ["bin/abinit"], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb b/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..c055778c8e3e05e3a5576bff202b90062d934395 --- /dev/null +++ b/easybuild/easyconfigs/a/ABySS/ABySS-1.5.2-goolf-1.4.10.eb @@ -0,0 +1,32 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Maxime Schmitt , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '1.5.2' + +homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] + +dependencies = [('Boost', '1.53.0')] + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb b/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb new file mode 100755 index 0000000000000000000000000000000000000000..6395f17b38d2e35896d2b5a8e14737237cebecd2 --- /dev/null +++ b/easybuild/easyconfigs/a/ADF/ADF-2009.01a.pc64_linux.intelmpi.eb @@ -0,0 +1,20 @@ +easyblock = 'Tarball' + +name = "ADF" +version = '2009.01a.pc64_linux.intelmpi' + +homepage = 'http://www.scm.com/' +description = "ADF is a premium-quality quantum chemistry software package based on Density Functional Theory (DFT)." + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(namelower)s%(version)s.bin.tgz'] + +dependencies = [('impi', '3.2.2.006')] + +sanity_check_paths = { + 'files': ['bin/adf', 'bin/adf.exe'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb b/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb new file mode 100644 index 0000000000000000000000000000000000000000..a27cf3bd195f755b9363dd8a834016928b2ac723 --- /dev/null +++ b/easybuild/easyconfigs/a/AutoDock_Vina/AutoDock_Vina-1.1.2_linux_x86.eb @@ -0,0 +1,25 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'AutoDock_Vina' +version = '1.1.2' +versionsuffix = '_linux_x86' + +homepage = 'http://vina.scripps.edu/index.html' +description = """ AutoDock Vina is an open-source program for doing molecular docking. """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://vina.scripps.edu/download/'] +sources = ['%s_%s%s.tgz' % (name.lower(), version.replace('.','_'), versionsuffix)] + +sanity_check_paths = { + 'files': ["bin/vina_split", "bin/vina"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..b57c1dcc838405d2e3732aceb6cbd7dc30048de3 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-4.9.2-2.25.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': 'GNU', 'version': '4.9.2-2.25'} + +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/Autoconf/Autoconf-2.69-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..af0a90aedb78be84b0e1efe9227d06447f610c05 --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GNU-5.1.0-2.25.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': 'GNU', 'version': '5.1.0-2.25'} + +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-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..f0e456c431987fee85e7afd1b128535e805ce7ae --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-4.9.2-2.25.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': 'GNU', 'version': '4.9.2-2.25'} + +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/Automake/Automake-1.15-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..1d63ee839dff2a16ed598b167aadb9cc7255be4b --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15-GNU-5.1.0-2.25.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': 'GNU', 'version': '5.1.0-2.25'} + +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-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..25b293c3c4fb1235a05172f2414ad2a7add5bc05 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-4.9.2-2.25.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': 'GNU', 'version': '4.9.2-2.25'} + +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-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..0d6c26a78c1a07f9750c421fff89738bf6c4a80f --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20150215-GNU-5.1.0-2.25.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': 'GNU', 'version': '5.1.0-2.25'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15'), # 20150105 + ('libtool', '2.4.6'), # 20150215 +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb new file mode 100644 index 0000000000000000000000000000000000000000..e1662e8bf27e897b781f6ba669d0f911701f672f --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.9.3-Java-1.7.0_79.eb @@ -0,0 +1,26 @@ +name = 'ant' +version = '1.9.3' + +homepage = 'http://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files + as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['apache-%(name)s-%(version)s-src.tar.gz'] +source_urls = ['http://archive.apache.org/dist/%(name)s/source/'] + +java = 'Java' +javaver = '1.7.0_79' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +builddependencies = [('JUnit', '4.11', versionsuffix)] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..b307dca6af305cabe58479ec0a0208b8304c2cf7 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.1-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 +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.1' + +homepage = 'http://www.htslib.org/' +description = """ Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising + SNP and short indel sequence variants """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [('http://sourceforge.net/projects/samtools/files/samtools/%(version)s', 'download')] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +parallel = 1 + +skipsteps = ['configure'] + +installopts = ' prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bcftools", "plot-vcfstats", "vcfutils.pl"]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..0c511d17e03a4508bcc0a4173ccbf2f508b61b60 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDTools/BEDTools-2.23.0-goolf-1.4.10.eb @@ -0,0 +1,32 @@ +# Author: Maxime Schmitt, University of Luxembourg +# +# Based on the work of: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'BEDTools' +version = '2.23.0' + +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': '1.4.10'} + +# https://github.com/arq5x/bedtools2/releases/download/v2.23.0/bedtools-2.23.0.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/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..37178f8aa58e052452669f9684430d441e5d8e1b --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.30-foss-2015a-Python-2.7.9.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/Luxembourg Centre for Systems Biomedicine +# 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 = "2.2.30" +versionsuffix = '-Python-2.7.9' + +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': '2015a'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +patches = ['%(name)s-%(version)s_basename-fixes.patch'] + +dependencies = [('Boost', '1.57.0', versionsuffix)] + +configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..e09b9fd29876e76b4e344581f4b17ff4e5b5b387 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.2.31-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: 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 = '2.2.31' +versionsuffix = '-Python-2.7.10' + +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': 'intel', 'version': '2015a'} + +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/%(version)s/'] + +patches = [ + '%(name)s-2.2.30_ictce-fixes.patch', + '%(name)s-2.2.30_basename-fixes.patch' +] + +dependencies = [('Boost', '1.58.0', versionsuffix)] + +configopts = '--with-boost=$EBROOTBOOST --with-64 --with-bin-release --without-debug --with-mt' + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastp", "bin/blastx"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..1318374418384cf7a77e6cb10572e1311f0264e2 --- /dev/null +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74-goolf-1.4.10.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'BSMAP' +version = '2.74' + +homepage = 'https://code.google.com/p/bsmap/' +description = """BSMAP is a short reads mapping software for bisulfite sequencing reads.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://bsmap.googlecode.com/files/'] +sources = [SOURCELOWER_TGZ] + +skipsteps = ['configure'] + +installopts = "DESTDIR=%(installdir)s" + +patches = [ + 'BSMAP-2.74_makefile-modif.patch', + 'BSMAP-2.74_parameters-cpp.patch', + 'BSMAP-2.74_samtools-deps.patch', +] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.7'), + ('SAMtools', '0.1.18'), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["bsmap", "methratio.py", "sam2bam.sh"]], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch new file mode 100644 index 0000000000000000000000000000000000000000..daf84a74d5b368a4b53aba678bea4d8fa5ae3fd0 --- /dev/null +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_makefile-modif.patch @@ -0,0 +1,22 @@ +Patch to point to the correct bin directory in the EASYBUILDINSTALLDIR and to +to the correct location of the ZLIB libraries +Thekla Loizou July 2015 +--- bsmap-2.74/makefile.orig 2012-09-20 23:01:57.000000000 +0300 ++++ bsmap-2.74/makefile 2014-12-16 09:24:16.033631393 +0200 +@@ -1,6 +1,6 @@ + CC= g++ + +-BIN = $(DESTDIR)/usr/bin ++BIN = $(DESTDIR)/bin + FLAGS= -DMAXHITS=1000 -DTHREAD -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -m64 + #FLAGS= -DMAXHITS=1000 -funroll-loops -Lsamtools -Isamtools -Lgzstream -Igzstream -O3 -Wall -Wno-strict-aliasing -m64 + +@@ -16,7 +16,7 @@ + bsmap: $(OBJS1) + (cd samtools; make) + (cd gzstream; make) +- $(CC) $(FLAGS) $^ -o $@ $(THREAD) -lbam -lz -lgzstream ++ $(CC) $(FLAGS) $^ -o $@ $(THREAD) -lbam -L$(EBROOTZLIB)/lib -lz -lgzstream + rm -f *.o + + clean: diff --git a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_parameters-cpp.patch b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_parameters-cpp.patch new file mode 100644 index 0000000000000000000000000000000000000000..21007be7d35fda4929ec5ec8a016d6eea9e4147e --- /dev/null +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_parameters-cpp.patch @@ -0,0 +1,9 @@ +Patch to include unitstd.h in the parameters for cpp +Thekla Loizou July 2015 +--- param.cpp.orig 2014-12-08 22:13:01.439639000 +0200 ++++ param.cpp 2014-12-08 22:14:20.305028000 +0200 +@@ -1,3 +1,4 @@ ++#include + #include "param.h" + #include + diff --git a/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_samtools-deps.patch b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_samtools-deps.patch new file mode 100644 index 0000000000000000000000000000000000000000..7475b92e928fc6a7324ae3ee69115797cda880b0 --- /dev/null +++ b/easybuild/easyconfigs/b/BSMAP/BSMAP-2.74_samtools-deps.patch @@ -0,0 +1,78 @@ +Patch to point to the correct locations of SAMTools dependencies +Thekla Loizou July 2015 +--- bsmap-2.74/samtools/Makefile.orig 2014-12-15 14:42:22.628493847 +0200 ++++ bsmap-2.74/samtools/Makefile 2014-12-15 14:42:51.729602124 +0200 +@@ -10,10 +10,11 @@ + bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \ + cut_target.o phase.o bam2depth.o + PROG= samtools +-INCLUDES= -I. ++INCLUDES= -I$(EBROOTNCURSES)/include -I$(EBROOTZLIB)/include -I. + SUBDIRS= . bcftools misc +-LIBPATH= +-#LIBCURSES= -lcurses # -lXCurses ++LIBPATH= -L$(EBROOTZLIB)/lib ++LIBCURSES= -L$(EBROOTNCURSES)/lib -lcurses -L$(EBROOTZLIB)/lib -lz # -lXCurses ++ + + .SUFFIXES:.c .o + +@@ -44,10 +45,10 @@ + $(CC) $(CFLAGS) -o $@ $(AOBJS) -Lbcftools $(LIBPATH) libbam.a -lbcf $(LIBCURSES) -lm -lz + + razip:razip.o razf.o $(KNETFILE_O) +- $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz ++ $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -L$(EBROOTZLIB)/lib -lz + + bgzip:bgzip.o bgzf.o $(KNETFILE_O) +- $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz ++ $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -L$(EBROOTZLIB)/lib -lz + + razip.o:razf.h + bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h +@@ -73,10 +74,10 @@ + + + libbam.1.dylib-local:$(LOBJS) +- libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz ++ libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -L$(EBROOTZLIB)/lib -lz + + libbam.so.1-local:$(LOBJS) +- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz ++ $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -L$(EBROOTZLIB)/lib -lz + + dylib: + @$(MAKE) cleanlocal; \ +--- bsmap-2.74/samtools/misc/Makefile.orig 2012-09-20 23:01:58.000000000 +0300 ++++ bsmap-2.74/samtools/misc/Makefile 2014-12-15 14:40:50.817493925 +0200 +@@ -28,13 +28,13 @@ + lib: + + seqtk:seqtk.o +- $(CC) $(CFLAGS) -o $@ seqtk.o -lm -lz ++ $(CC) $(CFLAGS) -o $@ seqtk.o -lm -L$(EBROOTZLIB)/lib -lz + + wgsim:wgsim.o +- $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz ++ $(CC) $(CFLAGS) -o $@ wgsim.o -lm -L$(EBROOTZLIB)/lib -lz + + md5fa:md5.o md5fa.o md5.h ../kseq.h +- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz ++ $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -L$(EBROOTZLIB)/lib -lz + + md5sum-lite:md5sum-lite.o + $(CC) $(CFLAGS) -o $@ md5sum-lite.o +@@ -43,10 +43,10 @@ + $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c + + maq2sam-short:maq2sam.c +- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz +- ++ $(CC) $(CFLAGS) -o $@ maq2sam.c -L$(EBROOTZLIB)/lib -lz ++ + maq2sam-long:maq2sam.c +- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz ++ $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -L$(EBROOTZLIB)/lib -lz + + md5fa.o:md5.h md5fa.c + $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c diff --git a/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..46e8bcb1a8d94aa8f1067d752bea7a8a18d88de1 --- /dev/null +++ b/easybuild/easyconfigs/b/Biggus/Biggus-0.11.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,22 @@ +easyblock = "PythonPackage" + +name = 'Biggus' +version = '0.11.0' + +homepage = 'https://github.com/SciTools/biggus' +description = """Virtual large arrays and lazy evaluation.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +pylibdir = 'lib/python%s/site-packages' % pythonshortver +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/Biggus/Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/b/Biggus/Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..4374be186cdbcb6e385487d041481679eeb0f0b7 --- /dev/null +++ b/easybuild/easyconfigs/b/Biggus/Biggus-0.5.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,22 @@ +easyblock = "PythonPackage" + +name = 'Biggus' +version = '0.5.0' + +homepage = 'https://github.com/SciTools/biggus' +description = """Virtual large arrays and lazy evaluation.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +pylibdir = 'lib/python%s/site-packages' % pythonshortver +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-goolf-1.4.10-Perl-5.16.3.eb index 35b31e9ad8b4f6ad8b5dbb2940125a24ad74b0e6..2de3974d8c3a969dfb258f37364ab8ae92dcd321 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-goolf-1.4.10-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-goolf-1.4.10-Perl-5.16.3.eb @@ -9,8 +9,8 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['bioperl-release-%s.tar.gz' % version.replace('.', '-')] perl = 'Perl' perlver = '5.16.3' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-4.1.13-Perl-5.16.3.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-4.1.13-Perl-5.16.3.eb index f16cc0e7a36d5844995a0593589f563e53e878ca..9d9654707f97c139be72a51bd97eb26150ece427 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-4.1.13-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-4.1.13-Perl-5.16.3.eb @@ -9,8 +9,8 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = ['http://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['bioperl-release-%s.tar.gz' % version.replace('.', '-')] perl = 'Perl' perlver = '5.16.3' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-5.3.0-Perl-5.16.3.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-5.3.0-Perl-5.16.3.eb index f989bdd896cb105756ad78d1e2f7b9bf35eae543..47381bc735760d2ba814389661af2ee683f6e0f2 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-5.3.0-Perl-5.16.3.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.1-ictce-5.3.0-Perl-5.16.3.eb @@ -9,8 +9,8 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['bioperl-release-%s.tar.gz' % version.replace('.', '-')] perl = 'Perl' perlver = '5.16.3' diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-ictce-5.5.0-Perl-5.18.2.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-ictce-5.5.0-Perl-5.18.2.eb index b2c6b6f6298df908842ad858b9bac0831eca1a33..5954f543932b69c0cd8091683fb51238fd73cd43 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-ictce-5.5.0-Perl-5.18.2.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.923-ictce-5.5.0-Perl-5.18.2.eb @@ -9,8 +9,8 @@ description = """Bioperl is the product of a community effort to produce Perl co toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['http://www.cpan.org/modules/by-module/Bio/CJFIELDS/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/bioperl/bioperl-live/archive/'] +sources = ['release-%s.tar.gz' % version.replace('.', '-')] perl = 'Perl' perlver = '5.18.2' diff --git a/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..337980614fbfd664844ef62098e2f683b84c0ed5 --- /dev/null +++ b/easybuild/easyconfigs/b/Bismark/Bismark-0.10.1-goolf-1.4.10.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = "Tarball" + +name = 'Bismark' +version = '0.10.1' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/bismark/' +description = """A tool to map bisulfite converted sequence reads and +determine cytosine methylation states""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ["http://www.bioinformatics.babraham.ac.uk/projects/bismark/"] +sources = ['%s_v%s.tar.gz' % (name.lower(), version) ] + +dependencies = [('Bowtie2', '2.0.2')] + +sanity_check_paths = { + 'files': ["bismark", "bismark2bedGraph", "bismark2report", "bismark_genome_preparation", + "bismark_methylation_extractor", "coverage2cytosine", "deduplicate_bismark"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-6.1.5.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-6.1.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..deba4d2a79e3b05a8453b3cca08ca00976d45ba9 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-ictce-6.1.5.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '2.7' + +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': '6.1.5'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [('M4', '1.4.16')] + +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-2.7-intel-2015a.eb b/easybuild/easyconfigs/b/Bison/Bison-2.7-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..48aa608e0d36475fea8d1e26b3928135a3726552 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-2.7-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '2.7' + +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': '2015a'} + +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-3.0.2-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..96873ab500996b03701faff43084216244b6516b --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.1.29.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +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': 'CrayGNU', 'version': '5.1.29'} + +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-3.0.2-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..79f11b47febbc88d82227cb3efb9850a95bf2792 --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.25.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +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': 'CrayGNU', 'version': '5.2.25'} + +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/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..67832ccafa4b44022726c2857e00a032c70ba2de --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-CrayGNU-5.2.40.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +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': 'CrayGNU', 'version': '5.2.40'} + +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-3.0.2-foss-2014b.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..821e3cc963d55bbd146a32ebcbaf0ee0149e0e7a --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2014b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +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': '2014b'} + +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-3.0.2-foss-2015a.eb b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0b270e9381ff0a5d78465bfb4d59e94fb039abfb --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.0.2-foss-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'Bison' +version = '3.0.2' + +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': '2015a'} + +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/Boost/Boost-1.55.0-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..8d26308267b848adc9509a6c86f27f2bf4ffe236 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2014b-Python-2.7.8.eb @@ -0,0 +1,26 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2014b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.8' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +osdependencies = ['zlib-devel'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..88a81a73e9b2486a7faef4d0ec8caad67229c1f4 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.55.0' + +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('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..644fd26b387107095983d8147dfeaacff0c6f555 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +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-1.55.0-ictce-7.1.2-Python-2.7.8.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..d29dcc1cdae5e793c3855bd382c45bb5196889e9 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-ictce-7.1.2-Python-2.7.8.eb @@ -0,0 +1,28 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'ictce', 'version': '7.1.2'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +patches = ['intellinuxjam_fPIC.patch', 'boost-impi5.patch'] + +pythonversion = '2.7.8' +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-1.58.0-foss-2015.05-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..24316a807ffee348d2e01f96a48b68baea3c3e6a --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015.05-Python-2.7.9.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..76622b0263731200d662f710e3a71d10d735c034 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.10.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +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('.'))] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..bbef8b760b3ac8240f9078c2e2961fca0159d225 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +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('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..bee3eb38e4f0257abd6366b81280cde8cc99f98a --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-goolf-1.7.20.eb @@ -0,0 +1,23 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +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-1.58.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..d48f0872ddcc24a13d88d152bc431050aa8c328f --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.10' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..a209577bba563ea28b75df363e7dac921d12fe0d --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.58.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +name = 'Boost' +version = '1.58.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + +pythonversion = '2.7.9' +versionsuffix = '-Python-%s' % pythonversion + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('Python', pythonversion), +] + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/Boost/boost-impi5.patch b/easybuild/easyconfigs/b/Boost/boost-impi5.patch new file mode 100644 index 0000000000000000000000000000000000000000..635da12964f8acf90c611cffea66d6709f1097c1 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/boost-impi5.patch @@ -0,0 +1,37 @@ +diff -ur boost_1_55_0.orig/tools/build/v2/tools/mpi.jam boost_1_55_0/tools/build/v2/tools/mpi.jam +--- boost_1_55_0.orig/tools/build/v2/tools/mpi.jam 2012-04-26 23:32:41.000000000 +0200 ++++ boost_1_55_0/tools/build/v2/tools/mpi.jam 2014-09-03 13:45:45.000000000 +0200 +@@ -301,6 +301,16 @@ + } + # OpenMPI and newer versions of LAM-MPI have -showme:compile and + # -showme:link. ++ # Look for MPICH ++ else if [ safe-shell-command "$(command) -show" ] ++ { ++ if $(.debug-configuration) ++ { ++ ECHO "Found MPICH wrapper compiler: $(command)" ; ++ } ++ compile_flags = [ SHELL "$(command) -compile_info" ] ; ++ link_flags = [ SHELL "$(command) -link_info" ] ; ++ } + else if [ safe-shell-command "$(command) -showme:compile" ] && + [ safe-shell-command "$(command) -showme:link" ] + { +@@ -327,16 +337,6 @@ + + result = [ SHELL "$(command) -showme" ] ; + } +- # Look for MPICH +- else if [ safe-shell-command "$(command) -show" ] +- { +- if $(.debug-configuration) +- { +- ECHO "Found MPICH wrapper compiler: $(command)" ; +- } +- compile_flags = [ SHELL "$(command) -compile_info" ] ; +- link_flags = [ SHELL "$(command) -link_info" ] ; +- } + # Sun HPC and Ibm POE + else if [ SHELL "$(command) -v 2>/dev/null" ] + { diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..0240ff0e2c2cedef6f93bbf1400c72e9a3b3152b --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.1-goolf-1.4.10.eb @@ -0,0 +1,19 @@ +#Modified from existing version by: +#Robert Schmidt +#Ottawa Hospital Research Institute - Bioinformatics Team + +name = 'Bowtie' +version = '1.1.1' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. +It aligns short DNA sequences (reads) to the human genome. +""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c3c415f11f0f8e3a050d0fc0c17b64f8f91b698d --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie/Bowtie-1.1.2-intel-2015a.eb @@ -0,0 +1,32 @@ +#Modified from existing version by: +#Robert Schmidt +#Ottawa Hospital Research Institute - Bioinformatics Team +easyblock = 'MakeCp' + +name = 'Bowtie' +version = '1.1.2' + +homepage = 'http://bowtie-bio.sourceforge.net/index.shtml' +description = """Bowtie is an ultrafast, memory-efficient short read aligner. +It aligns short DNA sequences (reads) to the human genome. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(namelower)s-%(version)s-src.zip'] +source_urls = ['http://download.sourceforge.net/bowtie-bio/'] + +patches = ['int64typedef.patch'] + +buildopts = 'CC="$CC" CXX="$CXX" CPP="$CXX"' + +files_to_copy = [(['bowtie', 'bowtie-build', 'bowtie-inspect'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/bowtie', 'bin/bowtie-inspect'], + 'dirs': [], +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..30dfc1896056ea87807b8d7ae8625639c77340b0 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-goolf-1.7.20.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 +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.5' + +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': 'goolf', 'version': '1.7.20'} + +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/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..cc4bd53b3af195625813f229498639fa5e1f0202 --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.5-intel-2015a.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 +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team + +easyblock = 'MakeCp' + +name = 'Bowtie2' +version = '2.2.5' + +homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +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/bibtexparser/bibtexparser-0.5-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..383c7de16ac8365e72662f39bfa14d9167cd6c1b --- /dev/null +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,20 @@ +easyblock = 'PythonPackage' + +name = 'bibtexparser' +version = '0.5' + +homepage = 'https://github.com/sciunto-org/python-bibtexparser' +description = """Bibtex parser in Python 2.7 and 3.x""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..4c591a3fc0c4d0754230ffb73a0a8c7efd0d2bb3 --- /dev/null +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.5-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,20 @@ +easyblock = 'PythonPackage' + +name = 'bibtexparser' +version = '0.5' + +homepage = 'https://github.com/sciunto-org/python-bibtexparser' +description = """Bibtex parser in Python 2.7 and 3.x""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..7060a6e07d4ed80085d1db31d5a47f05de67dd54 --- /dev/null +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,20 @@ +easyblock = 'PythonPackage' + +name = 'bibtexparser' +version = '0.6.0' + +homepage = 'https://github.com/sciunto-org/python-bibtexparser' +description = """Bibtex parser in Python 2.7 and 3.x""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..88ee53e88af00652d2b64c84e2d5a7a59e93f34d --- /dev/null +++ b/easybuild/easyconfigs/b/bibtexparser/bibtexparser-0.6.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,20 @@ +easyblock = 'PythonPackage' + +name = 'bibtexparser' +version = '0.6.0' + +homepage = 'https://github.com/sciunto-org/python-bibtexparser' +description = """Bibtex parser in Python 2.7 and 3.x""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb index 6d0b4d9315d4c2ad98fa5f00b926e8d8b084b799..09be4e251381a1486680b49c6af7103786803631 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goalf-1.1.0-no-OFED.eb @@ -18,11 +18,14 @@ version = '2.22' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils-2.22: GNU binary utilities" +toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'pic': True} + sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -toolchainopts = {'pic': True} +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb index 129afa50d15cd899b9af99c787be5761b36e06bc..037eea64d670577145cd3de25899bcc26f5d0e82 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-gompi-1.4.12-no-OFED.eb @@ -18,11 +18,14 @@ version = '2.22' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils-2.22: GNU binary utilities" +toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} +toolchainopts = {'pic': True} + sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -toolchainopts = {'pic': True} +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb index 98ff0c9aefe57dd5b08c6f0989a451b0132b70fb..6eefeecf7f105efe2cf079ce217cbdcca6cd9866 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.4.10.eb @@ -18,10 +18,13 @@ version = '2.22' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils-2.22: GNU binary utilities" +toolchain = {'name': 'goolf', 'version': '1.4.10'} + sources = ['binutils-%s.tar.bz2' % version] source_urls = [GNU_SOURCE] -toolchain = {'name': 'goolf', 'version': '1.4.10'} +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..1922cb5d1278e46e29a3390b39777eff79f9b58f --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.22-goolf-1.5.14.eb @@ -0,0 +1,35 @@ +## +# 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_07-02.html +## + +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.22' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils-2.22: GNU binary utilities" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} +toolchainopts = {'pic': True} + +sources = ['binutils-%(version)s.tar.bz2'] +source_urls = [GNU_SOURCE] + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a', 'lib64/libiberty.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb b/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb index 7e0429c8a13a77835fb99305727e9e8e67cb2dbb..f289f62f1b1330c3bf3ce51084f8544a58850083 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-foss-2014b.eb @@ -15,6 +15,9 @@ dependencies = [ ('zlib', '1.2.8'), ] +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' + binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] sanity_check_paths = { 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 35ffa05491581b0981afabfd12de4c06677aff95..90ee55811f8d090738cd56b78eb71cd0f1a755b3 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.24-intel-2014b.eb @@ -15,6 +15,9 @@ dependencies = [ ('zlib', '1.2.8'), ] +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' + # disable warning/error #175 ("subscript out of range") buildopts = 'CFLAGS="$CFLAGS -wd175"' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..6b906969bbe4ac006542096e6455dacaae619ed3 --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.25' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCC', 'version': '4.9.2-binutils-%(version)s'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' + +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb index e44a4bc4f7165314b19c49c8f82686da5432a9a2..3b30b6d478da13391e04008b7d4a12f1086be456 100644 --- a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb @@ -6,17 +6,24 @@ version = '2.25' homepage = 'http://directory.fsf.org/project/binutils/' description = "binutils: GNU binary utilities" +toolchain = {'name': 'GCC', 'version': '4.9.2'} + sources = [SOURCE_TAR_GZ] source_urls = [GNU_SOURCE] -toolchain = {'name': 'GCC', 'version': '4.9.2'} +# zlib required, but being linked instatically, so not a runtime dep +builddependencies = [('zlib', '1.2.8')] -dependencies = [ - ('zlib', '1.2.8'), -] +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' + +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + sanity_check_paths = { 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..e8d57cd5784e90049a3678763ac01ad004940d6f --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-5.1.0-binutils-2.25.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.25' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'GCC', 'version': '5.1.0-binutils-%(version)s'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +builddependencies = [ + # zlib required, but being linked instatically, so not a runtime dep + ('zlib', '1.2.8'), + # use same binutils version that was used when building GCC toolchain, to 'bootstrap' this binutils + ('binutils', version, '', True) +] + +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' + +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/binutils/binutils-2.25.eb b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..aa312b1626a655a5bfa34dc35efcff4567526cbc --- /dev/null +++ b/easybuild/easyconfigs/b/binutils/binutils-2.25.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'binutils' +version = '2.25' + +homepage = 'http://directory.fsf.org/project/binutils/' +description = "binutils: GNU binary utilities" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +# zlib required, but being linked instatically, so not a runtime dep +builddependencies = [('zlib', '1.2.8')] + +# statically link with zlib, to avoid runtime dependency on zlib +preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' +prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"' + +# make sure that system libraries are also considered by ld +configopts = '--with-sysroot=/' + +binlist = ['addr2line', 'ar', 'as', 'c++filt', 'elfedit', 'gprof', 'ld', 'ld.bfd', 'nm', + 'objcopy', 'objdump', 'ranlib', 'readelf', 'size', 'strings', 'strip' ] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binlist] + ['lib/libbfd.a', 'lib/libopcodes.a'] + + ['include/%s' % x for x in ['ansidecl.h', 'bfd.h', 'bfdlink.h', 'dis-asm.h', 'symcat.h']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb index 0a0256d97dd23a00ce548bfb222cc68afa048b17..428ecbe9cfe462dae187f1bfb328fa3f9d42cd0b 100644 --- a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb +++ b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10-extended.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2013-01.html ## -easyblock = "Toolchain" +easyblock = 'Bundle' name = 'biodeps' version = '1.6' diff --git a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10.eb b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10.eb index d8d026cace641bf05c38c8966de152381b03b889..6fcc534d72a27e821e128b09dcf48fa52d74bb4d 100644 --- a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-goolf-1.4.10.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2013-01.html ## -easyblock = "Toolchain" +easyblock = 'Bundle' name = 'biodeps' version = '1.6' diff --git a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb index 878f45a16dad588f1cb7b26eedbb3fe519415f1d..34a00add446855a520a05aa3cbc7156538aa7e60 100644 --- a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb +++ b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0-extended.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2013-01.html ## -easyblock = "Toolchain" +easyblock = 'Bundle' name = 'biodeps' version = '1.6' diff --git a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0.eb b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0.eb index 63eda1f427e0fa1a3d3c880752cbd5c4f15690db..1091497ff7ea58e55f91a3473bc0c0a03968c8c7 100644 --- a/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/b/biodeps/biodeps-1.6-ictce-5.3.0.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2013-01.html ## -easyblock = "Toolchain" +easyblock = 'Bundle' name = 'biodeps' version = '1.6' diff --git a/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..d339980b4f223943993e48e3ed58a9a18184a859 --- /dev/null +++ b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1-goolf-1.4.10.eb @@ -0,0 +1,46 @@ +# With <3 for EasyBuild +# +# EasyConfig for BLASR: +# ---------------------------------------------------------------------------- +# Copyright: 2013 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Petar Forai +# ---------------------------------------------------------------------------- + +easyblock = 'MakeCp' + +name = 'blasr' +version = 'smrtanalysis-2.1' + +homepage = 'https://github.com/PacificBiosciences/blasr' +description = """BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the + highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBio's + extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(version)s.tar.gz'] +source_urls = ['https://github.com/PacificBiosciences/blasr/archive/'] + +patches = ['blasr-%(version)s_non-static.patch'] + +dependencies = [('HDF5', '1.8.9')] + +buildopts = 'HDF5INCLUDEDIR=${EBROOTHDF5}/include HDF5LIBDIR=${EBROOTHDF5}/lib' + +binaries = [ + 'wordCounter', 'printReadWordCount', 'blasr', 'sdpMatcher', 'swMatcher', 'kbandMatcher', 'sawriter', + 'saquery', 'samodify', 'printTupleCountTable', 'malign', 'cmpPrintTupleCountTable', 'removeAdapters', + 'tabulateAlignment', 'samatcher', 'sals', 'saprinter', 'buildQualityValueProfile', 'extendAlign', + 'guidedalign', 'pbmask', +] + +files_to_copy = [(['alignment/bin/%s' % x for x in binaries], 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in binaries], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1_non-static.patch b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1_non-static.patch new file mode 100644 index 0000000000000000000000000000000000000000..03b7b3f2bbe519356f5a1674f87719487bddc34c --- /dev/null +++ b/easybuild/easyconfigs/b/blasr/blasr-smrtanalysis-2.1_non-static.patch @@ -0,0 +1,13 @@ +--- common.mk.orig 2013-11-08 15:19:36.848815000 +0100 ++++ common.mk 2013-11-08 15:19:54.854217000 +0100 +@@ -24,6 +24,7 @@ + ifeq ($(shell $(CC) -dumpversion | awk -F '.' '$$1*100+$$2>404{print "yes"}'),yes) + CPPOPTS += -fpermissive + endif +-ifneq ($(shell uname -s),Darwin) +- STATIC = -static +-endif ++# Why oh why ... ++#ifneq ($(shell uname -s),Darwin) ++# STATIC = -static ++#endif diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2015a.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0321acfcc558113ac0bb2f652de5ae87c9d60bd1 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2015a.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..a04591dedea2dabab6fa0f929e716be159d27f68 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.1.29.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': '5.1.29'} +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-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..3f96190606801772d44e63e8329012fe5cb9b6e8 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.25.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': 'CrayGNU', 'version': '5.2.25'} +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-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..58489cb68f9841a4501baa314d7f4c6f6c750ec1 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-CrayGNU-5.2.40.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': '5.2.40'} +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-2015.05.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..1c3c8d1851862117494715ee2a9c067517f8456f --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-foss-2015.05.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': '2015.05'} +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-goolf-1.7.20.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..718daa2bc0c40a5dc9c35935e193c46b395e7922 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-goolf-1.7.20.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': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.bzip.org/%(version)s/'] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014.06.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..567328a2d616ebd44759e4bfb2d2ce38a66396ae --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.6-intel-2014.06.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': '2014.06'} +toolchainopts = {'pic': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.bzip.org/%(version)s'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..155eb5a8aee415696369bf728fba55305175dfd7 --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2-intel-2015a.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': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, '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-37b2_fix-qgas-double-declared.patch', +] + +# MKL activated automatically when the ictce toolchain is used +build_options = "FULL COLFFT PIPF" + +# Chose from: huge, xxlarge, xlarge, large, medium (the default), small, xsmall, reduce +system_size = "medium" + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch new file mode 100644 index 0000000000000000000000000000000000000000..2c8d36a45f335744b44f9e69a330cabc63111b5b --- /dev/null +++ b/easybuild/easyconfigs/c/CHARMM/CHARMM-37b2_fix-qgas-double-declared.patch @@ -0,0 +1,53 @@ +reproduction of CHARMM SVN revision 272 (Check-in: http:/charmm.hanyang.ac.kr/6187) +renamed qgas variable in pbeq to qgas1 and updated references in energy +diff -ru c37b2.orig/source/energy/energy.src c37b2/source/energy/energy.src +--- c37b2.orig/source/energy/energy.src 2012-09-29 08:01:42.000000000 +0200 ++++ c37b2/source/energy/energy.src 2015-05-21 16:57:43.951197202 +0200 +@@ -266,7 +266,7 @@ + use param + use pathm + use mpathint, only: qpint, epint !##PATHINT +- use pbeq, only: qpbeq,qpbf,npbeq,qgsbp,pbforce,gsbp0,qgas,qsmbp,smbp0 !##PBEQ ++ use pbeq, only: qpbeq,qpbf,npbeq,qgsbp,pbforce,gsbp0,qgas1,qsmbp,smbp0 !##PBEQ + use pbound + use pert + use polarm, only: qpolar, polar1 !##POLAR +@@ -3203,7 +3203,7 @@ + + CALL PBFORCE(NATOM,X,Y,Z,CG,ETERM(PBELEC),ETERM(PBNP), & + DX,DY,DZ,NPBEQ,ecalls,.false. & +- ,QETERM(QMEL),ETERM(QMEL),QGAS & !##SCCDFTB ++ ,QETERM(QMEL),ETERM(QMEL),QGAS1 & !##SCCDFTB + ) + IF (TIMER.GT.1) & + CALL WRTTIM('Poisson Boltzmann Solvation energy times:') +diff -ru c37b2.orig/source/misc/pbeq.src c37b2/source/misc/pbeq.src +--- c37b2.orig/source/misc/pbeq.src 2012-08-08 20:08:30.000000000 +0200 ++++ c37b2/source/misc/pbeq.src 2015-05-21 16:55:47.871787533 +0200 +@@ -19,7 +19,7 @@ + !public :: pbeq0,pbforce,gsbp0,srdist + !QC: export more + public :: pbeq0,pbforce,gsbp0,srdist,m3,dm3,rpowerl2,cosmphi2,sinmphi2,& +- alpol2,dalpol2,lpol2,dlpol2,pbeq1,oldpbeq1,mayer,pbeq2,qgas, & ++ alpol2,dalpol2,lpol2,dlpol2,pbeq1,oldpbeq1,mayer,pbeq2,qgas1, & + pbeq_iniall,smbp0 + + !variables +@@ -115,7 +115,7 @@ + + ! The following is related to QM/MM implementation of gsbp and pb + ! Xiao_QC_UW0609 +- LOGICAL QPSC,QGAS ++ LOGICAL QPSC,QGAS1 + ##IF SCCDFTB + ! + ! COEFX -----> heap index for COEFX(NTPOL) +@@ -2734,7 +2734,7 @@ + ! XIAO_QC_UW0609 keyword for SCC/PB + MXTPSC = GTRMI(COMLYN,COMLEN,'MXPS',5000) + PSCTOL = GTRMF(COMLYN,COMLEN,'PSTL',1.0D-2) +- QGAS = INDXA(COMLYN,COMLEN,'IGAS').GT.0 ++ QGAS1 = INDXA(COMLYN,COMLEN,'IGAS').GT.0 + ! XIAO_QC_UW0609 add charge dependant radii + QCHDRAD = INDXA(COMLYN,COMLEN,'CHDR').GT.0 + IF (QCHDRAD) THEN diff --git a/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9408c50361728c93b17344d0b374918fddb26230 --- /dev/null +++ b/easybuild/easyconfigs/c/CLHEP/CLHEP-2.2.0.5-intel-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'CMakeMake' + +name = 'CLHEP' +version = '2.2.0.5' + +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': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TGZ] +source_urls = ['http://proj-clhep.web.cern.ch/proj-clhep/DISTRIBUTION/tarFiles/'] + +builddependencies = [('CMake', '3.2.2')] + +separate_build_dir = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..08b9903802b50b1c48d02f63c0f8fda070122374 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-2.8.12-foss-2014b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '2.8.12' + +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': '2014b'} + +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-3.0.0-foss-2014b.eb b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..872f8b4d7dab341b5923730930c018f6e49ac459 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2014b.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.0.0' + +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': 'foss', 'version': '2014b'} + +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-3.0.0-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c55a48656c2b7eba2de2ad9c1dc465c5857ab755 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-foss-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.0.0' + +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': 'foss', 'version': '2015a'} + +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-3.0.0-intel-2014.06.eb b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-intel-2014.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..447079089d936b15acbbe986e1b754f5788c8385 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.0.0-intel-2014.06.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.0.0' + +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': 'intel', 'version': '2014.06'} + +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-3.2.1-GCC-4.9.2.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.1-GCC-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..f556c35a247e2b50ed46b38804e8470f1cce183c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.1-GCC-4.9.2.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.1' + +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': '4.9.2'} + +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-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4982739fa2ab7b1106fd74f7b68c60068c446cd4 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.1-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.1' + +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': '2015a'} + +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-3.2.2-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..68df962efa687871ddddaeec1a9850346b4eafc2 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.1.29.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +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': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'dynamic': True} + +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-3.2.2-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..75190be28b5c848573e3fdf32fb4ff49253c168a --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +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': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'dynamic': True} + +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-3.2.2-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..275dc8cadadb1e9c3bf7f6d2a8f318b6ade52e9a --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-CrayGNU-5.2.40.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +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': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'dynamic': True} + +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-3.2.2-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d971d9f7a0a6358e208a3302cd1ee4da24302c6b --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.2-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.2' + +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': '2015a'} + +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-3.2.3-foss-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..e6f905f4098a3847b4fe46f1617f55ba6220dd3c --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-foss-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.3' + +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': '2015a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '5.9'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1k'), +] + +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-3.2.3-intel-2015a.eb b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5e1447f0f0fab7b743fad920befa5282f21791e7 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.2.3-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'CMake' +version = '3.2.3' + +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': 'intel', 'version': '2015a'} + +source_urls = ['http://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = '-- -DCMAKE_USE_OPENSSL=1' + +dependencies = [ + ('ncurses', '5.9'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + #('OpenSSL', '1.0.1k'), +] + +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/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb b/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..f772aaa29cdaed52dd453f8867154cee139cd1ad --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAfold/CONTRAfold-2.02-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 +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'CONTRAfold' +version = '2.02' + +homepage = 'http://contra.stanford.edu/contrafold/' +description = ''' CONditional TRAining for RNA Secondary Structure Prediction ''' + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [homepage] +sources = ['%s_v%s.tar.gz' % (name.lower(),version.replace('.','_'))] + +patches = ['contrafold-gcc47.patch'] + +start_dir = 'src' + +files_to_copy = [(['score_prediction', 'contrafold', 'score_directory.pl',\ + 'roc_area.pl', 'MakeDefaults.pl'], 'bin'), '../doc'] + +sanity_check_paths = { + 'files': ['bin/score_prediction', 'bin/contrafold'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CONTRAfold/contrafold-gcc47.patch b/easybuild/easyconfigs/c/CONTRAfold/contrafold-gcc47.patch new file mode 100644 index 0000000000000000000000000000000000000000..d484c76bfdbecf7fd1479723f76090af68e69030 --- /dev/null +++ b/easybuild/easyconfigs/c/CONTRAfold/contrafold-gcc47.patch @@ -0,0 +1,20 @@ +--- contrafold.orig/src/Makefile 2008-08-14 02:08:30.000000000 +0200 ++++ contrafold/src/Makefile 2014-02-04 13:51:29.041589171 +0100 +@@ -1,6 +1,6 @@ + CXX = g++ + +-CXXFLAGS = -O3 -DNDEBUG -W -pipe -Wundef -Winline --param large-function-growth=100000 -Wall ++CXXFLAGS = -O3 -DNDEBUG -W -pipe -Wundef -Winline --param large-function-growth=100000 -Wall -fpermissive + LINKFLAGS = -lm + GDLINKFLAGS = -lgd -lpng + +--- contrafold.orig/src/Utilities.cpp 2008-08-14 02:08:31.000000000 +0200 ++++ contrafold/src/Utilities.cpp 2014-02-04 14:09:09.082650184 +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-5.1.29.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..e1f9bdb729ac280e4ffb7cd4ea0c6b1a5696daf5 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.1.29.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.0' + +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': 'CrayGNU', 'version': '5.1.29'} +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', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# 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 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..43baa97a11a4003b107ffe43d08be06b7d80faca --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.25.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.0' + +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': 'CrayGNU', 'version': '5.2.25'} +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', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# 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 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..eea0ba5f731dbd8900fc765f4fdf3536d201d5ed --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2.6.0-CrayGNU-5.2.40.eb @@ -0,0 +1,38 @@ +name = 'CP2K' +version = '2.6.0' + +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': 'CrayGNU', 'version': '5.2.40'} +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', '2.2.1'), +] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +# 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 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-20130228-intel-2015a.eb b/easybuild/easyconfigs/c/CP2K/CP2K-20130228-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fd8d96a13d0cc18b5c58e4ae858a7e8bafbbc5cc --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-20130228-intel-2015a.eb @@ -0,0 +1,36 @@ +name = 'CP2K' +version = '20130228' + +homepage = 'http://cp2k.berlios.de/index.html' +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': '2015a'} +toolchainopts = {'pic': True} + +sources = ['CP2K-%(version)s.tar.gz'] + +patches = [ + 'CP2K-2013_fix_compile_date_lastcvs.patch', + 'do_regtest_nocompile.patch', +] + +dependencies = [ + ('FFTW', '3.3.3'), + ('Libint', '1.1.4'), +] + +builddependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7'), +] + +# don't use parallel make, results in compilation failure +# because Fortran module files aren't created before they are needed +parallel = 1 + +ignore_regtest_fails = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CP2K/CP2K-2013_fix_compile_date_lastcvs.patch b/easybuild/easyconfigs/c/CP2K/CP2K-2013_fix_compile_date_lastcvs.patch new file mode 100644 index 0000000000000000000000000000000000000000..7533a553087cd6b3bc47065640e9197379b3e7e7 --- /dev/null +++ b/easybuild/easyconfigs/c/CP2K/CP2K-2013_fix_compile_date_lastcvs.patch @@ -0,0 +1,11 @@ +--- cp2k/makefiles/Makefile.orig 2013-02-04 17:55:57.000000000 +0100 ++++ cp2k/makefiles/Makefile 2013-02-05 17:55:06.811020304 +0100 +@@ -200,7 +200,7 @@ + # + ifeq ($(CPPSHELL),) + CPPSHELL := -D__COMPILE_ARCH="\"$(ARCH)\""\ +- -D__COMPILE_DATE="\"$(shell date)\""\ ++ -D__COMPILE_DATE="\"$(shell date | sed 's/ /_/g'))\""\ + -D__COMPILE_HOST="\"$(shell hostname)\""\ + -D__COMPILE_REVISION="\"$(strip $(REVISION))\"" + endif diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb new file mode 100644 index 0000000000000000000000000000000000000000..76cb0b94f93ad8e194242f21948db74ec1df4039 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.0.37.eb @@ -0,0 +1,29 @@ +## +# 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 +# Authors:: George Tsouloupas , Fotis Georgatos , 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_2012-99.html +## + +name = 'CUDA' +version = '6.0.37' + +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'} + +# http://developer.download.nvidia.com/compute/cuda/6_0/rel/installers/cuda_6.0.37_linux_64.run +source_urls = ['http://developer.download.nvidia.com/compute/cuda/%(version_major)s_%(version_minor)s/rel/installers/'] +sources = ['%(namelower)s_%(version)s_linux_64.run'] +checksums = ['22f50793b6704fe987983302fa7d1707'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..920ee4c4faaaa53963d81d4c5260c23ffd8767c1 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-6.5.14.eb @@ -0,0 +1,30 @@ +## +# 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 +# Authors:: George Tsouloupas , Fotis Georgatos , 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_2012-99.html +## + +name = 'CUDA' +version = '6.5.14' + +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'} + +# eg. http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/cuda_6.5.14_linux_64.run +source_urls = ['http://developer.download.nvidia.com/compute/cuda/6_5/rel/installers/'] + +sources = ['%(namelower)s_%(version)s_linux_64.run'] +checksums = [('md5', '90b1b8f77313600cc294d9271741f4da')] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..665f1371cbdbf2eb8f7a0f9eb1815a7e6f00286b --- /dev/null +++ b/easybuild/easyconfigs/c/Check/Check-0.9.12-goolf-1.4.10.eb @@ -0,0 +1,23 @@ +# 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 = "Check" +version = "0.9.12" + +homepage = 'http://check.sourceforge.net' +description = """ Check is a unit testing framework for C. It features a simple interface + for defining unit tests, putting little in the way of the developer. Tests are run in a + separate address space, so both assertion failures and code errors that cause segmentation + faults or other signals can be caught. Test results are reportable in the following: + Subunit, TAP, XML, and a generic logging format.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..b2653a86750e60470f7c77bf9ed51b0d0f3af423 --- /dev/null +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-4.0.5-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'Circuitscape' +version = '4.0.5' + +homepage = 'http://www.circuitscape.org/' +description = """Circuitscape is a free, open-source program which borrows algorithms + from electronic circuit theory to predict patterns of movement, gene flow, + and genetic differentiation among plant and animal populations in + heterogeneous landscapes. Circuit theory complements least-cost path + approaches because it considers effects of all possible pathways + across a landscape simultaneously.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.8' +pyshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), + ('PyAMG', '2.2.1', versionsuffix), +] + +sanity_check_paths = { + 'files': ['lib/python%s/site-packages/%%(namelower)s/__init__.py' % pyshortver] + + ['bin/cs%s.py' % x for x in ['run', 'verify']], + 'dirs': ['lib/python%s/site-packages/%%(namelower)s' % pyshortver], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb index 445ace09850d17b8c0ac28919c403350b3ac5424..40f0a86d6f88f57be99c3c2828537ba9a17af9c6 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.0-GCC-4.9.2.eb @@ -30,7 +30,7 @@ sources = [ ] dependencies = [ - ('GMP', '6.0.0'), + ('GMP', '6.0.0a'), ('ISL', '0.14'), ] diff --git a/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..966759d71cd17ea26dc4cf0cbe3336c20850e610 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-3.6.1-GCC-4.9.2.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = "Clang" +version = "3.6.1" + +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': '4.9.2'} +# 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', '6.0.0a'), + ('ISL', '0.14'), +] + +builddependencies = [ + ('CMake', '3.2.1'), + ('Python', '2.7.9', '-bare'), + ('libxml2', '2.9.2'), +] + +assertions = True + +usepolly = True + +build_targets = ['X86'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..766d96d7565ce5fcec75e2965575dfafed7bb7e7 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.1.29.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayCCE' +version = '5.1.29' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-cray/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.0', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..7a2e621e2440b14e31b9813b195d8af0b624ae68 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.25.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayCCE' +version = '5.2.25' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-cray/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..b31f4b3a23e21c3914b7591f0410fa61abac45bd --- /dev/null +++ b/easybuild/easyconfigs/c/CrayCCE/CrayCCE-5.2.40.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayCCE' +version = '5.2.40' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-cray module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-cray/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..b3e7499933652aab16c7d7d2b0bf0947aca9e274 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.1.29.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayGNU' +version = '5.1.29' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.0', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..401574689493c1e220d00c29b5f73c0fceb033f3 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.25.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayGNU' +version = '5.2.25' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..dbbbbbd3039785c20044889424afa06cc658db48 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayGNU/CrayGNU-5.2.40.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayGNU' +version = '5.2.40' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-gnu module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-gnu/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..7c17b80f7ec94685ed65ed4c859dfc86d59450cd --- /dev/null +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.1.29.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayIntel' +version = '5.1.29' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-intel/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.0', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..edaac85f5493690b1950c031cfe784d266cf280e --- /dev/null +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.25.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayIntel' +version = '5.2.25' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-intel/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..5937accfe4587228d5357aa7e87a4555f1b707e0 --- /dev/null +++ b/easybuild/easyconfigs/c/CrayIntel/CrayIntel-5.2.40.eb @@ -0,0 +1,16 @@ +easyblock = 'Toolchain' + +name = 'CrayIntel' +version = '5.2.40' + +homepage = '(none)' +description = """Toolchain using Cray compiler wrapper, using PrgEnv-intel module.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('PrgEnv-intel/' + version, EXTERNAL_MODULE), # also loads cray-libsci + ('fftw/3.3.4.2', EXTERNAL_MODULE), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb index b1b5830754fac02a2f1b9ab65cc20b25ffb53be4..94eaf15f8dd907b211f15c47454a24c5c574e60d 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-3.4.3-gompi-1.4.12-no-OFED.eb @@ -1,11 +1,15 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## + easyblock = 'ConfigureMake' name = "Cube" @@ -20,9 +24,12 @@ description = """Cube, which is used as performance report explorer for Scalasca toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -# http://apps.fz-juelich.de/scalasca/releases/cube/3.4/dist/cube-3.4.3.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/3.4/dist'] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] + +checksums = [ + '703d4681851a5abf50946868f05e8f9e', # cube-3.4.3.tar.gz +] dependencies = [('Qt', '4.8.4')] diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb index a097385484cb9067ce8763e66296eac67e68a089..7159c84d00340784eaee2a3197754cf914269110 100644 --- a/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2-gompi-1.4.12-no-OFED.eb @@ -1,11 +1,15 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## + easyblock = 'EB_Score_minus_P' name = "Cube" @@ -20,18 +24,31 @@ description = """Cube, which is used as performance report explorer for Scalasca toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -# http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist/cube-4.2.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/4.2/dist'] +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-4.2_fix-Qt-version-check.patch', + 'Cube-4.2_fix-with-qt-check.patch', +] -patches = ['Cube-4.2_fix-Qt-version-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', '4.8.4')] -configopts = "QMAKE=$EBROOTQT/bin/qmake MOC=$EBROOTQT/bin/moc UIC=$EBROOTQT/bin/uic" +# 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", "lib/libcube4.so"], + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.so", "lib64/libcube4.so")], 'dirs': ["include/cube", "include/cubew"], } diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..7bda257ed231f7102fd0103e87be93c729b84284 --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2.3-goolf-1.5.14.eb @@ -0,0 +1,41 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Authors:: Jordi Blasco +# License:: New BSD +# +## + +easyblock = 'EB_Score_minus_P' + +name = "Cube" +version = "4.2.3" + +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'] + +checksums = [ + '8f95b9531f5a8f8134f279c2767c9b20', # cube-4.2.3.tar.gz +] + +dependencies = [('Qt', '4.8.4')] + +# 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.so", "lib64/libcube4.so")], + 'dirs': ["include/cube", "include/cubew"], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.2_fix-with-qt-check.patch b/easybuild/easyconfigs/c/Cube/Cube-4.2_fix-with-qt-check.patch new file mode 100644 index 0000000000000000000000000000000000000000..5ea89bb644d67e932173088816f56c554b36b6a5 --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.2_fix-with-qt-check.patch @@ -0,0 +1,209 @@ +--- build-backend/configure.orig 2013-08-02 13:20:33.000000000 +0200 ++++ build-backend/configure 2015-04-29 09:56:00.891697331 +0200 +@@ -19819,6 +19819,8 @@ $as_echo "$at_darwin" >&6; } + + # Find qmake. + ++ if test "x$QT_PATH" == "x"; then : ++ + for ac_prog in qmake-qt4 qmake + do + # Extract the first word of "$ac_prog", so it can be a program name with args. +@@ -19867,6 +19869,57 @@ done + test -n "$QMAKE" || QMAKE="missing" + + ++else ++ ++ for ac_prog in qmake ++do ++ # Extract the first word of "$ac_prog", so it can be a program name with args. ++set dummy $ac_prog; ac_word=$2 ++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 ++$as_echo_n "checking for $ac_word... " >&6; } ++if ${ac_cv_path_QMAKE+:} false; then : ++ $as_echo_n "(cached) " >&6 ++else ++ case $QMAKE in ++ [\\/]* | ?:[\\/]*) ++ ac_cv_path_QMAKE="$QMAKE" # Let the user override the test with a path. ++ ;; ++ *) ++ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR ++as_dummy="$QT_PATH:$QT_DIR:$PATH:$tmp_qt_paths" ++for as_dir in $as_dummy ++do ++ IFS=$as_save_IFS ++ test -z "$as_dir" && as_dir=. ++ for ac_exec_ext in '' $ac_executable_extensions; do ++ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ++ ac_cv_path_QMAKE="$as_dir/$ac_word$ac_exec_ext" ++ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 ++ break 2 ++ fi ++done ++ done ++IFS=$as_save_IFS ++ ++ ;; ++esac ++fi ++QMAKE=$ac_cv_path_QMAKE ++if test -n "$QMAKE"; then ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $QMAKE" >&5 ++$as_echo "$QMAKE" >&6; } ++else ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 ++$as_echo "no" >&6; } ++fi ++ ++ ++ test -n "$QMAKE" && break ++done ++test -n "$QMAKE" || QMAKE="missing" ++ ++ ++fi + if test x"$QMAKE" = xmissing; then + as_fn_error $? "Cannot find qmake in your PATH. Try to specify the exact path using the option --with-qt= or to switch off the compilation of gui using option --without-gui." "$LINENO" 5 + break +@@ -20309,7 +20362,59 @@ $as_echo "$at_cv_qt_build" >&6; } + + # Find moc (Meta Object Compiler). + +- for ac_prog in moc-qt4 moc ++ if test "x$QT_PATH" == "x"; then : ++ ++ for ac_prog in moc-qt4 moc ++do ++ # Extract the first word of "$ac_prog", so it can be a program name with args. ++set dummy $ac_prog; ac_word=$2 ++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 ++$as_echo_n "checking for $ac_word... " >&6; } ++if ${ac_cv_path_MOC+:} false; then : ++ $as_echo_n "(cached) " >&6 ++else ++ case $MOC in ++ [\\/]* | ?:[\\/]*) ++ ac_cv_path_MOC="$MOC" # Let the user override the test with a path. ++ ;; ++ *) ++ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR ++as_dummy="$PATH:$tmp_qt_paths" ++for as_dir in $as_dummy ++do ++ IFS=$as_save_IFS ++ test -z "$as_dir" && as_dir=. ++ for ac_exec_ext in '' $ac_executable_extensions; do ++ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ++ ac_cv_path_MOC="$as_dir/$ac_word$ac_exec_ext" ++ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 ++ break 2 ++ fi ++done ++ done ++IFS=$as_save_IFS ++ ++ ;; ++esac ++fi ++MOC=$ac_cv_path_MOC ++if test -n "$MOC"; then ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $MOC" >&5 ++$as_echo "$MOC" >&6; } ++else ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 ++$as_echo "no" >&6; } ++fi ++ ++ ++ test -n "$MOC" && break ++done ++test -n "$MOC" || MOC="missing" ++ ++ ++else ++ ++ for ac_prog in moc + do + # Extract the first word of "$ac_prog", so it can be a program name with args. + set dummy $ac_prog; ac_word=$2 +@@ -20356,6 +20461,8 @@ fi + done + test -n "$MOC" || MOC="missing" + ++ ++fi + if test x"$MOC" = xmissing; then + as_fn_error $? "Cannot find moc (Meta Object Compiler) in your PATH. Try using --with-qt." "$LINENO" 5 + break +@@ -20364,7 +20471,59 @@ test -n "$MOC" || MOC="missing" + + # Find uic (User Interface Compiler). + +- for ac_prog in uic-qt4 uic ++ if test "x$QT_PATH" == "x"; then : ++ ++ for ac_prog in uic-qt4 uic ++do ++ # Extract the first word of "$ac_prog", so it can be a program name with args. ++set dummy $ac_prog; ac_word=$2 ++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 ++$as_echo_n "checking for $ac_word... " >&6; } ++if ${ac_cv_path_UIC+:} false; then : ++ $as_echo_n "(cached) " >&6 ++else ++ case $UIC in ++ [\\/]* | ?:[\\/]*) ++ ac_cv_path_UIC="$UIC" # Let the user override the test with a path. ++ ;; ++ *) ++ as_save_IFS=$IFS; IFS=$PATH_SEPARATOR ++as_dummy="$PATH:$tmp_qt_paths" ++for as_dir in $as_dummy ++do ++ IFS=$as_save_IFS ++ test -z "$as_dir" && as_dir=. ++ for ac_exec_ext in '' $ac_executable_extensions; do ++ if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ++ ac_cv_path_UIC="$as_dir/$ac_word$ac_exec_ext" ++ $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 ++ break 2 ++ fi ++done ++ done ++IFS=$as_save_IFS ++ ++ ;; ++esac ++fi ++UIC=$ac_cv_path_UIC ++if test -n "$UIC"; then ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: $UIC" >&5 ++$as_echo "$UIC" >&6; } ++else ++ { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 ++$as_echo "no" >&6; } ++fi ++ ++ ++ test -n "$UIC" && break ++done ++test -n "$UIC" || UIC="missing" ++ ++ ++else ++ ++ for ac_prog in uic + do + # Extract the first word of "$ac_prog", so it can be a program name with args. + set dummy $ac_prog; ac_word=$2 +@@ -20411,6 +20570,8 @@ fi + done + test -n "$UIC" || UIC="missing" + ++ ++fi + if test x"$UIC" = xmissing; then + as_fn_error $? "Cannot find uic (User Interface Compiler) in your PATH. Try using --with-qt." "$LINENO" 5 + break diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..01eebc5f7e4e2b066bf6550339be1282e465b6a3 --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3-foss-2015a.eb @@ -0,0 +1,47 @@ +## +# 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 = "4.3" + +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': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] + +checksums = [ + 'ed4d6f3647eefa65fc194b5d1a5f4ffe', # cube-4.3.tar.gz +] + +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.so", "lib64/libcube4.so")], + 'dirs': ["include/cube", "include/cubew"], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000000000000000000000000000000000..560d4ea5c5f8d46862c8791dac23921bc8db5a36 --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,47 @@ +## +# 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 = "4.3" + +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': 'gompi', 'version': '1.4.12-no-OFED'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] + +checksums = [ + 'ed4d6f3647eefa65fc194b5d1a5f4ffe', # cube-4.3.tar.gz +] + +dependencies = [('Qt', '4.8.4')] + +# 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.so", "lib64/libcube4.so")], + 'dirs': ["include/cube", "include/cubew"], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb b/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b12da485bc27115bfdf88a5ff755a1ec5abae1e0 --- /dev/null +++ b/easybuild/easyconfigs/c/Cube/Cube-4.3.2-foss-2015a.eb @@ -0,0 +1,41 @@ +## +# 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 = "4.3.2" + +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': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] + +checksums = [ + 'a9119524df5a39e7a5bf6dee4de62e30', # cube-4.3.2.tar.gz +] + +dependencies = [('Qt', '4.8.6')] + +sanity_check_paths = { + 'files': ["bin/cube", ("lib/libcube4.a", "lib64/libcube4.a"), ("lib/libcube4.so", "lib64/libcube4.so")], + 'dirs': ["include/cube", "include/cubew"], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..96199f4bf20a56fe1a8489a05a3637e5502822dc --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb @@ -0,0 +1,45 @@ +## +# 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 +## + +name = 'Cufflinks' +version = "1.3.0" + +homepage = 'http://cufflinks.cbcb.umd.edu/' +description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] + +dependencies = [ + ('Boost', '1.51.0', '-Python-2.7.3'), + ('SAMtools', '0.1.18'), + ('Eigen', '3.1.1'), + ('zlib', '1.2.7'), +] + +patches = [ + 'Cufflinks_GCC-4.7.patch', + 'cufflinks-1.x-ldflags.patch' +] + +preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' + +sanity_check_paths = { + 'files': ['bin/cufflinks'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d0372e6f7036ef03b18931e96882e5a5a80096ed --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-foss-2015a.eb @@ -0,0 +1,29 @@ +name = 'Cufflinks' +version = '2.2.1' + +homepage = 'http://cole-trapnell-lab.github.io/cufflinks/' +description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] + +dependencies = [ + # issues with boost > 1.55, see https://github.com/cole-trapnell-lab/cufflinks/issues/3 + ('Boost', '1.55.0', '-Python-2.7.9'), + ('SAMtools', '0.1.19'), + ('Eigen', '3.2.3'), + ('zlib', '1.2.8'), +] + +preconfigopts = 'CPPFLAGS=-I$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-goolf-1.4.10.eb b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..3fdf2a09230495578758559129e37683df9a0ac1 --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/Cufflinks-2.2.1-goolf-1.4.10.eb @@ -0,0 +1,28 @@ +name = 'Cufflinks' +version = '2.2.1' + +homepage = 'http://cufflinks.cbcb.umd.edu/' +description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['cufflinks-%(version)s.tar.gz'] +source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/'] + +dependencies = [ + ('Boost', '1.51.0', '-Python-2.7.3'), + ('SAMtools', '0.1.19'), + ('Eigen', '3.1.1'), + ('zlib', '1.2.7'), +] + +configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib' +preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" ' + +sanity_check_paths = { + 'files': ['bin/cufflinks'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.x-ldflags.patch b/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.x-ldflags.patch new file mode 100644 index 0000000000000000000000000000000000000000..9c2bd9e9a203b4bd2a2b0fe6f1ce7ee4ca186a59 --- /dev/null +++ b/easybuild/easyconfigs/c/Cufflinks/cufflinks-1.x-ldflags.patch @@ -0,0 +1,45 @@ +diff -ru cufflinks-1.3.0/configure cufflinks-1.3.0_patched/configure +--- cufflinks-1.3.0/configure 2012-01-02 13:36:44.000000000 +0000 ++++ cufflinks-1.3.0_patched/configure 2015-01-27 18:32:24.810282390 +0000 +@@ -6386,7 +6386,8 @@ + CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}" + CXXFLAGS="$CFLAGS" + CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS" +-LDFLAGS="$ext_LDFLAGS" ++user_LDFLAGS="$LDFLAGS" ++LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}" + + # Checks for structures/functions that can be used to determine system memory + echo "$as_me:$LINENO: checking for struct sysinfo.totalram" >&5 +diff -ru cufflinks-1.3.0/src/Makefile.in cufflinks-1.3.0_patched/src/Makefile.in +--- cufflinks-1.3.0/src/Makefile.in 2012-01-02 13:36:43.000000000 +0000 ++++ cufflinks-1.3.0_patched/src/Makefile.in 2015-01-27 18:20:02.944386541 +0000 +@@ -438,24 +438,24 @@ + # (echo '#!$(PYTHON)'; sed '/^#!/d' $<) > $@ + cufflinks_SOURCES = cufflinks.cpp + cufflinks_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-cufflinks_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS) ++cufflinks_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS) + cuffcompare_SOURCES = cuffcompare.cpp + cuffcompare_LDADD = libgc.a + gffread_SOURCES = gffread.cpp + gffread_LDADD = libgc.a + cuffdiff_SOURCES = cuffdiff.cpp + cuffdiff_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-cuffdiff_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++cuffdiff_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + gtf_to_sam_SOURCES = gtf_to_sam.cpp + gtf_to_sam_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-gtf_to_sam_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++gtf_to_sam_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + #cuffcluster_SOURCES = cuffcluster.cpp + #cuffcluster_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) + #cuffcluster_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + compress_gtf_SOURCES = compress_gtf.cpp + compress_gtf_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) +-compress_gtf_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++compress_gtf_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + all: all-am + + .SUFFIXES: diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 83aec1d93634e7b2aa204f50a6f88b5761e5a7e4..01ad882b837d9f9f0ea0d51c1b26c004e0a068c4 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.16' -homepage = 'http://pypi.python.org/pypi/Cython/' +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.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb index 892d56aaa136889da5a673618c923d77dc9c9345..fa53744e7cf9e2d8f6e95ac9b91dbf1ab5d359fa 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-goolf-1.4.10-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.16' -homepage = 'http://pypi.python.org/pypi/Cython/' +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.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.0.6-Python-2.7.3.eb index b81a538f5c6e7993f7d72a41a50a7dd58fc9acac..33197474cec3bbe51a18187369278f1eb77bffce 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.0.6-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.16' -homepage = 'http://pypi.python.org/pypi/Cython/' +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.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.1.13-Python-2.7.3.eb index 6e94f41099893c1468ca76ed830dc1eef2f551f7..5cd50bc1ae5368c25b72a1425f9cf241699e342b 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-4.1.13-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.16' -homepage = 'http://pypi.python.org/pypi/Cython/' +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.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb index 5d1302c3c1ebdbb18a41bf6ee1fcc1f45296e0a3..f2fb277465351094a29d872b7aad9cb251ea1595 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.16-ictce-5.3.0-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.16' -homepage = 'http://pypi.python.org/pypi/Cython/' +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.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb index ebccd555bbeeae43e7fc88efcfc13b1a06618576..0e8ac631d070ab4b108be909cad85eb9385f3f45 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-goolf-1.4.10-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.19.1' -homepage = 'http://pypi.python.org/pypi/Cython/' +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.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-4.1.13-Python-2.7.3.eb index 3c845e984536516ad7b766d1a8db642b2f3dccdd..37ecdfbd483e67b9e4ab57413785103564b05fe9 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-4.1.13-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.19.1' -homepage = 'http://pypi.python.org/pypi/Cython/' +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.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb index 544e217059453b65e38ebd93442d020f5d0bbcce..6ba8ee3375981af9f61ca572e34e6c4374b53adc 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.1-ictce-5.3.0-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.19.1' -homepage = 'http://pypi.python.org/pypi/Cython/' +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.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb index 6d9476ba0f302754d5cdb8f29b86e69ba6d8bf5f..80955e4cc6f9e1ebb87cd0ebab3b65cfcb149f7e 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-0.19.2-ictce-5.5.0-Python-2.7.6.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = 'Cython' version = '0.19.2' -homepage = 'http://pypi.python.org/pypi/Cython/' +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.""" diff --git a/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..5b829d6a73d164579c66f55718c674d93f99d091 --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-0.22-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'Cython' +version = '0.22' + +homepage = 'https://pypi.python.org/pypi/Cython/' +description = """The Cython language makes writing C extensions for the Python language as easy as Python itself. +Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pythonver) +pyshortver = '.'.join(pythonver.split('.')[0:2]) +cythonlibdir = 'lib/python' + pyshortver + '/site-packages/Cython-%(version)s-py' + pyshortver + '-linux-x86_64.egg' + +dependencies = [(python, pythonver)] + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', '%s/%%(namelower)s.py' % cythonlibdir], + 'dirs': ['%s/%%(name)s' % cythonlibdir], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2014b.eb b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..00fec4f4d114791d69d862e922f383318da66298 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2014b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.37.1' + +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': '2014b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +#dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0ba45ba9e526d5225207c829ef7370ea107cc2fe --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.37.1-foss-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.37.1' + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +#dependencies = [('OpenSSL', '1.0.1i')] # OS dependency should be preferred for security reasons +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4e2d371a7115bb7b09002e94202bb5e4b25b5d83 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.41.0-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.41.0' + +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': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1m')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..f234e4353beecca8317a4b449ac9acf73058faa0 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-goolf-1.7.20.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.43.0' + +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': 'goolf', 'version': '1.7.20'} + +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=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..2dbc140a53cfcaf4bd3a95d2086a8db91ac8c739 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.43.0-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.43.0' + +homepage = 'http://curl.haxx.se' +description = """libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, + POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports + SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, + proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, + Kerberos), file transfer resume, http proxy tunneling and more.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://curl.haxx.se/download/'] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# dependencies = [('OpenSSL', '1.0.1p')] +# configopts = "--with-ssl=$EBROOTOPENSSL" + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..3638dbedbc6ba26e35130cd96f8b9e614c918257 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-goolf-1.7.20.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.12.18' + +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': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libpng', '1.6.12'), + ('freetype', '2.5.3'), + ('pixman', '0.32.6'), + ('fontconfig', '2.11.1'), + ('expat', '2.1.0'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no" + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c4afd6154b57cd027c512280708af02ddf4cdeb7 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-intel-2015a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = "cairo" +version = '1.12.18' + +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': '2015a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] + +dependencies = [ + ('libpng', '1.6.16'), + ('freetype', '2.5.5'), + ('zlib', '1.2.8'), + ('pixman', '0.32.6'), + ('fontconfig', '2.11.1'), + ('expat', '2.1.0'), + ('bzip2', '1.0.6'), +] + +builddependencies = [('Autotools', '20150119', '', ('GCC', '4.9.2'))] + +patches = ['cairo-1.12.18-pthread-check.patch'] + +preconfigopts = " autoconf configure.ac > configure && " + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no" + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch new file mode 100644 index 0000000000000000000000000000000000000000..9019afb9464eaeda9491f22a79efca74d95839f3 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.12.18-pthread-check.patch @@ -0,0 +1,17 @@ +# Make sure the configure script doesn't fail over a 'no version information available' warning +# by wpoely86@gmail.com +diff -ur cairo-1.12.18.orig/build/aclocal.cairo.m4 cairo-1.12.18/build/aclocal.cairo.m4 +--- cairo-1.12.18.orig/build/aclocal.cairo.m4 2013-03-15 21:29:27.000000000 +0100 ++++ cairo-1.12.18/build/aclocal.cairo.m4 2015-01-14 14:08:01.000000000 +0100 +@@ -101,9 +101,9 @@ + $1 + AC_LINK_IFELSE( + [AC_LANG_SOURCE([$_compile_program])], +- [cairo_cc_stderr=`test -f conftest.err && cat conftest.err` ++ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err | grep -v 'no version information available' ` + cairo_cc_flag=yes], +- [cairo_cc_stderr=`test -f conftest.err && cat conftest.err` ++ [cairo_cc_stderr=`test -f conftest.err && cat conftest.err | grep -v 'no version information available' ` + cairo_cc_flag=no]) + + if test "x$cairo_cc_stderr" != "x"; then diff --git a/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb new file mode 100644 index 0000000000000000000000000000000000000000..928b078aac4b112449fc8c1ceaa5be6863568b3d --- /dev/null +++ b/easybuild/easyconfigs/c/cramtools/cramtools-2.0-Java-1.7.0_80.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'cramtools' +version = '2.0' + +homepage = 'https://github.com/enasequence/cramtools/' +description = """CRAMTools is a set of Java tools and APIs for efficient compression of sequence +read data. Although this is intended as a stable version the code is released as +early access. Parts of the CRAMTools are experimental and may not be supported +in the future.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/enasequence/%(name)s/archive/'] + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +modloadmsg = "To execute cramtools run: java -jar \\${EBROOTCRAMTOOLS}/%(name)s-%(version)s.jar" + +sanity_check_paths = { + 'files': ["%(name)s-%(version)s.jar"], + 'dirs': ["lib"] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb index 77441b588107e8fdfc5ea582e49438f6dd54edd1..c519419dcf757ca545b6dd0b18501bb05308a8a0 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.3.eb @@ -17,8 +17,8 @@ description = """ cutadapt removes adapter sequences toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://cutadapt.googlecode.com/files/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.3' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb index e788568341014520611617d8bd63123896a219e4..f278de669b75bbe123facd55546fdb7364b900c1 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.3-goolf-1.4.10-Python-2.7.5.eb @@ -17,8 +17,8 @@ description = """ cutadapt removes adapter sequences toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://cutadapt.googlecode.com/files/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.5' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb index cf67752ee40007e211e98a330a48789fd066506c..a308b2113040ca38bca418c17a7269a85b9641d2 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-foss-2014b-Python-2.7.8.eb @@ -15,8 +15,8 @@ description = """ cutadapt removes adapter sequences from high-throughput sequen toolchain = {'name': 'foss', 'version': '2014b'} -source_urls = ['https://github.com/marcelm/cutadapt/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.8' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..a4f51697618d167202a3dc4baeb74b68e7dab78b --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.4.1-goolf-1.4.10-Python-2.7.5.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 (SIB) +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.4.1' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences + from high-throughput sequencing data. This is usually + necessary when the read length of the sequencing machine + is longer than the molecule that is sequenced, for + example when sequencing microRNAs. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.5' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb index f9435f3efa8157cea1567b831e7beaa4f35e30db..3303167a212712132abd6fe76644e37bd751796f 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-foss-2014b-Python-2.7.8.eb @@ -15,8 +15,8 @@ description = """ cutadapt removes adapter sequences from high-throughput sequen toolchain = {'name': 'foss', 'version': '2014b'} -source_urls = ['https://github.com/marcelm/cutadapt/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.8' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..dbc8a13634a2d846553c2d1832fb3e1671a92b60 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.5-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,33 @@ +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.5' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences + from high-throughput sequencing data. This is usually + necessary when the read length of the sequencing machine + is longer than the molecule that is sequenced, for + example when sequencing microRNAs. """ + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.8' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt','lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb index b165a51c0cccaf6b6be9256fad41eebfb5dc216e..83a8d8a50d11fa0846f0cf9ac57baa009790cdb3 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.6-foss-2014b-Python-2.7.8.eb @@ -15,8 +15,8 @@ description = """ cutadapt removes adapter sequences from high-throughput sequen toolchain = {'name': 'foss', 'version': '2014b'} -source_urls = ['https://github.com/marcelm/cutadapt/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.8' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb index fbe7a035d30187585bab2511e81350db59f3af58..f879b0939f257bf5e3af32327d0e82496bcb12b9 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7-foss-2014b-Python-2.7.8.eb @@ -15,8 +15,8 @@ description = """ cutadapt removes adapter sequences from high-throughput sequen toolchain = {'name': 'foss', 'version': '2014b'} -source_urls = ['https://github.com/marcelm/cutadapt/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.8' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb index a5093a2f2168f383708b0c387e5f6742f61ec02a..60048badc4d91fb70bc781525ab151f81450f1bc 100644 --- a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.7.1-foss-2014b-Python-2.7.8.eb @@ -15,8 +15,8 @@ description = """ cutadapt removes adapter sequences from high-throughput sequen toolchain = {'name': 'foss', 'version': '2014b'} -source_urls = ['https://github.com/marcelm/cutadapt/archive/'] -sources = ['v%(version)s.tar.gz'] +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] python = 'Python' pyver = '2.7.8' diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..a69f7bc2f85b976d02ba71f12be0640ed56d3347 --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-1.8.1-intel-2015a-Python-2.7.9.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 (SIB) +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'cutadapt' +version = '1.8.1' + +homepage = 'http://code.google.com/p/cutadapt/' +description = """ cutadapt removes adapter sequences from high-throughput sequencing data. + This is usually necessary when the read length of the sequencing machine is longer than + the molecule that is sequenced, for example when sequencing microRNAs. """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt','lib/python%s/site-packages/cutadapt/_align.so' % pyshortver], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..facf14e7e4331e4f7d9cc21bcb3f3db8c1e75a79 --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-Pg/DBD-Pg-3.4.1-intel-2014b-Perl-5.20.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PerlModule' + +name = 'DBD-Pg' +version = '3.4.1' + +homepage = 'http://search.cpan.org/~turnstep/DBD-Pg-3.4.1/' +description = """Perl binding for PostgreSQL""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://cpan.metacpan.org/authors/id/T/TU/TURNSTEP/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.20.0' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ("PostgreSQL", "9.3.5") +] + +options = {'modulename': 'DBD::Pg'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..2734b69ecf14a796ce307f7e71c28e2dbc4109a0 --- /dev/null +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-3.12.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,39 @@ +## +#This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## +easyblock = "PythonPackage" + +name = 'DendroPy' +version = '3.12.0' + +homepage = 'https://pypi.python.org/pypi/DendroPy/' +description = """A Python library for phylogenetics and phylogenetic computing: +reading, writing, simulation, processing and manipulation of phylogenetic trees +(phylogenies) and characters.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://pypi.python.org/packages/source/D/DendroPy/'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.3' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +sanity_check_paths = { + 'files': ['bin/cattrees.py','bin/long_branch_symmdiff.py','bin/sumlabels.py', + 'bin/sumtrees.py','bin/strict_consensus_merge.py'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-6.1.5.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-6.1.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..2f5d07d58fd5609038288cf391cba9d8fd36edb1 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.3.1-ictce-6.1.5.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.3.1' + +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': '6.1.5'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +dependencies = [ + ('flex', '2.5.37'), + ('Bison', '2.7'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2014b.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..9604d1fe3e7a01a257c59b907f5fd5cd842ba276 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2014b.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.7' + +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': '2014b'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2015a.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6fae2382dd0225658c93c6920012b285f0908c98 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.7-foss-2015a.eb @@ -0,0 +1,18 @@ +name = 'Doxygen' +version = '1.8.7' + +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': '2015a'} + +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +source_urls = ['http://ftp.stack.nl/pub/users/dimitri/'] + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.2'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb similarity index 67% rename from easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb rename to easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb index 526f2442cdd7e8c8e56f0b317332f460a831e895..ca072da66b97cf40efb62307a4a5ff7187e826b3 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2-clusterapps.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0-clusterapps.eb @@ -5,20 +5,21 @@ version = '1.5.2' versionsuffix = '-clusterapps' homepage = 'http://www.numericalrocks.com/index.php?option=com_content&task=blogcategory&id=25&Itemid=25' -description = """The e-Core technology simulates the natural processes of sedimentary rock formation; i.e. sedimentation, compaction and diagenesis.""" +description = """The e-Core technology simulates the natural processes of sedimentary rock formation; i.e. + sedimentation, compaction and diagenesis.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'ictce', 'version': '5.5.0'} -sources = ['%s-%s%s.tgz' % (name.lower(), version, versionsuffix)] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tgz'] patches = ['ecore-license-var.patch'] -comp = ('GCC', '4.6.3') -dependencies = [('OpenMPI', '1.4.5', '-no-OFED', comp)] +# needs to be 1.4.x, because it's linked with the libmpi_cxx.so.0 +dependencies = [('OpenMPI', '1.4.5')] sanity_check_paths = { 'files': ['arch/linux-rh5-x86_64/bin/%s' % x for x in ['absperm', 'FormationFactor', 'nmr', - 'orterun', 'packer', 'randomwalkffmpi', + 'orterun', 'packer', 'randomwalkffmpi', 'unpacker']] + \ ['absperm.sh', 'formationfactor.sh', 'nmr.sh', 'rw_formationfactor.sh'], 'dirs': [], diff --git a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0.eb similarity index 74% rename from easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb rename to easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0.eb index 382a1b327eb8c0d8c21a38ba201628f3b7f84b64..7c028041b8bfab81c7c099d20a5f69dee694a615 100644 --- a/easybuild/easyconfigs/e/ECore/ECore-1.5.2.eb +++ b/easybuild/easyconfigs/e/ECore/ECore-1.5.2-ictce-5.5.0.eb @@ -4,16 +4,16 @@ name = 'ECore' version = '1.5.2' homepage = 'http://www.numericalrocks.com/index.php?option=com_content&task=blogcategory&id=25&Itemid=25' -description = """The e-Core technology simulates the natural processes of sedimentary rock formation; i.e. sedimentation, compaction and diagenesis.""" +description = """The e-Core technology simulates the natural processes of sedimentary rock formation; i.e. + sedimentation, compaction and diagenesis.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = {'name': 'ictce', 'version': '5.5.0'} sources = [SOURCELOWER_TGZ] patches = ['ecore-license-var.patch'] -comp = ('GCC', '4.6.3') -dependencies = [('OpenMPI', '1.4.5', '-no-OFED', comp)] +dependencies = [('OpenMPI', '1.4.5')] sanity_check_paths = { 'files': ["ecore.sh", 'noarch/launch.sh'] + \ diff --git a/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..e763143dc4fa3f42339d698e9eb9e3ef598014a8 --- /dev/null +++ b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'EMAN2' +version = '2.11' + +homepage = 'http://blake.bcm.edu/emanwiki/EMAN2' +description = """EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite + with a primary focus on processing data from transmission electron microscopes. """ + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = ['http://ncmi.bcm.edu/ncmi/software/counter_222/software_130/'] +sources = ['eman%(version)s.source.tar.gz'] + +pyver = '2.7.9' +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + # FFTW provided via toolchain + ('GSL', '1.16'), + ('Python', pyver), # also provides numpy + ('Boost', '1.58.0', versionsuffix), + ('IPython', '3.2.0', versionsuffix), + ('HDF5', '1.8.15-patch1'), + ('freetype', '2.6'), + # optional + ('PyQt', '4.11.4', versionsuffix), + ('LibTIFF', '4.0.4'), + ('libpng', '1.6.17'), +] +builddependencies = [('CMake', '3.2.3')] + +start_dir = 'eman2' +separate_build_dir = True + +configopts = "-DEMAN_INSTALL_PREFIX=%(installdir)s -DENABLE_FTGL=OFF" + +sanity_check_paths = { + 'files': ['bin/e2proc2d.py', 'bin/e2proc3d.py', 'bin/e2bdb.py', 'bin/e2iminfo.py', 'bin/e2display.py', + 'bin/e2filtertool.py'], + 'dirs': ['examples', 'include', 'lib', 'test/rt'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..82523c603be6ea880d88a59c94742006333ca6f8 --- /dev/null +++ b/easybuild/easyconfigs/e/EMAN2/EMAN2-2.11-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'EMAN2' +version = '2.11' + +homepage = 'http://blake.bcm.edu/emanwiki/EMAN2' +description = """EMAN2 is the successor to EMAN1. It is a broadly based greyscale scientific image processing suite + with a primary focus on processing data from transmission electron microscopes. """ + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://ncmi.bcm.edu/ncmi/software/counter_222/software_130/'] +sources = ['eman%(version)s.source.tar.gz'] + +pyver = '2.7.9' +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('FFTW', '3.3.4'), + ('GSL', '1.16'), + ('Python', pyver), # also provides numpy + ('Boost', '1.58.0', versionsuffix), + ('IPython', '3.2.0', versionsuffix), + ('HDF5', '1.8.15-patch1'), + ('freetype', '2.6'), + # optional + ('PyQt', '4.11.4', versionsuffix), + ('LibTIFF', '4.0.4'), + ('libpng', '1.6.17'), +] +builddependencies = [('CMake', '3.2.3')] + +start_dir = 'eman2' +separate_build_dir = True + +configopts = "-DEMAN_INSTALL_PREFIX=%(installdir)s -DENABLE_FTGL=OFF" + +sanity_check_paths = { + 'files': ['bin/e2proc2d.py', 'bin/e2proc3d.py', 'bin/e2bdb.py', 'bin/e2iminfo.py', 'bin/e2display.py', + 'bin/e2filtertool.py'], + 'dirs': ['examples', 'include', 'lib', 'test/rt'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..f270612d5f3fb42b24c61890c2353e5d5d0ea9f4 --- /dev/null +++ b/easybuild/easyconfigs/e/ETSF_IO/ETSF_IO-1.0.4-goolf-1.4.10.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'ETSF_IO' +version = '1.0.4' + +homepage = 'http://www.etsf.eu/resources/software/libraries_and_tools' +description = """A library of F90 routines to read/write the ETSF file +format has been written. It is called ETSF_IO and available under LGPL. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://www.etsf.eu/system/files'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-netcdf-prefix=$EBROOTNETCDF " +configopts += "--with-netcdf-libs='-L$EBROOTNETCDF/lib -lnetcdf -lnetcdff' " +configopts += " --with-netcdf-incs='-I$EBROOTNETCDF/include'" + +dependencies = [ ('netCDF', '4.1.3') ] + +sanity_check_paths = { + 'files': ["bin/etsf_io"], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb index 375a69f41eca1d646c216999d2a7e68d635d7314..6a13fbccbd8f4401050c007bfe00c0c768de2fcb 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb index ceb0952d37427123085ba43df093cccd8dd4d32e..1fc508215ccbf06470f74092ed8e9c8d2367abaa 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.1.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb index 335d94e6fbc14839e4501a1441b3dabda14c6f00..aefe4f346169f8d120fedd616ce8a984c2e09d15 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.0.2.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb index 22d8fd70bd3d0ed0c8944c93002e0867a7fef042..aec17460aa5dbe6a99ebc81c0ea21db0c7a50ff2 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.1.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb index 99d04a46aab447526b495a1dbdad0526cc5d5890..12381b6467594e51e7c0a72eecc2f1d6ebec76de 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.10.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb index e4ebd91d1b8db3aa041de6d98accce61522e9c95..a8ef6b164a9b964adc76ea4709d4f46fae4c46d2 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb index 798cd20488a430f475fe59334a916bce6fb5e888..d2df7f198825649c26f9ce01b169590df6c6010c 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.11.1.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb index b7092a63e95e6451641fc54007bd7482f451f570..345d210d28808482b1fa55a0bf8244ea57b7447e 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb index f8cd7d18f270b1e41b08bf71cfabae6b2a9ccdff..97720876b9ae4bc7c55cf787f3073fd784124f4d 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.12.1.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb index 1b3cf50b1a0bf8abe53940824e4df12b5d366b98..0b5ba14c24eed3339f2a622a8466928f9021a46d 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.13.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb index 8ceec790c8abe8ec71acff450e1cb0cddec23ec7..0176f2b558445f29da406a73f2c9a06f1bed41a1 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.14.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb index cfc44c499c7d7fb5cc08fc1820eafd4f26af942e..3ae286c658871ad20c35f7910f70818b4a7450c9 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb index 0f2a68be4b340a6007fc304bde1ca1deee865bab..b4fb5e015c40291f83a276909dd6a54b20cabf0f 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.1.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb index d44b604d2779e2427af50d3f7ce716f977701221..9025d6b24b1a952859671c6dac582c7de33d073b 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.15.2.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb index 248cce692e371fbced98b5b20d2acea238623899..2ac7d84426f452b786006f90244590b7344f1533 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb index 83ed95495c269b2085752878c59c84ba94c3d578..a7a958a3ca37af9073ef83136407ee753917c692 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.1.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb index 8f07608f0357c3c412db9e00b2e79808dc7e0b8d..26fbe953cd40b2e80848e9f7bae8a13973c24dde 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.16.2.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb index 8d013d194160902aebaa587b22d85b3d2948a047..84e658abed364e84e951911969e8a03347d18326 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.2.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb index 4a22f26fd3c486f44a06271bf95953e5d88122ab..62ec5081923f69af3e279506575765af3afb9f65 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.3.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb index a94a92c65741dd1e717e830bf79764cfa1f0574b..f56094b5c06e2855738001b40c4f9b40fd07fd23 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.4.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb index 07838d802093345272554f358539c7ffb14407ef..df9a262ab241c02e8d96c97f9e51b57ddb739036 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.5.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb index fd30e9820cea543649ae5db7aef314d05764bbfb..9082a71a46b95b067d70f4ddf4b6e8e8ef51b612 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.6.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb index 39be41a74ebd3175635324feb7f18aa08b355042..a2164fa02d00ab10b3cf30fa8200066ef7474747 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.7.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb index 1fe6136b55a969255b458f2e7972d6b016cff1ed..8fa4a0a750ccd89e7243a5398430ba224c677f32 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb index 629ec16acb28b00074b69dcd9c8484bad2f495a9..1774b8976ce94d947dbcbfa6a015d6fbfab41e79 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.1.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb index 15551872f9edf4b22127e5c9ed6cbfdb94d00d39..d990801ac27b0292808f1d37168d26d57b2755f0 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.8.2.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb index 4047b507602a697bf75b094f41da40f6c206d448..97801124aa8f501633c3c5e1f1487259c730f6ad 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-1.9.0.eb @@ -11,9 +11,9 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb index 25286293192979e4f6fc921992fe4cfc809f7763..81d586f625359afef09048a9fda3bddeffa566c1 100644 --- a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.0.0.eb @@ -11,10 +11,10 @@ description = """EasyBuild is a software build and installation framework toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = [ - 'http://pypi.python.org/packages/source/v/vsc-base/', - 'http://pypi.python.org/packages/source/e/easybuild-framework/', - 'http://pypi.python.org/packages/source/e/easybuild-easyblocks/', - 'http://pypi.python.org/packages/source/e/easybuild-easyconfigs/', + 'https://pypi.python.org/packages/source/v/vsc-base/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', ] # order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) sources = [ diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..cb8c19e6065a5e2ecce964efe38aa511437550a2 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.1.0' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'https://pypi.python.org/packages/source/v/vsc-base/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.2.0.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-2.1.1.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..632563276e8bf65636e0eb936506eaa92b8dff46 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.1.1.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.1.1' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'https://pypi.python.org/packages/source/v/vsc-base/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.2.2.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-2.2.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..116950af4bdc21e32a31a82db11b1fd43995a663 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-2.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '2.2.0' + +homepage = 'http://hpcugent.github.com/easybuild/' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + 'https://pypi.python.org/packages/source/v/vsc-base/', + 'https://pypi.python.org/packages/source/e/easybuild-framework/', + 'https://pypi.python.org/packages/source/e/easybuild-easyblocks/', + 'https://pypi.python.org/packages/source/e/easybuild-easyconfigs/', +] +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +sources = [ + 'vsc-base-2.2.3.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-2015a.eb b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9cca953ebc6cc2b9652bb63d0d44c727845fc488 --- /dev/null +++ b/easybuild/easyconfigs/e/Eigen/Eigen-3.2.3-foss-2015a.eb @@ -0,0 +1,14 @@ +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': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [BITBUCKET_SOURCE] +sources = ['%(version)s.tar.bz2'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..a1c5928f0bf84c89e93acc15c41b9a4bad728227 --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2014b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'eudev' +version = '3.0' + +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': 'intel', 'version': '2014b'} +toolchainopts = {'cstd': 'c99'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] +patches = ['%(name)s-%(version)s_pre-2.6.34_kernel.patch'] + +builddependencies = [ + ('gperf', '3.0.4'), +] + +osdependencies = [('kernel-headers', 'linux-libc-dev')] + +configopts = '--disable-blkid --disable-selinux --disable-gudev --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/eudev/eudev-3.0-intel-2015a.eb b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5108981bdd56eec3bf4f1e4f0863d1da9041657c --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0-intel-2015a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'eudev' +version = '3.0' + +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': 'intel', 'version': '2015a'} +toolchainopts = {'cstd': 'c99'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://dev.gentoo.org/~blueness/%(name)s/'] +patches = ['%(name)s-%(version)s_pre-2.6.34_kernel.patch'] + +builddependencies = [ + ('gperf', '3.0.4'), +] + +osdependencies = [('kernel-headers', 'linux-libc-dev')] + +configopts = '--disable-blkid --disable-selinux --disable-gudev --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/eudev/eudev-3.0_pre-2.6.34_kernel.patch b/easybuild/easyconfigs/e/eudev/eudev-3.0_pre-2.6.34_kernel.patch new file mode 100644 index 0000000000000000000000000000000000000000..7fb7da7902ec1055cf43563c81cd494c99146393 --- /dev/null +++ b/easybuild/easyconfigs/e/eudev/eudev-3.0_pre-2.6.34_kernel.patch @@ -0,0 +1,16 @@ +#inspiration from http://repository.timesys.com/buildsources/u/udev/udev-181/udev-181-define-trigger-happy.patch +#BTN_TRIGGER_HAPPY is not defined in /usr/include/linux/input.h for pre 2.6.34 kernels +# B. Hajgato April 30 2015 +--- eudev-3.0/src/udev/udev-builtin-input_id.c.org 2015-04-30 09:11:07.990269206 +0200 ++++ eudev-3.0/src/udev/udev-builtin-input_id.c 2015-04-30 09:12:19.407272116 +0200 +@@ -33,6 +33,10 @@ + #include "udev.h" + #include "util.h" + ++#ifndef BTN_TRIGGER_HAPPY ++#define BTN_TRIGGER_HAPPY 0x2c0 ++#endif ++ + /* we must use this kernel-compatible implementation */ + #define BITS_PER_LONG (sizeof(unsigned long) * 8) + #define NBITS(x) ((((x)-1)/BITS_PER_LONG)+1) diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-GCC-4.9.2.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-GCC-4.9.2.eb index e10b56409eb58cb594601b968ed5d0e9f9de4aca..5ec94cc9029280d946d4447b1d7f488721f2e03b 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-GCC-4.9.2.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmpolf-1.1.6.eb index 32e37ffc4edf4d72fa8f6c468e9f4ebea6bad521..ff49fa9059b914ce7083e5c8182218e1f2b04d78 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmpolf-1.1.6.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'cgmpolf', 'version': '1.1.6'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.1.12rc1.eb index a5482a0de8196a47ae468e85733224382bafd65a..e94cc361d056bb92100152296bc4ac7f83fe55ac 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.1.12rc1.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'cgmvolf', 'version': '1.1.12rc1'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.2.7.eb index 77192999ec000a3356969ccad3c65b6f3190acc1..faee47738eff45910095d40eb66ccac5528ff7bd 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgmvolf-1.2.7.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'cgmvolf', 'version': '1.2.7'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgoolf-1.1.7.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgoolf-1.1.7.eb index 7548d8a26401c3067f1d3a8478e28bd698bb2f5d..292f27fff34869b758cf47cf49fa29f2a25ef6df 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-cgoolf-1.1.7.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'cgoolf', 'version': '1.1.7'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2014b.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2014b.eb index 35e32ef7da9f15d30642fb37534fd654fa235ef1..e68977279be5953fc0dcbe1246ba8e7aea4034fd 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2014b.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2014b.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'foss', 'version': '2014b'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015a.eb index 1381b2b8cd48ef5fe54b880d02afde4726c98e18..600e38e8b5a4254367b192c996815b7eaefe5c29 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015a.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-foss-2015a.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12.eb index 1df1944fe7205fb9f68ac4d22fea7e94b3604df6..5bf238017307474af7c1e0dc9cb9c0672f50824a 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'gmvolf', 'version': '1.7.12'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12rc1.eb index 23118879c5adbc9d177d0caf8986b51d151b8150..1e273d6bd7bd7a7a58ab6bad19b5a559e117f186 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-gmvolf-1.7.12rc1.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'gmvolf', 'version': '1.7.12rc1'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-goalf-1.1.0-no-OFED.eb index 207aea5fd5a68b8b639e9b4d1e1060170cec2792..7fee445ae4f29ed9c1e48ea3c0e6032ff943877f 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-goalf-1.1.0-no-OFED.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.4.10.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.4.10.eb index ccfb1c69db5457dbbf23c5190eca645ff0aaba96..c409db262d572186f9b46015dfa77b6717a3c575 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.4.10.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.7.20.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..721806cde96cd288552e64da1d3717bcdcccf91d --- /dev/null +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-goolf-1.7.20.eb @@ -0,0 +1,16 @@ +easyblock = 'ConfigureMake' + +name = 'expat' +version = '2.1.0' + +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': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-3.2.2.u3.eb index 3d951c24c9c6e56dc1565df78607b33ae5390ca7..988d22cea6d5a0ab555770ccef9024c39f1985bf 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-3.2.2.u3.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.0.6.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.0.6.eb index 6fe54d636de4a4380d9260357a9e96ad94ff56d0..40d2dd346f6c50bdfffde9a6f09bc603af32bbe7 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.0.6.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'ictce', 'version': '4.0.6'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.1.13.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.1.13.eb index f59fe3f2c07c9fd46b6756271c04dd68ef9744ac..659d23c4d01fa8e6ff1a21517d7d7e916a6c76b9 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-4.1.13.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'ictce', 'version': '4.1.13'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.3.0.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.3.0.eb index 77172614002c45cb32b77872a30d89e91a4698da..c97465c9f1a528268437475ecf04818ffe2b96e0 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.3.0.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.5.0.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.5.0.eb index 45acf6dd3e2061e3d4771dbf4a456c1609d570d8..7960b1c2df66b92d92cf51183f24144a7839ae01 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-ictce-5.5.0.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2014b.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2014b.eb index f76c746c5e41e388b265ddd75939aafcec87fad5..1c0523995adef6edcc067c7fa998efd5746de32e 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2014b.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2014b.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb index 0eb1188648fb11375d3dbb7eed57dfee24dcdba0..084ab12246354e7539e78cf9d3efbdf5dc2f83c6 100644 --- a/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb +++ b/easybuild/easyconfigs/e/expat/expat-2.1.0-intel-2015a.eb @@ -8,6 +8,7 @@ description = """Expat is an XML parser library written in C. It is a stream-ori registers handlers for things the parser might find in the XML document (like start tags)""" toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] source_urls = [SOURCEFORGE_SOURCE] diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..13d9d1cb72c6032c4494d7b048c85486eb2bd9a8 --- /dev/null +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-intel-2015a.eb @@ -0,0 +1,45 @@ +## +# 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 = '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': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +altname = name.lower().replace('-','_') +source_urls = ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'] +sources = ['%s-%%(version)s.tar.bz2' % altname] + +dependencies = [('libgtextutils', '0.6.1')]; + +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-6.0.1-no-OFED.eb b/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb new file mode 100644 index 0000000000000000000000000000000000000000..f0c72251831e710652fe08705ced7bfaf8f9237b --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.0.1-no-OFED.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'FDS' +version = '6.0.1' +versionsuffix = '-no-OFED' + +homepage = 'https://code.google.com/p/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': 'dummy', 'version': 'dummy'} + +# download .sh from https://bintray.com/nist-fire-research/releases/FDS-SMV/6.0.1/view/files to create tarball +sources = ['FDS_6.0.1-SMV_6.1.5_linux64.tar.gz'] + +dependencies = [('OpenMPI', '1.6.5-GCC-4.8.2-no-OFED')] + +skipsteps= ['configure', 'build'] + +sanity_check_paths = { + 'files': ['bin/fds', 'bin/fds_mpi'], + 'dirs': [], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb b/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..2179b3462c5026e5428f5b38c8b649408056ae6f --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-r17534-intel-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = 'r17534' + +homepage = 'https://code.google.com/p/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': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCE_TAR_GZ] +patches = ['FDS-%(version)s_makefile.patch'] + +unpack_options = '--strip-components=1' + +start_dir = 'FDS_Compilation' + +parallel = 1 + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +modextrapaths = {'PATH': 'FDS_Compilation'} + +sanity_check_paths = { + 'files': ['FDS_Compilation/fds'], + 'dirs': [], +} +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FDS/FDS-r17534_makefile.patch b/easybuild/easyconfigs/f/FDS/FDS-r17534_makefile.patch new file mode 100644 index 0000000000000000000000000000000000000000..dea4f7695ff857c313cf4004dd5734ef2ea83976 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-r17534_makefile.patch @@ -0,0 +1,16 @@ +diff -ru fds-r17534.orig/FDS_Compilation/makefile fds-r17534/FDS_Compilation/makefile +--- fds-r17534.orig/FDS_Compilation/makefile 2013-11-21 17:36:53.000000000 +0100 ++++ fds-r17534/FDS_Compilation/makefile 2015-05-19 13:01:04.892548269 +0200 +@@ -29,9 +29,9 @@ + + # General Purpose Rules + +-no_target: +- @echo \******** You did not specify a make target \******** +- @echo Please read the comments at the top of the makefile ++no_target: FCOMPL = $(F90) ++no_target: setup $(obj_serial) ++ $(FCOMPL) $(FFLAGS) $(LFLAGS) -o fds $(obj_serial) + + setup: + %.o : %.mod 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 new file mode 100644 index 0000000000000000000000000000000000000000..e84a122aebc05f69826c3aa61d56f2599afc0ea1 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-goolf-1.4.10.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = 'r18915' + +homepage = 'https://code.google.com/p/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': 'goolf', 'version': '1.4.10'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCE_TAR_GZ] +patches = ['FDS-%(version)s_makefile.patch'] + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +modextrapaths = {'PATH': 'FDS_Source'} + +sanity_check_paths = { + 'files': ['FDS_Source/fds'], + 'dirs': [], +} +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 new file mode 100644 index 0000000000000000000000000000000000000000..78ff82e688427bbecb93df11e1a214fd39b37f54 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915-ictce-5.5.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = 'r18915' + +homepage = 'https://code.google.com/p/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': 'ictce', 'version': '5.5.0'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCE_TAR_GZ] +patches = ['FDS-%(version)s_makefile.patch'] + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +modextrapaths = {'PATH': 'FDS_Source'} + +sanity_check_paths = { + 'files': ['FDS_Source/fds'], + 'dirs': [], +} +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FDS/FDS-r18915_makefile.patch b/easybuild/easyconfigs/f/FDS/FDS-r18915_makefile.patch new file mode 100644 index 0000000000000000000000000000000000000000..d7106bff9fb8c987655546d5346a968832dd4e28 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-r18915_makefile.patch @@ -0,0 +1,15 @@ +--- FDS_Compilation/makefile.orig (revision 18916) ++++ FDS_Compilation/makefile (working copy) +@@ -29,9 +29,9 @@ + + # General Purpose Rules + +-no_target: +- @echo \******** You did not specify a make target \******** +- @echo Please read the comments at the top of the makefile ++no_target: FCOMPL = $(F90) ++no_target: setup $(obj_serial) ++ $(FCOMPL) $(FFLAGS) $(LFLAGS) -o fds $(obj_serial) + + setup: + %.o : %.mod diff --git a/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb b/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0b9177003ef75c79044c3b2695de66342407cb47 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-r22681-intel-2015a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = 'r22681' + +homepage = 'https://code.google.com/p/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': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCE_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 + +modextrapaths = {'PATH': 'FDS_Compilation'} + +sanity_check_paths = { + 'files': ['FDS_Compilation/fds'], + 'dirs': [], +} +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-intel-2015a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..10fd990805ef6562229d1fc20f1bfeff124997cb --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.3-intel-2015a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'FFTW' +version = '3.3.3' + +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': '2015a'} +toolchainopts = {'optarch': True, '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/FFTW/FFTW-3.3.4-gompi-1.5.16.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.16.eb new file mode 100644 index 0000000000000000000000000000000000000000..6ae444ae025f221e3e5c742284084a0c5aabf013 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-1.5.16.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': '1.5.16'} +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-2015.05.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..0d9c4ae7b5904fee76bb5264740d09c9ad7265fa --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.4-gompi-2015.05.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': '2015.05'} +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/FIAT/FIAT-1.5.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/f/FIAT/FIAT-1.5.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..03fe5cf7a1bc322769d8ae010431f0b14cf242b0 --- /dev/null +++ b/easybuild/easyconfigs/f/FIAT/FIAT-1.5.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'FIAT' +version = '1.5.0' + +homepage = 'ttps://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': '2015a'} + +source_urls = ['https://bitbucket.org/fenics-project/fiat/downloads'] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('ScientificPython', '2.9.4', versionsuffix), + ('sympy', '0.7.6', versionsuffix), +] + +options = {'modulename': name} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/FIAT' % pythonshortversion], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb new file mode 100644 index 0000000000000000000000000000000000000000..b6d3efe3ac3d447eda5e4587ff5973b4a2de8cb1 --- /dev/null +++ b/easybuild/easyconfigs/f/FPM/FPM-1.3.3-Ruby-2.1.6.eb @@ -0,0 +1,20 @@ +easyblock = 'RubyGem' + +name = 'FPM' +version = '1.3.3' + +rubyver = '2.1.6' +versionsuffix = '-Ruby-%s' % rubyver + +homepage = 'https://github.com/jordansissel/fpm' +description = """Effing package management! Build packages for multiple platforms (deb, rpm, etc) with great ease + and sanity.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://rubygems.org/downloads/'] +sources = ['%(namelower)s-%(version)s.gem'] + +dependencies = [('Ruby', rubyver)] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.8-intel-2015a.eb b/easybuild/easyconfigs/f/FSL/FSL-5.0.8-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..dd4d60386c27390da26ea8dbed0814588fc9d10d --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.8-intel-2015a.eb @@ -0,0 +1,24 @@ +name = 'FSL' +version = '5.0.8' + +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': 'intel', 'version': '2015a'} + +source_urls = ["http://www.fmrib.ox.ac.uk/fsldownloads/"] +sources = ['%(namelower)s-%(version)s-sources.tar.gz'] + +patches = [ + 'FSL-%(version)s_makefile_fixes.patch', + 'FSL-%(version)s_ictce-wd803.patch', + 'FSL_icc_nan-inf_fix.patch', +] + +dependencies = [ + ('freeglut', '2.8.1'), + ('expat', '2.1.0'), + ('libX11', '1.6.3', '-Python-2.7.9'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.8_ictce-wd803.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.8_ictce-wd803.patch new file mode 100644 index 0000000000000000000000000000000000000000..c798885107eb8f382fd1ceab9f33f7241bf37f92 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.8_ictce-wd803.patch @@ -0,0 +1,300 @@ +diff -ru fsl.orig/fsl/config/apple-darwin10-gcc4.2/systemvars.mk fsl/config/apple-darwin10-gcc4.2/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin10-gcc4.2/systemvars.mk 2013-05-15 00:14:37.710187000 +0200 ++++ fsl/config/apple-darwin10-gcc4.2/systemvars.mk 2013-05-15 00:19:46.085324000 +0200 +@@ -15,7 +15,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ++OPTFLAGS := ${CFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/apple-darwin11-gcc4.2/systemvars.mk fsl/config/apple-darwin11-gcc4.2/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin11-gcc4.2/systemvars.mk 2012-03-21 12:30:53.000000000 +0100 ++++ fsl/config/apple-darwin11-gcc4.2/systemvars.mk 2013-05-15 00:19:48.066557000 +0200 +@@ -15,7 +15,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 ++OPTFLAGS := -O3 -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -ansi -pedantic + ANSI_FLAGS = ${GNU_ANSI_FLAGS} +diff -ru fsl.orig/fsl/config/apple-darwin12-gcc4.2/systemvars.mk fsl/config/apple-darwin12-gcc4.2/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin12-gcc4.2/systemvars.mk 2013-04-09 18:00:32.000000000 +0200 ++++ fsl/config/apple-darwin12-gcc4.2/systemvars.mk 2013-05-15 00:19:49.812861000 +0200 +@@ -15,7 +15,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 ++OPTFLAGS := -O3 -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -ansi -pedantic + ANSI_FLAGS = ${GNU_ANSI_FLAGS} +diff -ru fsl.orig/fsl/config/apple-darwin7-gcc3.1/systemvars.mk fsl/config/apple-darwin7-gcc3.1/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin7-gcc3.1/systemvars.mk 2013-05-15 00:14:37.712623000 +0200 ++++ fsl/config/apple-darwin7-gcc3.1/systemvars.mk 2013-05-15 00:19:51.866756000 +0200 +@@ -17,7 +17,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -traditional-cpp -Wall -Wno-long-long -Wno-long-double -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/apple-darwin7-gcc3.3/systemvars.mk fsl/config/apple-darwin7-gcc3.3/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin7-gcc3.3/systemvars.mk 2013-05-15 00:14:37.737794000 +0200 ++++ fsl/config/apple-darwin7-gcc3.3/systemvars.mk 2013-05-15 00:19:53.537845000 +0200 +@@ -17,7 +17,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -Wno-long-double -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/apple-darwin8-gcc4.0/systemvars.mk fsl/config/apple-darwin8-gcc4.0/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin8-gcc4.0/systemvars.mk 2013-05-15 00:14:37.745810000 +0200 ++++ fsl/config/apple-darwin8-gcc4.0/systemvars.mk 2013-05-15 00:19:55.229757000 +0200 +@@ -17,7 +17,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ++OPTFLAGS := ${CFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -Wno-long-double -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/apple-darwin9-gcc4.0/systemvars.mk fsl/config/apple-darwin9-gcc4.0/systemvars.mk +--- fsl.orig/fsl/config/apple-darwin9-gcc4.0/systemvars.mk 2013-05-15 00:14:37.751696000 +0200 ++++ fsl/config/apple-darwin9-gcc4.0/systemvars.mk 2013-05-15 00:19:57.417620000 +0200 +@@ -17,7 +17,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ++OPTFLAGS := ${CFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -Wno-long-long -Wno-long-double -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/generic/systemvars.mk fsl/config/generic/systemvars.mk +--- fsl.orig/fsl/config/generic/systemvars.mk 2013-05-15 00:14:37.757155000 +0200 ++++ fsl/config/generic/systemvars.mk 2013-05-15 00:19:59.724851000 +0200 +@@ -25,7 +25,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/gnu_64-gcc4.4/systemvars.mk fsl/config/gnu_64-gcc4.4/systemvars.mk +--- fsl.orig/fsl/config/gnu_64-gcc4.4/systemvars.mk 2011-04-19 10:47:52.000000000 +0200 ++++ fsl/config/gnu_64-gcc4.4/systemvars.mk 2013-05-15 00:20:03.204842000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk +--- fsl.orig/fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk 2013-05-15 00:14:37.763457000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk 2013-05-15 00:20:05.347565000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-deprecated + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk +--- fsl.orig/fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk 2013-05-15 00:14:37.769108000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk 2013-05-15 00:20:06.913095000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-deprecated + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk +--- fsl.orig/fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk 2013-05-15 00:14:37.775138000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk 2013-05-15 00:20:08.480567000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-deprecated + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_32-gcc2.96/systemvars.mk fsl/config/linux_32-gcc2.96/systemvars.mk +--- fsl.orig/fsl/config/linux_32-gcc2.96/systemvars.mk 2013-05-15 00:14:37.781755000 +0200 ++++ fsl/config/linux_32-gcc2.96/systemvars.mk 2013-05-15 00:20:10.043882000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_32-gcc3.2/systemvars.mk fsl/config/linux_32-gcc3.2/systemvars.mk +--- fsl.orig/fsl/config/linux_32-gcc3.2/systemvars.mk 2013-05-15 00:14:37.787130000 +0200 ++++ fsl/config/linux_32-gcc3.2/systemvars.mk 2013-05-15 00:20:11.484066000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_32-gcc3.3/systemvars.mk fsl/config/linux_32-gcc3.3/systemvars.mk +--- fsl.orig/fsl/config/linux_32-gcc3.3/systemvars.mk 2013-05-15 00:14:37.794387000 +0200 ++++ fsl/config/linux_32-gcc3.3/systemvars.mk 2013-05-15 00:20:12.921148000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_32-gcc3.4/systemvars.mk fsl/config/linux_32-gcc3.4/systemvars.mk +--- fsl.orig/fsl/config/linux_32-gcc3.4/systemvars.mk 2013-05-15 00:14:37.799247000 +0200 ++++ fsl/config/linux_32-gcc3.4/systemvars.mk 2013-05-15 00:20:14.478184000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_32-gcc4.0/systemvars.mk fsl/config/linux_32-gcc4.0/systemvars.mk +--- fsl.orig/fsl/config/linux_32-gcc4.0/systemvars.mk 2013-05-15 00:14:37.805358000 +0200 ++++ fsl/config/linux_32-gcc4.0/systemvars.mk 2013-05-15 00:20:16.819361000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_32-gcc4.1/systemvars.mk fsl/config/linux_32-gcc4.1/systemvars.mk +--- fsl.orig/fsl/config/linux_32-gcc4.1/systemvars.mk 2013-05-15 00:14:37.811876000 +0200 ++++ fsl/config/linux_32-gcc4.1/systemvars.mk 2013-05-15 00:20:18.322853000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_64-gcc3.4/systemvars.mk fsl/config/linux_64-gcc3.4/systemvars.mk +--- fsl.orig/fsl/config/linux_64-gcc3.4/systemvars.mk 2013-05-15 00:14:37.817395000 +0200 ++++ fsl/config/linux_64-gcc3.4/systemvars.mk 2013-05-15 00:20:20.465845000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_64-gcc4.0/systemvars.mk fsl/config/linux_64-gcc4.0/systemvars.mk +--- fsl.orig/fsl/config/linux_64-gcc4.0/systemvars.mk 2013-05-15 00:14:37.823453000 +0200 ++++ fsl/config/linux_64-gcc4.0/systemvars.mk 2013-05-15 00:20:22.065237000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_64-gcc4.1/systemvars.mk fsl/config/linux_64-gcc4.1/systemvars.mk +--- fsl.orig/fsl/config/linux_64-gcc4.1/systemvars.mk 2013-05-15 00:14:37.829561000 +0200 ++++ fsl/config/linux_64-gcc4.1/systemvars.mk 2013-05-15 00:20:23.601865000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_64-gcc4.2/systemvars.mk fsl/config/linux_64-gcc4.2/systemvars.mk +--- fsl.orig/fsl/config/linux_64-gcc4.2/systemvars.mk 2013-05-15 00:14:37.835868000 +0200 ++++ fsl/config/linux_64-gcc4.2/systemvars.mk 2013-05-15 00:20:25.058756000 +0200 +@@ -27,7 +27,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/linux_64-gcc4.4/systemvars.mk fsl/config/linux_64-gcc4.4/systemvars.mk +--- fsl.orig/fsl/config/linux_64-gcc4.4/systemvars.mk 2012-08-22 17:17:13.000000000 +0200 ++++ fsl/config/linux_64-gcc4.4/systemvars.mk 2013-05-15 00:20:26.561348000 +0200 +@@ -29,7 +29,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = -g + GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk +--- fsl.orig/fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk 2013-05-15 00:14:37.841452000 +0200 ++++ fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk 2013-05-15 00:20:28.072793000 +0200 +@@ -12,7 +12,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O6 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -ru fsl.orig/fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk +--- fsl.orig/fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk 2013-05-15 00:14:37.847832000 +0200 ++++ fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk 2013-05-15 00:20:29.505593000 +0200 +@@ -12,7 +12,7 @@ + ARCHLDFLAGS = -static + DEPENDFLAGS = -MM + +-OPTFLAGS = -O6 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS := ${CFLAGS} ${ARCHFLAGS} -wd803 + MACHDBGFLAGS = + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn diff --git a/easybuild/easyconfigs/f/FSL/FSL-5.0.8_makefile_fixes.patch b/easybuild/easyconfigs/f/FSL/FSL-5.0.8_makefile_fixes.patch new file mode 100644 index 0000000000000000000000000000000000000000..908f2f420516c6bbae420e87dcf128d2ea65a354 --- /dev/null +++ b/easybuild/easyconfigs/f/FSL/FSL-5.0.8_makefile_fixes.patch @@ -0,0 +1,343 @@ +diff -ru fsl.orig/config/apple-darwin10-gcc4.2/systemvars.mk fsl/config/apple-darwin10-gcc4.2/systemvars.mk +--- fsl.orig/config/apple-darwin10-gcc4.2/systemvars.mk 2009-11-03 18:02:14.000000000 +0100 ++++ fsl/config/apple-darwin10-gcc4.2/systemvars.mk 2013-05-14 22:43:15.344366000 +0200 +@@ -3,8 +3,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +diff -ru fsl.orig/config/apple-darwin7-gcc3.1/systemvars.mk fsl/config/apple-darwin7-gcc3.1/systemvars.mk +--- fsl.orig/config/apple-darwin7-gcc3.1/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/apple-darwin7-gcc3.1/systemvars.mk 2013-05-14 22:43:15.363590000 +0200 +@@ -7,8 +7,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +diff -ru fsl.orig/config/apple-darwin7-gcc3.3/systemvars.mk fsl/config/apple-darwin7-gcc3.3/systemvars.mk +--- fsl.orig/config/apple-darwin7-gcc3.3/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/apple-darwin7-gcc3.3/systemvars.mk 2013-05-14 22:43:15.385466000 +0200 +@@ -7,8 +7,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +diff -ru fsl.orig/config/apple-darwin8-gcc4.0/systemvars.mk fsl/config/apple-darwin8-gcc4.0/systemvars.mk +--- fsl.orig/config/apple-darwin8-gcc4.0/systemvars.mk 2007-12-19 15:40:57.000000000 +0100 ++++ fsl/config/apple-darwin8-gcc4.0/systemvars.mk 2013-05-14 22:43:15.402328000 +0200 +@@ -3,8 +3,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +diff -ru fsl.orig/config/apple-darwin9-gcc4.0/systemvars.mk fsl/config/apple-darwin9-gcc4.0/systemvars.mk +--- fsl.orig/config/apple-darwin9-gcc4.0/systemvars.mk 2007-12-19 15:33:53.000000000 +0100 ++++ fsl/config/apple-darwin9-gcc4.0/systemvars.mk 2013-05-14 22:43:15.415331000 +0200 +@@ -3,8 +3,8 @@ + + # Compiler dependent variables + +-CC = cc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = + CXXSTATICFLAGS = + +diff -ru fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk +--- fsl.orig/config/generic/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/generic/systemvars.mk 2013-05-14 22:43:15.438919000 +0200 +@@ -16,8 +16,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.2/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk +--- fsl.orig/config/i686-pc-cygwin-gcc3.2/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.2/systemvars.mk 2013-05-14 22:43:15.455595000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc-2 +-CXX = c++-2 ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.3/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk +--- fsl.orig/config/i686-pc-cygwin-gcc3.3/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.3/systemvars.mk 2013-05-14 22:43:15.473639000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/i686-pc-cygwin-gcc3.4/systemvars.mk fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk +--- fsl.orig/config/i686-pc-cygwin-gcc3.4/systemvars.mk 2007-07-13 13:00:20.000000000 +0200 ++++ fsl/config/i686-pc-cygwin-gcc3.4/systemvars.mk 2013-05-14 22:43:15.494398000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_32-gcc2.96/systemvars.mk fsl/config/linux_32-gcc2.96/systemvars.mk +--- fsl.orig/config/linux_32-gcc2.96/systemvars.mk 2007-07-25 17:21:07.000000000 +0200 ++++ fsl/config/linux_32-gcc2.96/systemvars.mk 2013-05-14 22:43:15.507210000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_32-gcc3.2/systemvars.mk fsl/config/linux_32-gcc3.2/systemvars.mk +--- fsl.orig/config/linux_32-gcc3.2/systemvars.mk 2007-07-25 17:21:08.000000000 +0200 ++++ fsl/config/linux_32-gcc3.2/systemvars.mk 2013-05-14 22:43:15.524309000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_32-gcc3.3/systemvars.mk fsl/config/linux_32-gcc3.3/systemvars.mk +--- fsl.orig/config/linux_32-gcc3.3/systemvars.mk 2007-07-25 17:21:09.000000000 +0200 ++++ fsl/config/linux_32-gcc3.3/systemvars.mk 2013-05-14 22:43:15.539643000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_32-gcc3.4/systemvars.mk fsl/config/linux_32-gcc3.4/systemvars.mk +--- fsl.orig/config/linux_32-gcc3.4/systemvars.mk 2007-07-25 17:21:10.000000000 +0200 ++++ fsl/config/linux_32-gcc3.4/systemvars.mk 2013-05-14 22:43:15.559881000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_32-gcc4.0/systemvars.mk fsl/config/linux_32-gcc4.0/systemvars.mk +--- fsl.orig/config/linux_32-gcc4.0/systemvars.mk 2007-07-25 17:21:11.000000000 +0200 ++++ fsl/config/linux_32-gcc4.0/systemvars.mk 2013-05-14 22:43:15.573696000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_32-gcc4.1/systemvars.mk fsl/config/linux_32-gcc4.1/systemvars.mk +--- fsl.orig/config/linux_32-gcc4.1/systemvars.mk 2012-04-20 11:37:28.000000000 +0200 ++++ fsl/config/linux_32-gcc4.1/systemvars.mk 2013-05-14 22:43:15.590022000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_64-gcc3.4/systemvars.mk fsl/config/linux_64-gcc3.4/systemvars.mk +--- fsl.orig/config/linux_64-gcc3.4/systemvars.mk 2007-07-25 17:21:12.000000000 +0200 ++++ fsl/config/linux_64-gcc3.4/systemvars.mk 2013-05-14 22:43:15.605655000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_64-gcc4.0/systemvars.mk fsl/config/linux_64-gcc4.0/systemvars.mk +--- fsl.orig/config/linux_64-gcc4.0/systemvars.mk 2007-07-25 17:21:13.000000000 +0200 ++++ fsl/config/linux_64-gcc4.0/systemvars.mk 2013-05-14 22:43:15.624046000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_64-gcc4.1/systemvars.mk fsl/config/linux_64-gcc4.1/systemvars.mk +--- fsl.orig/config/linux_64-gcc4.1/systemvars.mk 2007-07-25 11:19:45.000000000 +0200 ++++ fsl/config/linux_64-gcc4.1/systemvars.mk 2013-05-14 22:43:15.635678000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_64-gcc4.2/systemvars.mk fsl/config/linux_64-gcc4.2/systemvars.mk +--- fsl.orig/config/linux_64-gcc4.2/systemvars.mk 2008-06-26 15:25:42.000000000 +0200 ++++ fsl/config/linux_64-gcc4.2/systemvars.mk 2013-05-14 22:43:15.648658000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/linux_64-gcc4.4/systemvars.mk fsl/config/linux_64-gcc4.4/systemvars.mk +--- fsl.orig/config/linux_64-gcc4.4/systemvars.mk 2012-08-22 17:17:13.000000000 +0200 ++++ fsl/config/linux_64-gcc4.4/systemvars.mk 2014-06-14 23:23:58.456480000 +0200 +@@ -18,8 +18,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +diff -ru fsl.orig/config/sparc-solaris2.8-gcc2.95/systemvars.mk fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk +--- fsl.orig/config/sparc-solaris2.8-gcc2.95/systemvars.mk 2007-07-13 13:00:21.000000000 +0200 ++++ fsl/config/sparc-solaris2.8-gcc2.95/systemvars.mk 2013-05-14 22:43:15.658171000 +0200 +@@ -5,8 +5,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + + ARCHFLAGS = -mv8 -ffast-math -fomit-frame-pointer + +diff -ru fsl.orig/config/sparc-solaris2.9-gcc2.95/systemvars.mk fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk +--- fsl.orig/config/sparc-solaris2.9-gcc2.95/systemvars.mk 2007-07-13 13:00:21.000000000 +0200 ++++ fsl/config/sparc-solaris2.9-gcc2.95/systemvars.mk 2013-05-14 22:43:15.674176000 +0200 +@@ -5,8 +5,8 @@ + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC := ${CC} ++CXX := ${CXX} + + ARCHFLAGS = -mv8 -ffast-math -fomit-frame-pointer + ARCHLDFLAGS = -static +diff -ru fsl.orig/src/libmeshutils/Makefile fsl/src/libmeshutils/Makefile +--- fsl.orig/src/libmeshutils/Makefile 2012-07-23 15:25:20.000000000 +0200 ++++ fsl/src/libmeshutils/Makefile 2013-05-14 22:43:15.320209000 +0200 +@@ -3,7 +3,7 @@ + + PROJNAME = meshUtils + +-LD_LIBRARY_PATH=${FSLDIR}/lib ++#LD_LIBRARY_PATH=${FSLDIR}/lib + + USRINCFLAGS = -I${INC_NEWMAT} -I${INC_ZLIB} -I${INC_PROB} -I${INC_BOOST} + USRLDFLAGS = -L${LIB_PROB} -L${LIB_NEWMAT} -L${LIB_ZLIB} +diff -ru fsl.orig/src/melodic/Makefile fsl/src/melodic/Makefile +--- fsl.orig/src/melodic/Makefile 2013-03-13 21:22:35.000000000 +0100 ++++ fsl/src/melodic/Makefile 2013-05-14 22:44:13.016352000 +0200 +@@ -3,7 +3,7 @@ + include ${FSLCONFDIR}/default.mk + + OPTFLAGS = -O3 -Wno-deprecated -ggdb +-OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui ++#OPTFLAGS_alphaev6-dec-osf5.0-gcc2.95.2 = -O3 -mieee -mfp-trap-mode=sui + + PROJNAME = melodic + +--- fsl/src/film/Makefile.orig 2014-06-15 00:43:34.908901000 +0200 ++++ fsl/src/film/Makefile 2014-06-15 00:43:52.303973000 +0200 +@@ -26,7 +26,7 @@ + ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} ftoz.o ${LIBS} + + film_gls:${OBJS} film_gls.o +- ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls.o ${LIBS} -l giftiio ++ ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls.o ${LIBS} -lgiftiio + + film_gls_res:${OBJS} film_gls_res.o + ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${OBJS} film_gls_res.o ${LIBS} diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb index 0e1e6d0fb4fe43ac53cf331f2e704ec5bdc69794..67920d1a2d3e0f12d62cc577ac28f50196774447 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-goolf-1.4.10.eb @@ -16,7 +16,7 @@ sources = ['%(name)s-%(version)s.c'] skipsteps = ['source'] -cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %(source)s -o FastTree')] +cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %(source)s -o %(name)s')] files_to_copy = [(['FastTree'], 'bin')] diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb index 5fb2a1352d9bc24c3bc7e77016715e76a7452f74..b7b0c003396fccfc5c0d8e0bb20b56935af545de 100644 --- a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.7-ictce-5.5.0.eb @@ -16,7 +16,7 @@ sources = ['%(name)s-%(version)s.c'] skipsteps = ['source'] -cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %(source)s -o FastTree')] +cmds_map = [('FastTree.*.c', '$CC -DOPENMP $CFLAGS $LIBS %(source)s -o %(name)s')] files_to_copy = [(['FastTree'], 'bin')] diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..9ff730ebeda8b1096f7e370f983285c321dcc2c4 --- /dev/null +++ b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.2.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_Java' + +name = 'fastqc' +version = '0.11.2' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'] +sources = ['%(name)s_v%(version)s.zip'] + +dependencies = [('Java', '1.7.0_60')] + +postinstallcmds = ["chmod -R a+rx %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['fastqc'], + 'dirs': [], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..c5f20b91654926eb90d7d61fbb9671bdbc67d835 --- /dev/null +++ b/easybuild/easyconfigs/f/fastqc/fastqc-0.11.3.eb @@ -0,0 +1,27 @@ +easyblock = 'EB_Java' + +name = 'fastqc' +version = '0.11.3' + +homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'] +sources = ['%(name)s_v%(version)s.zip'] + +dependencies = [('Java', '1.7.0_80')] + +postinstallcmds = ["chmod -R a+rx %(installdir)s/fastqc %(installdir)s/run_fastqc.bat"] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['fastqc'], + 'dirs': [], +} + +sanity_check_commands = [('fastqc', '-v')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb index 50633eb59802cbdefbad3fbe6707ec1448ce49c2..7bcbad6706befeb5e6cef38df6b8338d078c540d 100644 --- a/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/f/fastqz/fastqz-1.5-GCC-4.8.2.eb @@ -30,7 +30,7 @@ dependencies = [('ZPAQ', '7.00')] skipsteps = ['source'] cmds_map = [ - ('fastqz%s.cpp' % minver, '$CXX $CFLAGS -lpthread %(source)s $EBROOTZPAQ/include/libzpaq.cpp -o fastqz'), + ('fastqz%s.cpp' % minver, '$CXX $CFLAGS -lpthread %(source)s $EBROOTZPAQ/include/libzpaq.cpp -o %(name)s'), ('fapack.cpp', '$CXX $CFLAGS -s %(source)s -o %(target)s') ] diff --git a/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..36569d20af714fca2d0ff0500931e39465ec8b4a --- /dev/null +++ b/easybuild/easyconfigs/f/ffmpeg/ffmpeg-2.4-intel-2014.06.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'ffmpeg' +version = '2.4' + +homepage = 'https://www.ffmpeg.org/' +description = """A complete, cross-platform solution to record, convert and stream audio and video.""" + +toolchain = {'name': 'intel', 'version': '2014.06'} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['http://ffmpeg.org/releases/'] + +configopts = '--enable-pic --enable-shared --enable-gpl --enable-version3 --enable-nonfree --cc="$CC" --cxx="$CXX"' + +dependencies = [ + ('NASM', '2.11.05'), + ('zlib', '1.2.8'), +] + +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']], + 'dirs': ['include'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5d430a5301ff2097bd77b34744024402eba4b2a2 --- /dev/null +++ b/easybuild/easyconfigs/f/fixesproto/fixesproto-5.0-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'fixesproto' +version = '5.0' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org FixesProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/xfixesproto.h', 'include/X11/extensions/xfixeswire.h'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-6.1.5.eb b/easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-6.1.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..15e30d50fbf4ec3af759be277af207e5faace014 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.37-ictce-6.1.5.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.37' + +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': 'ictce', 'version': '6.1.5'} +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-2.5.37-intel-2015a.eb b/easybuild/easyconfigs/f/flex/flex-2.5.37-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..086db50be89e50c7884e0598c0629094dc4cfe04 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.37-intel-2015a.eb @@ -0,0 +1,14 @@ +name = 'flex' +version = '2.5.37' + +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': '2015a'} +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-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..a6d2ced89c431f1f7c6f6da2afcd8a5941a407a7 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.1.29.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': 'CrayGNU', 'version': '5.1.29'} +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-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..e9455b96ac13377f52d6e2c087092067459a0ed9 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.25.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': 'CrayGNU', 'version': '5.2.25'} +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-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..470ec059e0012130b28cf6d879d2ef0d0e47f370 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-CrayGNU-5.2.40.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': 'CrayGNU', 'version': '5.2.40'} +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-foss-2014b.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..6a24b017aa79cbb8a179bb5730ccdb950543b29b --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2014b.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': 'foss', 'version': '2014b'} +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-foss-2015.05.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..208a02e5403e45baf0640fa33ec53981b1c802b5 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015.05.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': 'foss', 'version': '2015.05'} +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-foss-2015a.eb b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f9226ff5f3631f67338c0176482e53e3ed58e4e3 --- /dev/null +++ b/easybuild/easyconfigs/f/flex/flex-2.5.39-foss-2015a.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': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..e77da2e1fe8e9bdc91c4533bcc71cddafbadac5e --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = "fontconfig" +version = '2.11.1' + +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': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype','2.5.3'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..54455c5111b2db7d9079598f1df06f44467dbeef --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.1-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = "fontconfig" +version = '2.11.1' + +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': '2015a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype', '2.5.5'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2015a.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..77235f32a1aa63f8dfb6d9b9ada8d93ede3786fa --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.11.93-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = "fontconfig" +version = '2.11.93' + +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': '2015a'} + +source_urls = ['http://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('expat', '2.1.0'), + ('freetype', '2.5.5'), +] + +configopts = '--disable-docs ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/foss/foss-2015.05.eb b/easybuild/easyconfigs/f/foss/foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..e468cc0b439653c08cc643fb3823564bb78ec8e3 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2015.05.eb @@ -0,0 +1,39 @@ +easyblock = "Toolchain" + +name = 'foss' +version = '2015.05' + +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 = '4.9.2' +binutilsver = '2.25' +tcver = '%s-binutils-%s' % (gccver, binutilsver) + +blaslib = 'OpenBLAS' +blasver = '0.2.14' +blas = '%s-%s' % (blaslib, blasver) +blassuff = '-LAPACK-3.5.0' + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc_ver = "%s" % version +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +# 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, '-binutils-%s' % binutilsver), + ('binutils', binutilsver, '', ('GCC', tcver)), + ('OpenMPI', '1.8.5', '', ('GNU', '%s-%s' % (gccver, binutilsver))), + (blaslib, blasver, blassuff, ('GNU', '%s-%s' % (gccver, binutilsver))), + ('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/frealign/frealign-9.09-intel-2015a-avx-mp.eb b/easybuild/easyconfigs/f/frealign/frealign-9.09-intel-2015a-avx-mp.eb new file mode 100644 index 0000000000000000000000000000000000000000..a6b21fbfffcfb90e35d9168e8f6a6aefde4115cd --- /dev/null +++ b/easybuild/easyconfigs/f/frealign/frealign-9.09-intel-2015a-avx-mp.eb @@ -0,0 +1,31 @@ +easyblock = 'MakeCp' + +name = 'frealign' +version = '9.09' +versionsuffix = '-avx-mp' + +homepage = 'http://grigoriefflab.janelia.org/frealign' +description = """Frealign is a program for high-resolution refinement of 3D reconstructions from cryo-EM images of + single particles.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://grigoriefflab.janelia.org/sites/default/files/'] +sources = ['frealign_v%(version)s_150422.tar.gz'] + +start_dir = 'src' + +parallel = 1 + +# clean all included binaries first +prebuildopts = "rm ../bin/* && " +buildopts = "-f Makefile_linux_avx_intel_mp_static" + +files_to_copy = ['bin'] + +sanity_check_paths = { + 'files': ['bin/resample_mp.exe', 'bin/merge_3d_mp.exe', 'bin/frealign_v%(version_major)s_mp.exe'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-intel-2015a.eb b/easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f501cd2fef4b62782e6d82fa759b0d94b58a8a34 --- /dev/null +++ b/easybuild/easyconfigs/f/freeglut/freeglut-2.8.1-intel-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'freeglut' +version = '2.8.1' + +homepage = 'http://freeglut.sourceforge.net/' +description = "freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library." + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://prdownloads.sourceforge.net/%(name)s'] + +dependencies = [('libXi', '1.7.4')] + +sanity_check_paths = { + 'files': ['lib/libglut.a', 'lib/libglut.so'], + 'dirs': ['include/GL'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..c5fb92d43c4f151bdbf760adc52541f881e8a87a --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.5.3-goolf-1.7.20.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.5.3' + +homepage = 'http://freetype.org' +description = """FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and + portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display + servers, font conversion tools, text image generation tools, and many other products as well.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.12')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3678616622f855c37aeabec97a8ae35f4c8ce5fe --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-foss-2015a.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.6' + +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': '2015a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.17')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb b/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6a1b7e739c956a04be39b4b3c1439138e742eece --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.6-intel-2015a.eb @@ -0,0 +1,21 @@ +name = 'freetype' +version = '2.6' + +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': '2015a'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [('libpng', '1.6.17')] + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', 'lib/libfreetype.so', 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb b/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb new file mode 100644 index 0000000000000000000000000000000000000000..13de380c1b550861e16910f07b1fcfe65ac645ae --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-3.0-0-Java-1.7.0_10.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 Cyprus Institute +# Authors:: Thekla Loizou +# 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 = 'Tarball' + +name = 'GATK' +version = '3.0-0' + +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 = ['%s-%s.tar.bz2' % ("GenomeAnalysisTK", version)] + +java = 'Java' +javaver = '1.7.0_10' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +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 new file mode 100644 index 0000000000000000000000000000000000000000..8bb06bd90a35aaeb7a12ba19b72e6356cbf63681 --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.2.3.eb @@ -0,0 +1,109 @@ +easyblock = 'Bundle' + +name = 'GC3Pie' +version = '2.2.3' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c"import %(ext_name)s"', '') + +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +exts_list = [ + ('setuptools', '17.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.13.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', '2.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '0.7.9', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '0.8.7', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.9.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '0.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.15.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), +] + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyshortver, 'lib64/python%s/site-packages' % pyshortver]} + +# 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/gc3utils'], + 'dirs': ['lib/python%(pyver)s/site-packages/gc3pie-%%(version)s-py%(pyver)s.egg/gc3libs' % {'pyver': pyshortver}], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..6fee6c35e89d1154273ceb311f5dbea15c59d1a6 --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.3.eb @@ -0,0 +1,111 @@ +easyblock = 'Bundle' + +name = 'GC3Pie' +version = '2.3' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c"import %(ext_name)s"', '') + +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +exts_list = [ + ('setuptools', '18.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', 'devel', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '1.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.38.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '1.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.26.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), +] + +pyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver]} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver +sanity_check_paths = { + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + 'dirs': [], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..8a1d9386f8ef8d4d2d480e4fec0bd2bcf8149847 --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.0.eb @@ -0,0 +1,111 @@ +easyblock = 'Bundle' + +name = 'GC3Pie' +version = '2.4.0' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c"import %(ext_name)s"', '') + +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +exts_list = [ + ('setuptools', '18.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', 'devel', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '1.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.38.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '1.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '1.3', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.26.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), +] + +pyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver]} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver +sanity_check_paths = { + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + 'dirs': [], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..b62aa2387d6f8806ade0be67e3e1375fbc1476a4 --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.1.eb @@ -0,0 +1,111 @@ +easyblock = 'Bundle' + +name = 'GC3Pie' +version = '2.4.1' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c"import %(ext_name)s"', '') + +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +exts_list = [ + ('setuptools', '18.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', 'devel', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '1.0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.38.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.23.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), +] + +pyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver]} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver +sanity_check_paths = { + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + 'dirs': [], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..e73e2257cc55e8b263e900b27ee5702259fc5d32 --- /dev/null +++ b/easybuild/easyconfigs/g/GC3Pie/GC3Pie-2.4.2.eb @@ -0,0 +1,111 @@ +easyblock = 'Bundle' + +name = 'GC3Pie' +version = '2.4.2' + +homepage = 'https://gc3pie.readthedocs.org' +description = """GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution + environments.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_filter = ('python -c"import %(ext_name)s"', '') + +# allow use of system Python +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +exts_list = [ + ('setuptools', '18.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + # required for paramiko + ('ecdsa', '0.13', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + # required for paramiko + ('pycrypto', '2.6.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pycrypto/'], + 'modulename': 'Crypto', + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('PrettyTable', '0.7.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/PrettyTable/'], + 'source_tmpl': 'prettytable-%(version)s.tar.gz', + }), + ('pyCLI', 'devel', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyCLI/'], + 'modulename': 'cli', + }), + ('SQLAlchemy', '1.0.8', { + 'source_urls': ['https://pypi.python.org/packages/source/S/SQLAlchemy/'], + }), + ('parsedatetime', '1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/p/parsedatetime/'], + }), + ('boto', '2.38.0', { + 'source_urls': ['https://pypi.python.org/packages/source/b/boto/'], + }), + # required for pbr + ('pip', '7.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + # required for python-novaclient + ('pbr', '1.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + # required for python-novaclient + ('Babel', '2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/B/Babel/'], + }), + # required for python-novaclient + ('simplejson', '3.8.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/simplejson/'], + }), + # required for python-novaclient + ('requests', '2.7.0', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + }), + # required for python-novaclient + ('iso8601', '0.1.10', { + 'source_urls': ['https://pypi.python.org/packages/source/i/iso8601/'], + }), + # required for python-novaclient + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + # required for python-novaclient + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('python-novaclient', '2.23.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/python-novaclient/'], + 'modulename': 'novaclient', + }), + (name.lower(), version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gc3pie/'], + 'modulename': 'gc3libs', + }), +] + +pyver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +# on RHEL-based systems, some extensions get installed to lib, some to lib64 +modextrapaths = {'PYTHONPATH': ['lib/python%s/site-packages' % pyver, 'lib64/python%s/site-packages' % pyver]} + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +eggname = 'gc3pie-%%(version)s-py%s.egg' % pyver +sanity_check_paths = { + 'files': ['bin/gc3utils', + ('lib/python%s/site-packages/%s' % (pyver, eggname), 'lib64/python%s/site-packages/%s' % (pyver, eggname))], + 'dirs': [], +} + +sanity_check_commands = [('gc3utils', 'info --version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb b/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..719bc6f3153e1237155c22ecca4522fd903e8d62 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.5.2.eb @@ -0,0 +1,37 @@ +name = "GCC" +version = '4.5.2' + +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': 'dummy'} + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(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 +] +sources = [ + SOURCELOWER_TAR_GZ, + 'gmp-5.0.2.tar.gz', + 'mpfr-3.0.1.tar.gz', + 'mpc-0.8.2.tar.gz', +] + +checksums = [ + 'e31fe695d7235f11fb5a63eafdfbfe88', # gcc-4.5.2.tar.gz + '87e73447afdc2ca5cefd987da865da51', # gmp-5.0.2.tar.gz + 'e9c191fc46a4f5741f8a0a11ab33b8bf', # mpfr-3.0.1.tar.gz + 'e98267ebd5648a39f881d66797122fb6', # mpc-0.8.2.tar.gz +] + +languages = ['c', 'c++', 'fortran'] + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +withlto = False + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb b/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..f310421ff2f2ab48f7d4c21d5a216e75c9f73ce4 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.6.0.eb @@ -0,0 +1,35 @@ +name = "GCC" +version = '4.6.0' + +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': 'dummy'} + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(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 +] +sources = [ + SOURCELOWER_TAR_GZ, + 'gmp-5.0.4.tar.bz2', + 'mpfr-3.0.1.tar.gz', + 'mpc-0.9.tar.gz', +] + +checksums = [ + '009f59ee0f9c8100c12939140698cf33', # gcc-4.6.0.tar.gz + '50c3edcb7c9438e04377ee9a1a061b79', # gmp-5.0.4.tar.bz2 + 'e9c191fc46a4f5741f8a0a11ab33b8bf', # mpfr-3.0.1.tar.gz + '0d6acab8d214bd7d1fbbc593e83dd00d', # mpc-0.9.tar.gz +] + +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 new file mode 100644 index 0000000000000000000000000000000000000000..861866153237fa8bb6e7c9ada3237e0589fe83ad --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.8.5.eb @@ -0,0 +1,35 @@ +name = "GCC" +version = '4.8.5' + +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': 'dummy'} + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(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 +] +sources = [ + SOURCELOWER_TAR_GZ, + 'gmp-5.1.3.tar.bz2', + 'mpfr-3.1.2.tar.gz', + 'mpc-1.0.1.tar.gz', +] + +checksums = [ + 'bfe56e74d31d25009c8fb55fd3ca7e01', # gcc-4.8.5.tar.gz + 'a082867cbca5e898371a97bb27b31fea', # gmp-5.1.3.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'b32a2e1a3daa392372fbd586d1ed3679', # mpc-1.0.1.tar.gz +] + +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-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..4985b9228e2dc28a36621c2abb6330005889afa0 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.2-binutils-2.25.eb @@ -0,0 +1,45 @@ +name = "GCC" +version = '4.9.2' + +binutilsver = '2.25' +versionsuffix = '-binutils-%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': ''} + +mpfr_version = '3.1.2' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(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 +] +sources = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.2.tar.gz', +] + +builddependencies = [('binutils', binutilsver)] + +patches = [('mpfr-%s-allpatches-20140630.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + '4df8ee253b7f3863ad0b86359cd39c43', # gcc-4.9.2.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz + '21958aaf3d242e51b2f45cefcb9560d9', # mpfr-3.1.2-allpatches-20140630.patch +] + +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 new file mode 100644 index 0000000000000000000000000000000000000000..759f134bcc6554ea09caed6b0eb0282658430714 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-4.9.3.eb @@ -0,0 +1,40 @@ +name = "GCC" +version = '4.9.3' + +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': 'dummy'} + +mpfr_version = '3.1.2' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(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 +] +sources = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.2.tar.gz', +] + +patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + '6f831b4d251872736e8e9cc09746f327', # gcc-4.9.3.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + '68fadff3358fb3e7976c7a398a0af4c3', # mpc-1.0.2.tar.gz + '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch +] + +languages = ['c', 'c++', 'fortran'] + +# building GCC sometimes fails if make parallelism is too high, so let's limit it +maxparallel = 4 + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..8bbf0ea88e7755cbc48981ead7cadf5f0b405f6b --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0-binutils-2.25.eb @@ -0,0 +1,55 @@ +name = "GCC" +version = '5.1.0' + +binutilsver = '2.25' +versionsuffix = '-binutils-%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': ''} + +mpfr_version = '3.1.2' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(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 +] + +sources = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.14.tar.bz2', +] + +builddependencies = [ + ('M4', '1.4.17'), + ('binutils', binutilsver), +] + +patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +checksums = [ + 'd5525b1127d07d215960e6051c5da35e', # gcc-5.1.0.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'acd347243fca5609e3df37dba47fd0bb', # isl-0.14.tar.bz2 + '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch +] + +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 new file mode 100644 index 0000000000000000000000000000000000000000..a69c58da2c59ea2dbfd2013b502eab93a8e43b60 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.1.0.eb @@ -0,0 +1,49 @@ +name = "GCC" +version = '5.1.0' + +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 = '3.1.2' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(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 +] + +sources = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.14.tar.bz2', +] + +patches = [('mpfr-%s-allpatches-20141204.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +builddependencies = [('M4', '1.4.17')] + +checksums = [ + 'd5525b1127d07d215960e6051c5da35e', # gcc-5.1.0.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '181aa7bb0e452c409f2788a4a7f38476', # mpfr-3.1.2.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'acd347243fca5609e3df37dba47fd0bb', # isl-0.14.tar.bz2 + '58aec98d15982f9744a043d2f1c5af82', # mpfr-3.1.2-allpatches-20141204.patch +] + +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 new file mode 100644 index 0000000000000000000000000000000000000000..c25b63f7b1fd3d926eda88ef886de6f153214890 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-5.2.0.eb @@ -0,0 +1,49 @@ +name = 'GCC' +version = '5.2.0' + +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 = '3.1.3' + +source_urls = [ + 'http://ftpmirror.gnu.org/%(namelower)s/%(namelower)s-%(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 +] + +sources = [ + SOURCELOWER_TAR_BZ2, + 'gmp-6.0.0a.tar.bz2', + 'mpfr-%s.tar.gz' % mpfr_version, + 'mpc-1.0.3.tar.gz', + 'isl-0.14.tar.bz2', +] + +patches = [('mpfr-%s-allpatches-20150717.patch' % mpfr_version, '../mpfr-%s' % mpfr_version)] + +builddependencies = [('M4', '1.4.17')] + +checksums = [ + 'a51bcfeb3da7dd4c623e27207ed43467', # gcc-5.2.0.tar.bz2 + 'b7ff2d88cae7f8085bd5006096eed470', # gmp-6.0.0a.tar.bz2 + '7b650781f0a7c4a62e9bc8bdaaa0018b', # mpfr-3.1.l.tar.gz + 'd6a1d5f8ddea3abd2cc3e98f58352d26', # mpc-1.0.3.tar.gz + 'acd347243fca5609e3df37dba47fd0bb', # isl-0.14.tar.bz2 + 'e502185ebb22b41c528f183bb22a7569', # mpfr-3.1.3-allpatches-20150717.patch +] + +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-system.eb b/easybuild/easyconfigs/g/GCC/GCC-system.eb new file mode 100644 index 0000000000000000000000000000000000000000..b24177d7132df72b011aaebf4e731d9047544eae --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/GCC-system.eb @@ -0,0 +1,23 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2015 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# License:: 3-clause BSD +## + +easyblock = 'SystemCompiler' + +name = 'GCC' +# using 'system' as a version instructs the SystemCompiler easyblock to derive the actual compiler version, +# and define $EBVERSION* accordingly (yet generate a module named GCC/system); +# if an actual version is specified here, it will be checked against the version of the system compiler that was found +version = 'system' + +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': 'dummy'} + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/GCC/mpfr-3.1.2-allpatches-20141204.patch b/easybuild/easyconfigs/g/GCC/mpfr-3.1.2-allpatches-20141204.patch new file mode 100644 index 0000000000000000000000000000000000000000..df1aaea4345f24eb0cffdf756fe278cf99f58416 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/mpfr-3.1.2-allpatches-20141204.patch @@ -0,0 +1,1628 @@ +# All mpfr patches as of 2014-12-04 +# taken from their website: http://www.mpfr.org/mpfr-current/#download +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/PATCHES 2013-09-26 10:52:52.000000000 +0000 +@@ -0,0 +1 @@ ++exp_2 +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2013-03-13 15:37:28.000000000 +0000 ++++ mpfr-3.1.2-b/VERSION 2013-09-26 10:52:52.000000000 +0000 +@@ -1 +1 @@ +-3.1.2 ++3.1.2-p1 +diff -Naurd mpfr-3.1.2-a/src/exp_2.c mpfr-3.1.2-b/src/exp_2.c +--- mpfr-3.1.2-a/src/exp_2.c 2013-03-13 15:37:28.000000000 +0000 ++++ mpfr-3.1.2-b/src/exp_2.c 2013-09-26 10:52:52.000000000 +0000 +@@ -204,7 +204,7 @@ + for (k = 0; k < K; k++) + { + mpz_mul (ss, ss, ss); +- exps <<= 1; ++ exps *= 2; + exps += mpz_normalize (ss, ss, q); + } + mpfr_set_z (s, ss, MPFR_RNDN); +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2013-03-13 15:37:37.000000000 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2013-09-26 10:52:52.000000000 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2" ++#define MPFR_VERSION_STRING "3.1.2-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2013-03-13 15:37:34.000000000 +0000 ++++ mpfr-3.1.2-b/src/version.c 2013-09-26 10:52:52.000000000 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2"; ++ return "3.1.2-p1"; + } +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2013-09-26 10:56:55.000000000 +0000 ++++ mpfr-3.1.2-b/PATCHES 2013-09-26 10:56:55.000000000 +0000 +@@ -0,0 +1 @@ ++fits-smallneg +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/VERSION 2013-09-26 10:56:55.000000000 +0000 +@@ -1 +1 @@ +-3.1.2-p1 ++3.1.2-p2 +diff -Naurd mpfr-3.1.2-a/src/fits_u.h mpfr-3.1.2-b/src/fits_u.h +--- mpfr-3.1.2-a/src/fits_u.h 2013-03-13 15:37:35.000000000 +0000 ++++ mpfr-3.1.2-b/src/fits_u.h 2013-09-26 10:56:55.000000000 +0000 +@@ -32,17 +32,20 @@ + int res; + + if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (f))) +- /* Zero always fit */ +- return MPFR_IS_ZERO (f) ? 1 : 0; +- else if (MPFR_IS_NEG (f)) +- /* Negative numbers don't fit */ +- return 0; +- /* now it fits if +- (a) f <= MAXIMUM +- (b) round(f, prec(slong), rnd) <= MAXIMUM */ ++ return MPFR_IS_ZERO (f) ? 1 : 0; /* Zero always fits */ + + e = MPFR_GET_EXP (f); + ++ if (MPFR_IS_NEG (f)) ++ return e >= 1 ? 0 /* f <= -1 does not fit */ ++ : rnd != MPFR_RNDN ? MPFR_IS_LIKE_RNDU (rnd, -1) /* directed mode */ ++ : e < 0 ? 1 /* f > -1/2 fits in MPFR_RNDN */ ++ : mpfr_powerof2_raw(f); /* -1/2 fits, -1 < f < -1/2 don't */ ++ ++ /* Now it fits if ++ (a) f <= MAXIMUM ++ (b) round(f, prec(slong), rnd) <= MAXIMUM */ ++ + /* first compute prec(MAXIMUM); fits in an int */ + for (s = MAXIMUM, prec = 0; s != 0; s /= 2, prec ++); + +diff -Naurd mpfr-3.1.2-a/src/fits_uintmax.c mpfr-3.1.2-b/src/fits_uintmax.c +--- mpfr-3.1.2-a/src/fits_uintmax.c 2013-03-13 15:37:33.000000000 +0000 ++++ mpfr-3.1.2-b/src/fits_uintmax.c 2013-09-26 10:56:55.000000000 +0000 +@@ -27,51 +27,19 @@ + #include "mpfr-intmax.h" + #include "mpfr-impl.h" + +-#ifdef _MPFR_H_HAVE_INTMAX_T +- +-/* We can't use fits_u.h <= mpfr_cmp_ui */ +-int +-mpfr_fits_uintmax_p (mpfr_srcptr f, mpfr_rnd_t rnd) +-{ +- mpfr_exp_t e; +- int prec; +- uintmax_t s; +- mpfr_t x; +- int res; +- +- if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (f))) +- /* Zero always fit */ +- return MPFR_IS_ZERO (f) ? 1 : 0; +- else if (MPFR_IS_NEG (f)) +- /* Negative numbers don't fit */ +- return 0; +- /* now it fits if +- (a) f <= MAXIMUM +- (b) round(f, prec(slong), rnd) <= MAXIMUM */ +- +- e = MPFR_GET_EXP (f); +- +- /* first compute prec(MAXIMUM); fits in an int */ +- for (s = MPFR_UINTMAX_MAX, prec = 0; s != 0; s /= 2, prec ++); +- +- /* MAXIMUM needs prec bits, i.e. MAXIMUM = 2^prec - 1 */ +- +- /* if e <= prec - 1, then f < 2^(prec-1) < MAXIMUM */ +- if (e <= prec - 1) +- return 1; ++/* Note: though mpfr-impl.h is included in fits_u.h, we also include it ++ above so that it gets included even when _MPFR_H_HAVE_INTMAX_T is not ++ defined; this is necessary to avoid an empty translation unit, which ++ is forbidden by ISO C. Without this, a failing test can be reproduced ++ by creating an invalid stdint.h somewhere in the default include path ++ and by compiling MPFR with "gcc -ansi -pedantic-errors". */ + +- /* if e >= prec + 1, then f >= 2^prec > MAXIMUM */ +- if (e >= prec + 1) +- return 0; ++#ifdef _MPFR_H_HAVE_INTMAX_T + +- MPFR_ASSERTD (e == prec); ++#define FUNCTION mpfr_fits_uintmax_p ++#define MAXIMUM MPFR_UINTMAX_MAX ++#define TYPE uintmax_t + +- /* hard case: first round to prec bits, then check */ +- mpfr_init2 (x, prec); +- mpfr_set (x, f, rnd); +- res = MPFR_GET_EXP (x) == e; +- mpfr_clear (x); +- return res; +-} ++#include "fits_u.h" + + #endif +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2013-09-26 10:56:55.000000000 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p1" ++#define MPFR_VERSION_STRING "3.1.2-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/src/version.c 2013-09-26 10:56:55.000000000 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p1"; ++ return "3.1.2-p2"; + } +diff -Naurd mpfr-3.1.2-a/tests/tfits.c mpfr-3.1.2-b/tests/tfits.c +--- mpfr-3.1.2-a/tests/tfits.c 2013-03-13 15:37:45.000000000 +0000 ++++ mpfr-3.1.2-b/tests/tfits.c 2013-09-26 10:56:55.000000000 +0000 +@@ -33,155 +33,176 @@ + #include "mpfr-intmax.h" + #include "mpfr-test.h" + +-#define ERROR1 { printf("Initial error for x="); mpfr_dump(x); exit(1); } +-#define ERROR2 { printf("Error for x="); mpfr_dump(x); exit(1); } ++#define ERROR1(N) \ ++ do \ ++ { \ ++ printf("Error %d for rnd = %s and x = ", N, \ ++ mpfr_print_rnd_mode ((mpfr_rnd_t) r)); \ ++ mpfr_dump(x); \ ++ exit(1); \ ++ } \ ++ while (0) + + static void check_intmax (void); + + int + main (void) + { +- mpfr_t x; ++ mpfr_t x, y; ++ int i, r; + + tests_start_mpfr (); + + mpfr_init2 (x, 256); ++ mpfr_init2 (y, 8); + +- /* Check NAN */ +- mpfr_set_nan (x); +- if (mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR1; ++ RND_LOOP (r) ++ { + +- /* Check INF */ +- mpfr_set_inf (x, 1); +- if (mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR1; ++ /* Check NAN */ ++ mpfr_set_nan (x); ++ if (mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (1); ++ if (mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (2); ++ if (mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (3); ++ if (mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (4); ++ if (mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (5); ++ if (mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (6); + +- /* Check Zero */ +- MPFR_SET_ZERO (x); +- if (!mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check INF */ ++ mpfr_set_inf (x, 1); ++ if (mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (7); ++ if (mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (8); ++ if (mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (9); ++ if (mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (10); ++ if (mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (11); ++ if (mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (12); + +- /* Check small op */ +- mpfr_set_str1 (x, "1@-1"); +- if (!mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check Zero */ ++ MPFR_SET_ZERO (x); ++ if (!mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (13); ++ if (!mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (14); ++ if (!mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (15); ++ if (!mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (16); ++ if (!mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (17); ++ if (!mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (18); + +- /* Check 17 */ +- mpfr_set_ui (x, 17, MPFR_RNDN); +- if (!mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check small positive op */ ++ mpfr_set_str1 (x, "1@-1"); ++ if (!mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (19); ++ if (!mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (20); ++ if (!mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (21); ++ if (!mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (22); ++ if (!mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (23); ++ if (!mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (24); + +- /* Check all other values */ +- mpfr_set_ui (x, ULONG_MAX, MPFR_RNDN); +- mpfr_mul_2exp (x, x, 1, MPFR_RNDN); +- if (mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR1; +- mpfr_mul_2exp (x, x, 40, MPFR_RNDN); +- if (mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR1; ++ /* Check 17 */ ++ mpfr_set_ui (x, 17, MPFR_RNDN); ++ if (!mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (25); ++ if (!mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (26); ++ if (!mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (27); ++ if (!mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (28); ++ if (!mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (29); ++ if (!mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (30); + +- mpfr_set_ui (x, ULONG_MAX, MPFR_RNDN); +- if (!mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_ui (x, LONG_MAX, MPFR_RNDN); +- if (!mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_ui (x, UINT_MAX, MPFR_RNDN); +- if (!mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_ui (x, INT_MAX, MPFR_RNDN); +- if (!mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_ui (x, USHRT_MAX, MPFR_RNDN); +- if (!mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_ui (x, SHRT_MAX, MPFR_RNDN); +- if (!mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check all other values */ ++ mpfr_set_ui (x, ULONG_MAX, MPFR_RNDN); ++ mpfr_mul_2exp (x, x, 1, MPFR_RNDN); ++ if (mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (31); ++ if (mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (32); ++ mpfr_mul_2exp (x, x, 40, MPFR_RNDN); ++ if (mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (33); ++ if (mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (34); ++ if (mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (35); ++ if (mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (36); ++ if (mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (37); + +- mpfr_set_si (x, 1, MPFR_RNDN); +- if (!mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR2; ++ mpfr_set_ui (x, ULONG_MAX, MPFR_RNDN); ++ if (!mpfr_fits_ulong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (38); ++ mpfr_set_ui (x, LONG_MAX, MPFR_RNDN); ++ if (!mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (39); ++ mpfr_set_ui (x, UINT_MAX, MPFR_RNDN); ++ if (!mpfr_fits_uint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (40); ++ mpfr_set_ui (x, INT_MAX, MPFR_RNDN); ++ if (!mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (41); ++ mpfr_set_ui (x, USHRT_MAX, MPFR_RNDN); ++ if (!mpfr_fits_ushort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (42); ++ mpfr_set_ui (x, SHRT_MAX, MPFR_RNDN); ++ if (!mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (43); + +- /* Check negative value */ +- mpfr_set_si (x, -1, MPFR_RNDN); +- if (!mpfr_fits_sint_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_sshort_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_slong_p (x, MPFR_RNDN)) +- ERROR2; +- if (mpfr_fits_uint_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_ushort_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_ulong_p (x, MPFR_RNDN)) +- ERROR1; ++ mpfr_set_si (x, 1, MPFR_RNDN); ++ if (!mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (44); ++ if (!mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (45); ++ ++ /* Check negative op */ ++ for (i = 1; i <= 4; i++) ++ { ++ int inv; ++ ++ mpfr_set_si_2exp (x, -i, -2, MPFR_RNDN); ++ mpfr_rint (y, x, (mpfr_rnd_t) r); ++ inv = MPFR_NOTZERO (y); ++ if (!mpfr_fits_ulong_p (x, (mpfr_rnd_t) r) ^ inv) ++ ERROR1 (46); ++ if (!mpfr_fits_slong_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (47); ++ if (!mpfr_fits_uint_p (x, (mpfr_rnd_t) r) ^ inv) ++ ERROR1 (48); ++ if (!mpfr_fits_sint_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (49); ++ if (!mpfr_fits_ushort_p (x, (mpfr_rnd_t) r) ^ inv) ++ ERROR1 (50); ++ if (!mpfr_fits_sshort_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (51); ++ } ++ } + + mpfr_clear (x); ++ mpfr_clear (y); + + check_intmax (); + +@@ -189,85 +210,98 @@ + return 0; + } + +-static void check_intmax (void) ++static void ++check_intmax (void) + { + #ifdef _MPFR_H_HAVE_INTMAX_T +- mpfr_t x; ++ mpfr_t x, y; ++ int i, r; + +- mpfr_init2 (x, sizeof (uintmax_t)*CHAR_BIT); ++ mpfr_init2 (x, sizeof (uintmax_t) * CHAR_BIT); ++ mpfr_init2 (y, 8); + +- /* Check NAN */ +- mpfr_set_nan (x); +- if (mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR1; ++ RND_LOOP (r) ++ { ++ /* Check NAN */ ++ mpfr_set_nan (x); ++ if (mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (52); ++ if (mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (53); + +- /* Check INF */ +- mpfr_set_inf (x, 1); +- if (mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR1; ++ /* Check INF */ ++ mpfr_set_inf (x, 1); ++ if (mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (54); ++ if (mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (55); + +- /* Check Zero */ +- MPFR_SET_ZERO (x); +- if (!mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check Zero */ ++ MPFR_SET_ZERO (x); ++ if (!mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (56); ++ if (!mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (57); + +- /* Check small op */ +- mpfr_set_str1 (x, "1@-1"); +- if (!mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check positive small op */ ++ mpfr_set_str1 (x, "1@-1"); ++ if (!mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (58); ++ if (!mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (59); + +- /* Check 17 */ +- mpfr_set_ui (x, 17, MPFR_RNDN); +- if (!mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR2; +- if (!mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR2; ++ /* Check 17 */ ++ mpfr_set_ui (x, 17, MPFR_RNDN); ++ if (!mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (60); ++ if (!mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (61); + +- /* Check hugest */ +- mpfr_set_ui_2exp (x, 42, sizeof (uintmax_t) * 32, MPFR_RNDN); +- if (mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR1; +- if (mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR1; ++ /* Check hugest */ ++ mpfr_set_ui_2exp (x, 42, sizeof (uintmax_t) * 32, MPFR_RNDN); ++ if (mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (62); ++ if (mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (63); + +- /* Check all other values */ +- mpfr_set_uj (x, MPFR_UINTMAX_MAX, MPFR_RNDN); +- mpfr_add_ui (x, x, 1, MPFR_RNDN); +- if (mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR1; +- mpfr_set_uj (x, MPFR_UINTMAX_MAX, MPFR_RNDN); +- if (!mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_sj (x, MPFR_INTMAX_MAX, MPFR_RNDN); +- mpfr_add_ui (x, x, 1, MPFR_RNDN); +- if (mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR1; +- mpfr_set_sj (x, MPFR_INTMAX_MAX, MPFR_RNDN); +- if (!mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_set_sj (x, MPFR_INTMAX_MIN, MPFR_RNDN); +- if (!mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR2; +- mpfr_sub_ui (x, x, 1, MPFR_RNDN); +- if (mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR1; ++ /* Check all other values */ ++ mpfr_set_uj (x, MPFR_UINTMAX_MAX, MPFR_RNDN); ++ mpfr_add_ui (x, x, 1, MPFR_RNDN); ++ if (mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (64); ++ mpfr_set_uj (x, MPFR_UINTMAX_MAX, MPFR_RNDN); ++ if (!mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (65); ++ mpfr_set_sj (x, MPFR_INTMAX_MAX, MPFR_RNDN); ++ mpfr_add_ui (x, x, 1, MPFR_RNDN); ++ if (mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (66); ++ mpfr_set_sj (x, MPFR_INTMAX_MAX, MPFR_RNDN); ++ if (!mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (67); ++ mpfr_set_sj (x, MPFR_INTMAX_MIN, MPFR_RNDN); ++ if (!mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (68); ++ mpfr_sub_ui (x, x, 1, MPFR_RNDN); ++ if (mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (69); + +- /* Check negative value */ +- mpfr_set_si (x, -1, MPFR_RNDN); +- if (!mpfr_fits_intmax_p (x, MPFR_RNDN)) +- ERROR2; +- if (mpfr_fits_uintmax_p (x, MPFR_RNDN)) +- ERROR1; ++ /* Check negative op */ ++ for (i = 1; i <= 4; i++) ++ { ++ int inv; ++ ++ mpfr_set_si_2exp (x, -i, -2, MPFR_RNDN); ++ mpfr_rint (y, x, (mpfr_rnd_t) r); ++ inv = MPFR_NOTZERO (y); ++ if (!mpfr_fits_uintmax_p (x, (mpfr_rnd_t) r) ^ inv) ++ ERROR1 (70); ++ if (!mpfr_fits_intmax_p (x, (mpfr_rnd_t) r)) ++ ERROR1 (71); ++ } ++ } + + mpfr_clear (x); ++ mpfr_clear (y); + #endif + } +- +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2013-10-09 13:34:21.000000000 +0000 ++++ mpfr-3.1.2-b/PATCHES 2013-10-09 13:34:21.000000000 +0000 +@@ -0,0 +1 @@ ++clang-divby0 +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/VERSION 2013-10-09 13:34:21.000000000 +0000 +@@ -1 +1 @@ +-3.1.2-p2 ++3.1.2-p3 +diff -Naurd mpfr-3.1.2-a/src/mpfr-impl.h mpfr-3.1.2-b/src/mpfr-impl.h +--- mpfr-3.1.2-a/src/mpfr-impl.h 2013-03-13 15:37:36.000000000 +0000 ++++ mpfr-3.1.2-b/src/mpfr-impl.h 2013-10-09 13:34:21.000000000 +0000 +@@ -468,8 +468,16 @@ + #define MPFR_LIMBS_PER_FLT ((IEEE_FLT_MANT_DIG-1)/GMP_NUMB_BITS+1) + + /* Visual C++ doesn't support +1.0/0.0, -1.0/0.0 and 0.0/0.0 +- at compile time. */ +-#if defined(_MSC_VER) && defined(_WIN32) && (_MSC_VER >= 1200) ++ at compile time. ++ Clang with -fsanitize=undefined is a bit similar due to a bug: ++ http://llvm.org/bugs/show_bug.cgi?id=17381 ++ but even without its sanitizer, it may be better to use the ++ double_zero version until IEEE 754 division by zero is properly ++ supported: ++ http://llvm.org/bugs/show_bug.cgi?id=17000 ++*/ ++#if (defined(_MSC_VER) && defined(_WIN32) && (_MSC_VER >= 1200)) || \ ++ defined(__clang__) + static double double_zero = 0.0; + # define DBL_NAN (double_zero/double_zero) + # define DBL_POS_INF ((double) 1.0/double_zero) +@@ -501,6 +509,8 @@ + (with Xcode 2.4.1, i.e. the latest one). */ + #define LVALUE(x) (&(x) == &(x) || &(x) != &(x)) + #define DOUBLE_ISINF(x) (LVALUE(x) && ((x) > DBL_MAX || (x) < -DBL_MAX)) ++/* The DOUBLE_ISNAN(x) macro is also valid on long double x ++ (assuming that the compiler isn't too broken). */ + #ifdef MPFR_NANISNAN + /* Avoid MIPSpro / IRIX64 / gcc -ffast-math (incorrect) optimizations. + The + must not be replaced by a ||. With gcc -ffast-math, NaN is +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2013-10-09 13:34:21.000000000 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p2" ++#define MPFR_VERSION_STRING "3.1.2-p3" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2013-09-26 10:52:52.000000000 +0000 ++++ mpfr-3.1.2-b/src/version.c 2013-10-09 13:34:21.000000000 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p2"; ++ return "3.1.2-p3"; + } +diff -Naurd mpfr-3.1.2-a/tests/tget_flt.c mpfr-3.1.2-b/tests/tget_flt.c +--- mpfr-3.1.2-a/tests/tget_flt.c 2013-03-13 15:37:44.000000000 +0000 ++++ mpfr-3.1.2-b/tests/tget_flt.c 2013-10-09 13:34:21.000000000 +0000 +@@ -28,9 +28,17 @@ + main (void) + { + mpfr_t x, y; +- float f, g, infp; ++ float f, g; + int i; ++#if !defined(MPFR_ERRDIVZERO) ++ float infp; ++#endif ++ ++ tests_start_mpfr (); + ++#if !defined(MPFR_ERRDIVZERO) ++ /* The definition of DBL_POS_INF involves a division by 0. This makes ++ "clang -O2 -fsanitize=undefined -fno-sanitize-recover" fail. */ + infp = (float) DBL_POS_INF; + if (infp * 0.5 != infp) + { +@@ -38,8 +46,7 @@ + fprintf (stderr, "(this is probably a compiler bug, please report)\n"); + exit (1); + } +- +- tests_start_mpfr (); ++#endif + + mpfr_init2 (x, 24); + mpfr_init2 (y, 24); +@@ -353,6 +360,7 @@ + printf ("expected %.8e, got %.8e\n", g, f); + exit (1); + } ++#if !defined(MPFR_ERRDIVZERO) + f = mpfr_get_flt (x, MPFR_RNDN); /* first round to 2^128 (even rule), + thus we should get +Inf */ + g = infp; +@@ -376,6 +384,7 @@ + printf ("expected %.8e, got %.8e\n", g, f); + exit (1); + } ++#endif + + mpfr_clear (x); + mpfr_clear (y); +diff -Naurd mpfr-3.1.2-a/tests/tset_ld.c mpfr-3.1.2-b/tests/tset_ld.c +--- mpfr-3.1.2-a/tests/tset_ld.c 2013-03-13 15:37:44.000000000 +0000 ++++ mpfr-3.1.2-b/tests/tset_ld.c 2013-10-09 13:34:21.000000000 +0000 +@@ -47,8 +47,11 @@ + static int + Isnan_ld (long double d) + { +- double e = (double) d; +- if (DOUBLE_ISNAN (e)) ++ /* Do not convert d to double as this can give an overflow, which ++ may confuse compilers without IEEE 754 support (such as clang ++ -fsanitize=undefined), or trigger a trap if enabled. ++ The DOUBLE_ISNAN macro should work fine on long double. */ ++ if (DOUBLE_ISNAN (d)) + return 1; + LONGDOUBLE_NAN_ACTION (d, goto yes); + return 0; +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2013-11-15 00:51:49.211333830 +0000 ++++ mpfr-3.1.2-b/PATCHES 2013-11-15 00:51:49.323334999 +0000 +@@ -0,0 +1 @@ ++printf-alt0 +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2013-11-15 00:51:49.211333830 +0000 ++++ mpfr-3.1.2-b/VERSION 2013-11-15 00:51:49.323334999 +0000 +@@ -1 +1 @@ +-3.1.2-p3 ++3.1.2-p4 +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2013-11-15 00:51:49.211333830 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2013-11-15 00:51:49.323334999 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p3" ++#define MPFR_VERSION_STRING "3.1.2-p4" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/vasprintf.c mpfr-3.1.2-b/src/vasprintf.c +--- mpfr-3.1.2-a/src/vasprintf.c 2013-03-13 15:37:37.000000000 +0000 ++++ mpfr-3.1.2-b/src/vasprintf.c 2013-11-15 00:51:49.267334408 +0000 +@@ -1040,7 +1040,7 @@ + } + + /* Determine the different parts of the string representation of the regular +- number P when SPEC.SPEC is 'e', 'E', 'g', or 'G'. ++ number P when spec.spec is 'e', 'E', 'g', or 'G'. + DEC_INFO contains the previously computed exponent and string or is NULL. + + return -1 if some field > INT_MAX */ +@@ -1167,7 +1167,7 @@ + } + + /* Determine the different parts of the string representation of the regular +- number P when SPEC.SPEC is 'f', 'F', 'g', or 'G'. ++ number P when spec.spec is 'f', 'F', 'g', or 'G'. + DEC_INFO contains the previously computed exponent and string or is NULL. + + return -1 if some field of number_parts is greater than INT_MAX */ +@@ -1559,7 +1559,7 @@ + /* fractional part */ + { + np->point = MPFR_DECIMAL_POINT; +- np->fp_trailing_zeros = (spec.spec == 'g' && spec.spec == 'G') ? ++ np->fp_trailing_zeros = (spec.spec == 'g' || spec.spec == 'G') ? + spec.prec - 1 : spec.prec; + } + else if (spec.alt) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2013-11-15 00:51:49.211333830 +0000 ++++ mpfr-3.1.2-b/src/version.c 2013-11-15 00:51:49.323334999 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p3"; ++ return "3.1.2-p4"; + } +diff -Naurd mpfr-3.1.2-a/tests/tsprintf.c mpfr-3.1.2-b/tests/tsprintf.c +--- mpfr-3.1.2-a/tests/tsprintf.c 2013-03-13 15:37:44.000000000 +0000 ++++ mpfr-3.1.2-b/tests/tsprintf.c 2013-11-15 00:51:49.267334408 +0000 +@@ -456,10 +456,16 @@ + check_sprintf ("1.999900 ", "%-#10.7RG", x); + check_sprintf ("1.9999 ", "%-10.7RG", x); + mpfr_set_ui (x, 1, MPFR_RNDN); ++ check_sprintf ("1.", "%#.1Rg", x); ++ check_sprintf ("1. ", "%-#5.1Rg", x); ++ check_sprintf (" 1.0", "%#5.2Rg", x); + check_sprintf ("1.00000000000000000000000000000", "%#.30Rg", x); + check_sprintf ("1", "%.30Rg", x); + mpfr_set_ui (x, 0, MPFR_RNDN); +- check_sprintf ("0.000000000000000000000000000000", "%#.30Rg", x); ++ check_sprintf ("0.", "%#.1Rg", x); ++ check_sprintf ("0. ", "%-#5.1Rg", x); ++ check_sprintf (" 0.0", "%#5.2Rg", x); ++ check_sprintf ("0.00000000000000000000000000000", "%#.30Rg", x); + check_sprintf ("0", "%.30Rg", x); + + /* following tests with precision 53 bits */ +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2013-12-01 11:07:49.575329762 +0000 ++++ mpfr-3.1.2-b/PATCHES 2013-12-01 11:07:49.751331625 +0000 +@@ -0,0 +1 @@ ++custom_init_set +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2013-12-01 11:07:49.571329714 +0000 ++++ mpfr-3.1.2-b/VERSION 2013-12-01 11:07:49.747331585 +0000 +@@ -1 +1 @@ +-3.1.2-p4 ++3.1.2-p5 +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2013-12-01 11:07:49.571329714 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2013-12-01 11:07:49.747331585 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p4" ++#define MPFR_VERSION_STRING "3.1.2-p5" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +@@ -861,7 +861,7 @@ + _t = (mpfr_kind_t) _k; \ + _s = 1; \ + } else { \ +- _t = (mpfr_kind_t) -k; \ ++ _t = (mpfr_kind_t) - _k; \ + _s = -1; \ + } \ + _e = _t == MPFR_REGULAR_KIND ? (e) : \ +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2013-12-01 11:07:49.575329762 +0000 ++++ mpfr-3.1.2-b/src/version.c 2013-12-01 11:07:49.747331585 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p4"; ++ return "3.1.2-p5"; + } +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2014-04-15 21:56:49.609057464 +0000 ++++ mpfr-3.1.2-b/PATCHES 2014-04-15 21:56:49.697059857 +0000 +@@ -0,0 +1 @@ ++li2-return +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2014-04-15 21:56:49.609057464 +0000 ++++ mpfr-3.1.2-b/VERSION 2014-04-15 21:56:49.697059857 +0000 +@@ -1 +1 @@ +-3.1.2-p5 ++3.1.2-p6 +diff -Naurd mpfr-3.1.2-a/src/li2.c mpfr-3.1.2-b/src/li2.c +--- mpfr-3.1.2-a/src/li2.c 2013-03-13 15:37:32.000000000 +0000 ++++ mpfr-3.1.2-b/src/li2.c 2014-04-15 21:56:49.653058661 +0000 +@@ -630,5 +630,5 @@ + return mpfr_check_range (y, inexact, rnd_mode); + } + +- MPFR_ASSERTN (0); /* should never reach this point */ ++ MPFR_RET_NEVER_GO_HERE (); + } +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2014-04-15 21:56:49.609057464 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2014-04-15 21:56:49.697059857 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p5" ++#define MPFR_VERSION_STRING "3.1.2-p6" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2014-04-15 21:56:49.609057464 +0000 ++++ mpfr-3.1.2-b/src/version.c 2014-04-15 21:56:49.697059857 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p5"; ++ return "3.1.2-p6"; + } +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2014-04-15 22:04:57.090286262 +0000 ++++ mpfr-3.1.2-b/PATCHES 2014-04-15 22:04:57.162288198 +0000 +@@ -0,0 +1 @@ ++exp3 +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2014-04-15 22:04:57.086286154 +0000 ++++ mpfr-3.1.2-b/VERSION 2014-04-15 22:04:57.162288198 +0000 +@@ -1 +1 @@ +-3.1.2-p6 ++3.1.2-p7 +diff -Naurd mpfr-3.1.2-a/src/exp3.c mpfr-3.1.2-b/src/exp3.c +--- mpfr-3.1.2-a/src/exp3.c 2013-03-13 15:37:34.000000000 +0000 ++++ mpfr-3.1.2-b/src/exp3.c 2014-04-15 22:04:57.126287230 +0000 +@@ -283,7 +283,7 @@ + } + } + +- if (mpfr_can_round (shift_x > 0 ? t : tmp, realprec, MPFR_RNDD, MPFR_RNDZ, ++ if (mpfr_can_round (shift_x > 0 ? t : tmp, realprec, MPFR_RNDN, MPFR_RNDZ, + MPFR_PREC(y) + (rnd_mode == MPFR_RNDN))) + { + inexact = mpfr_set (y, shift_x > 0 ? t : tmp, rnd_mode); +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2014-04-15 22:04:57.086286154 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2014-04-15 22:04:57.162288198 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p6" ++#define MPFR_VERSION_STRING "3.1.2-p7" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2014-04-15 22:04:57.090286262 +0000 ++++ mpfr-3.1.2-b/src/version.c 2014-04-15 22:04:57.162288198 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p6"; ++ return "3.1.2-p7"; + } +diff -Naurd mpfr-3.1.2-a/tests/texp.c mpfr-3.1.2-b/tests/texp.c +--- mpfr-3.1.2-a/tests/texp.c 2013-03-13 15:37:44.000000000 +0000 ++++ mpfr-3.1.2-b/tests/texp.c 2014-04-15 22:04:57.126287230 +0000 +@@ -150,6 +150,22 @@ + exit (1); + } + ++ mpfr_set_prec (x, 118); ++ mpfr_set_str_binary (x, "0.1110010100011101010000111110011000000000000000000000000000000000000000000000000000000000000000000000000000000000000000E-86"); ++ mpfr_set_prec (y, 118); ++ mpfr_exp_2 (y, x, MPFR_RNDU); ++ mpfr_exp_3 (x, x, MPFR_RNDU); ++ if (mpfr_cmp (x, y)) ++ { ++ printf ("mpfr_exp_2 and mpfr_exp_3 differ for prec=118\n"); ++ printf ("mpfr_exp_2 gives "); ++ mpfr_out_str (stdout, 2, 0, y, MPFR_RNDN); ++ printf ("\nmpfr_exp_3 gives "); ++ mpfr_out_str (stdout, 2, 0, x, MPFR_RNDN); ++ printf ("\n"); ++ exit (1); ++ } ++ + mpfr_clear (x); + mpfr_clear (y); + return 0; +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2014-04-15 22:20:32.243481506 +0000 ++++ mpfr-3.1.2-b/PATCHES 2014-04-15 22:22:32.418722707 +0000 +@@ -0,0 +1 @@ ++gmp6-compat +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2014-04-15 22:20:20.755171478 +0000 ++++ mpfr-3.1.2-b/VERSION 2014-04-15 22:21:45.225450147 +0000 +@@ -1 +1 @@ +-3.1.2-p7 ++3.1.2-p8 +diff -Naurd mpfr-3.1.2-a/configure mpfr-3.1.2-b/configure +--- mpfr-3.1.2-a/configure 2013-03-13 15:38:20.000000000 +0000 ++++ mpfr-3.1.2-b/configure 2014-04-15 22:21:38.821277476 +0000 +@@ -14545,26 +14545,30 @@ + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext + fi + +-if test "$use_gmp_build" = yes ; then +- { $as_echo "$as_me:${as_lineno-$LINENO}: checking for valid GMP_NUMB_BITS" >&5 +-$as_echo_n "checking for valid GMP_NUMB_BITS... " >&6; } +- if test "$cross_compiling" = yes; then : ++{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for GMP_NUMB_BITS and sizeof(mp_limb_t) consistency" >&5 ++$as_echo_n "checking for GMP_NUMB_BITS and sizeof(mp_limb_t) consistency... " >&6; } ++if test "$cross_compiling" = yes; then : + { $as_echo "$as_me:${as_lineno-$LINENO}: result: can't test" >&5 + $as_echo "can't test" >&6; } + else + cat confdefs.h - <<_ACEOF >conftest.$ac_ext + /* end confdefs.h. */ + ++#include + #include + #include "gmp.h" +-#include "gmp-impl.h" + + int + main () + { + +- return GMP_NUMB_BITS == BYTES_PER_MP_LIMB * CHAR_BIT +- && sizeof(mp_limb_t) == BYTES_PER_MP_LIMB ? 0 : 1; ++ if (GMP_NUMB_BITS == sizeof(mp_limb_t) * CHAR_BIT) ++ return 0; ++ fprintf (stderr, "GMP_NUMB_BITS = %ld\n", (long) GMP_NUMB_BITS); ++ fprintf (stderr, "sizeof(mp_limb_t) = %ld\n", (long) sizeof(mp_limb_t)); ++ fprintf (stderr, "sizeof(mp_limb_t) * CHAR_BIT = %ld != GMP_NUMB_BITS\n", ++ (long) (sizeof(mp_limb_t) * CHAR_BIT)); ++ return 1; + + ; + return 0; +@@ -14577,14 +14581,14 @@ + + { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + $as_echo "no" >&6; } +- as_fn_error $? "GMP_NUMB_BITS is incorrect. +-You probably need to change some of the GMP or MPFR compile options." "$LINENO" 5 ++ as_fn_error $? "GMP_NUMB_BITS and sizeof(mp_limb_t) are not consistent. ++You probably need to change some of the GMP or MPFR compile options. ++See 'config.log' for details (search for GMP_NUMB_BITS)." "$LINENO" 5 + fi + rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ + conftest.$ac_objext conftest.beam conftest.$ac_ext + fi + +-fi + + + if test "$dont_link_with_gmp" = yes ; then +diff -Naurd mpfr-3.1.2-a/configure.ac mpfr-3.1.2-b/configure.ac +--- mpfr-3.1.2-a/configure.ac 2013-03-13 15:37:46.000000000 +0000 ++++ mpfr-3.1.2-b/configure.ac 2013-03-13 15:37:46.000000000 +0000 +@@ -435,23 +435,29 @@ + ]) + fi + +-dnl Check for valid GMP_NUMB_BITS and BYTES_PER_MP_LIMB ++dnl Check for GMP_NUMB_BITS and sizeof(mp_limb_t) consistency. ++dnl Problems may occur if gmp.h was generated with some ABI ++dnl and is used with another ABI (or if nails are used). + dnl This test doesn't need to link with libgmp (at least it shouldn't). +-if test "$use_gmp_build" = yes ; then +- AC_MSG_CHECKING(for valid GMP_NUMB_BITS) +- AC_RUN_IFELSE([AC_LANG_PROGRAM([[ ++AC_MSG_CHECKING(for GMP_NUMB_BITS and sizeof(mp_limb_t) consistency) ++AC_RUN_IFELSE([AC_LANG_PROGRAM([[ ++#include + #include + #include "gmp.h" +-#include "gmp-impl.h" + ]], [[ +- return GMP_NUMB_BITS == BYTES_PER_MP_LIMB * CHAR_BIT +- && sizeof(mp_limb_t) == BYTES_PER_MP_LIMB ? 0 : 1; ++ if (GMP_NUMB_BITS == sizeof(mp_limb_t) * CHAR_BIT) ++ return 0; ++ fprintf (stderr, "GMP_NUMB_BITS = %ld\n", (long) GMP_NUMB_BITS); ++ fprintf (stderr, "sizeof(mp_limb_t) = %ld\n", (long) sizeof(mp_limb_t)); ++ fprintf (stderr, "sizeof(mp_limb_t) * CHAR_BIT = %ld != GMP_NUMB_BITS\n", ++ (long) (sizeof(mp_limb_t) * CHAR_BIT)); ++ return 1; + ]])], [AC_MSG_RESULT(yes)], [ + AC_MSG_RESULT(no) +- AC_MSG_ERROR([GMP_NUMB_BITS is incorrect. +-You probably need to change some of the GMP or MPFR compile options.])], ++ AC_MSG_ERROR([GMP_NUMB_BITS and sizeof(mp_limb_t) are not consistent. ++You probably need to change some of the GMP or MPFR compile options. ++See 'config.log' for details (search for GMP_NUMB_BITS).])], + [AC_MSG_RESULT([can't test])]) +-fi + + + dnl We really need to link using libtool. But it is impossible with the current +diff -Naurd mpfr-3.1.2-a/src/init2.c mpfr-3.1.2-b/src/init2.c +--- mpfr-3.1.2-a/src/init2.c 2013-03-13 15:37:32.000000000 +0000 ++++ mpfr-3.1.2-b/src/init2.c 2014-04-15 22:21:06.220398489 +0000 +@@ -30,11 +30,11 @@ + + /* Check if we can represent the number of limbs + * associated to the maximum of mpfr_prec_t*/ +- MPFR_ASSERTN( MP_SIZE_T_MAX >= (MPFR_PREC_MAX/BYTES_PER_MP_LIMB) ); ++ MPFR_ASSERTN( MP_SIZE_T_MAX >= (MPFR_PREC_MAX/MPFR_BYTES_PER_MP_LIMB) ); + +- /* Check for correct GMP_NUMB_BITS and BYTES_PER_MP_LIMB */ +- MPFR_ASSERTN( GMP_NUMB_BITS == BYTES_PER_MP_LIMB * CHAR_BIT +- && sizeof(mp_limb_t) == BYTES_PER_MP_LIMB ); ++ /* Check for correct GMP_NUMB_BITS and MPFR_BYTES_PER_MP_LIMB */ ++ MPFR_ASSERTN( GMP_NUMB_BITS == MPFR_BYTES_PER_MP_LIMB * CHAR_BIT ++ && sizeof(mp_limb_t) == MPFR_BYTES_PER_MP_LIMB ); + + MPFR_ASSERTN (mp_bits_per_limb == GMP_NUMB_BITS); + +diff -Naurd mpfr-3.1.2-a/src/mpfr-gmp.h mpfr-3.1.2-b/src/mpfr-gmp.h +--- mpfr-3.1.2-a/src/mpfr-gmp.h 2013-03-13 15:37:32.000000000 +0000 ++++ mpfr-3.1.2-b/src/mpfr-gmp.h 2014-04-15 22:21:06.220398489 +0000 +@@ -72,7 +72,6 @@ + #endif + + /* Define some macros */ +-#define BYTES_PER_MP_LIMB (GMP_NUMB_BITS/CHAR_BIT) + + #define MP_LIMB_T_MAX (~(mp_limb_t)0) + +@@ -96,19 +95,19 @@ + #define SHRT_HIGHBIT SHRT_MIN + + /* MP_LIMB macros */ +-#define MPN_ZERO(dst, n) memset((dst), 0, (n)*BYTES_PER_MP_LIMB) +-#define MPN_COPY_DECR(dst,src,n) memmove((dst),(src),(n)*BYTES_PER_MP_LIMB) +-#define MPN_COPY_INCR(dst,src,n) memmove((dst),(src),(n)*BYTES_PER_MP_LIMB) ++#define MPN_ZERO(dst, n) memset((dst), 0, (n)*MPFR_BYTES_PER_MP_LIMB) ++#define MPN_COPY_DECR(dst,src,n) memmove((dst),(src),(n)*MPFR_BYTES_PER_MP_LIMB) ++#define MPN_COPY_INCR(dst,src,n) memmove((dst),(src),(n)*MPFR_BYTES_PER_MP_LIMB) + #define MPN_COPY(dst,src,n) \ + do \ + { \ + if ((dst) != (src)) \ + { \ + MPFR_ASSERTD ((char *) (dst) >= (char *) (src) + \ +- (n) * BYTES_PER_MP_LIMB || \ ++ (n) * MPFR_BYTES_PER_MP_LIMB || \ + (char *) (src) >= (char *) (dst) + \ +- (n) * BYTES_PER_MP_LIMB); \ +- memcpy ((dst), (src), (n) * BYTES_PER_MP_LIMB); \ ++ (n) * MPFR_BYTES_PER_MP_LIMB); \ ++ memcpy ((dst), (src), (n) * MPFR_BYTES_PER_MP_LIMB); \ + } \ + } \ + while (0) +diff -Naurd mpfr-3.1.2-a/src/mpfr-impl.h mpfr-3.1.2-b/src/mpfr-impl.h +--- mpfr-3.1.2-a/src/mpfr-impl.h 2013-10-09 13:34:21.000000000 +0000 ++++ mpfr-3.1.2-b/src/mpfr-impl.h 2014-04-15 22:21:06.220398489 +0000 +@@ -191,7 +191,7 @@ + # endif + #endif + +- ++#define MPFR_BYTES_PER_MP_LIMB (GMP_NUMB_BITS/CHAR_BIT) + + /****************************************************** + ******************** Check GMP *********************** +@@ -930,7 +930,7 @@ + #define MPFR_SET_ALLOC_SIZE(x, n) \ + ( ((mp_size_t*) MPFR_MANT(x))[-1] = n) + #define MPFR_MALLOC_SIZE(s) \ +- ( sizeof(mpfr_size_limb_t) + BYTES_PER_MP_LIMB * ((size_t) s) ) ++ ( sizeof(mpfr_size_limb_t) + MPFR_BYTES_PER_MP_LIMB * ((size_t) s) ) + #define MPFR_SET_MANT_PTR(x,p) \ + (MPFR_MANT(x) = (mp_limb_t*) ((mpfr_size_limb_t*) p + 1)) + #define MPFR_GET_REAL_PTR(x) \ +@@ -964,7 +964,7 @@ + #endif + + #define MPFR_TMP_LIMBS_ALLOC(N) \ +- ((mp_limb_t *) MPFR_TMP_ALLOC ((size_t) (N) * BYTES_PER_MP_LIMB)) ++ ((mp_limb_t *) MPFR_TMP_ALLOC ((size_t) (N) * MPFR_BYTES_PER_MP_LIMB)) + + /* temporary allocate 1 limb at xp, and initialize mpfr variable x */ + /* The temporary var doesn't have any size field, but it doesn't matter +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2014-04-15 22:20:20.755171478 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2014-04-15 22:21:45.225450147 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p7" ++#define MPFR_VERSION_STRING "3.1.2-p8" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/mul.c mpfr-3.1.2-b/src/mul.c +--- mpfr-3.1.2-a/src/mul.c 2013-03-13 15:37:37.000000000 +0000 ++++ mpfr-3.1.2-b/src/mul.c 2014-04-15 22:21:06.224398597 +0000 +@@ -106,7 +106,7 @@ + MPFR_ASSERTD(tn <= k); + + /* Check for no size_t overflow*/ +- MPFR_ASSERTD((size_t) k <= ((size_t) -1) / BYTES_PER_MP_LIMB); ++ MPFR_ASSERTD((size_t) k <= ((size_t) -1) / MPFR_BYTES_PER_MP_LIMB); + MPFR_TMP_MARK(marker); + tmp = MPFR_TMP_LIMBS_ALLOC (k); + +@@ -301,7 +301,7 @@ + MPFR_ASSERTD (tn <= k); /* tn <= k, thus no int overflow */ + + /* Check for no size_t overflow*/ +- MPFR_ASSERTD ((size_t) k <= ((size_t) -1) / BYTES_PER_MP_LIMB); ++ MPFR_ASSERTD ((size_t) k <= ((size_t) -1) / MPFR_BYTES_PER_MP_LIMB); + MPFR_TMP_MARK (marker); + tmp = MPFR_TMP_LIMBS_ALLOC (k); + +diff -Naurd mpfr-3.1.2-a/src/stack_interface.c mpfr-3.1.2-b/src/stack_interface.c +--- mpfr-3.1.2-a/src/stack_interface.c 2013-03-13 15:37:32.000000000 +0000 ++++ mpfr-3.1.2-b/src/stack_interface.c 2014-04-15 22:21:06.220398489 +0000 +@@ -26,7 +26,7 @@ + size_t + mpfr_custom_get_size (mpfr_prec_t prec) + { +- return MPFR_PREC2LIMBS (prec) * BYTES_PER_MP_LIMB; ++ return MPFR_PREC2LIMBS (prec) * MPFR_BYTES_PER_MP_LIMB; + } + + #undef mpfr_custom_init +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2014-04-15 22:20:20.755171478 +0000 ++++ mpfr-3.1.2-b/src/version.c 2014-04-15 22:21:45.225450147 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p7"; ++ return "3.1.2-p8"; + } +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2014-06-30 15:15:25.533266905 +0000 ++++ mpfr-3.1.2-b/PATCHES 2014-06-30 15:15:25.617269178 +0000 +@@ -0,0 +1 @@ ++div-overflow +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2014-06-30 15:15:25.529266797 +0000 ++++ mpfr-3.1.2-b/VERSION 2014-06-30 15:15:25.617269178 +0000 +@@ -1 +1 @@ +-3.1.2-p8 ++3.1.2-p9 +diff -Naurd mpfr-3.1.2-a/src/div.c mpfr-3.1.2-b/src/div.c +--- mpfr-3.1.2-a/src/div.c 2013-03-13 15:37:33.000000000 +0000 ++++ mpfr-3.1.2-b/src/div.c 2014-06-30 15:15:25.585268312 +0000 +@@ -750,7 +750,9 @@ + truncate_check_qh: + if (qh) + { +- qexp ++; ++ if (MPFR_LIKELY (qexp < MPFR_EXP_MAX)) ++ qexp ++; ++ /* else qexp is now incorrect, but one will still get an overflow */ + q0p[q0size - 1] = MPFR_LIMB_HIGHBIT; + } + goto truncate; +@@ -765,7 +767,9 @@ + inex = 1; /* always here */ + if (mpn_add_1 (q0p, q0p, q0size, MPFR_LIMB_ONE << sh)) + { +- qexp ++; ++ if (MPFR_LIKELY (qexp < MPFR_EXP_MAX)) ++ qexp ++; ++ /* else qexp is now incorrect, but one will still get an overflow */ + q0p[q0size - 1] = MPFR_LIMB_HIGHBIT; + } + +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2014-06-30 15:15:25.533266905 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2014-06-30 15:15:25.613269070 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p8" ++#define MPFR_VERSION_STRING "3.1.2-p9" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2014-06-30 15:15:25.533266905 +0000 ++++ mpfr-3.1.2-b/src/version.c 2014-06-30 15:15:25.613269070 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p8"; ++ return "3.1.2-p9"; + } +diff -Naurd mpfr-3.1.2-a/tests/tdiv.c mpfr-3.1.2-b/tests/tdiv.c +--- mpfr-3.1.2-a/tests/tdiv.c 2013-03-13 15:37:44.000000000 +0000 ++++ mpfr-3.1.2-b/tests/tdiv.c 2014-06-30 15:15:25.585268312 +0000 +@@ -1104,6 +1104,96 @@ + #define RAND_FUNCTION(x) mpfr_random2(x, MPFR_LIMB_SIZE (x), randlimb () % 100, RANDS) + #include "tgeneric.c" + ++static void ++test_extreme (void) ++{ ++ mpfr_t x, y, z; ++ mpfr_exp_t emin, emax; ++ mpfr_prec_t p[4] = { 8, 32, 64, 256 }; ++ int xi, yi, zi, j, r; ++ unsigned int flags, ex_flags; ++ ++ emin = mpfr_get_emin (); ++ emax = mpfr_get_emax (); ++ ++ mpfr_set_emin (MPFR_EMIN_MIN); ++ mpfr_set_emax (MPFR_EMAX_MAX); ++ ++ for (xi = 0; xi < 4; xi++) ++ { ++ mpfr_init2 (x, p[xi]); ++ mpfr_setmax (x, MPFR_EMAX_MAX); ++ MPFR_ASSERTN (mpfr_check (x)); ++ for (yi = 0; yi < 4; yi++) ++ { ++ mpfr_init2 (y, p[yi]); ++ mpfr_setmin (y, MPFR_EMIN_MIN); ++ for (j = 0; j < 2; j++) ++ { ++ MPFR_ASSERTN (mpfr_check (y)); ++ for (zi = 0; zi < 4; zi++) ++ { ++ mpfr_init2 (z, p[zi]); ++ RND_LOOP (r) ++ { ++ mpfr_clear_flags (); ++ mpfr_div (z, x, y, (mpfr_rnd_t) r); ++ flags = __gmpfr_flags; ++ MPFR_ASSERTN (mpfr_check (z)); ++ ex_flags = MPFR_FLAGS_OVERFLOW | MPFR_FLAGS_INEXACT; ++ if (flags != ex_flags) ++ { ++ printf ("Bad flags in test_extreme on z = a/b" ++ " with %s and\n", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) r)); ++ printf ("a = "); ++ mpfr_dump (x); ++ printf ("b = "); ++ mpfr_dump (y); ++ printf ("Expected flags:"); ++ flags_out (ex_flags); ++ printf ("Got flags: "); ++ flags_out (flags); ++ printf ("z = "); ++ mpfr_dump (z); ++ exit (1); ++ } ++ mpfr_clear_flags (); ++ mpfr_div (z, y, x, (mpfr_rnd_t) r); ++ flags = __gmpfr_flags; ++ MPFR_ASSERTN (mpfr_check (z)); ++ ex_flags = MPFR_FLAGS_UNDERFLOW | MPFR_FLAGS_INEXACT; ++ if (flags != ex_flags) ++ { ++ printf ("Bad flags in test_extreme on z = a/b" ++ " with %s and\n", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) r)); ++ printf ("a = "); ++ mpfr_dump (y); ++ printf ("b = "); ++ mpfr_dump (x); ++ printf ("Expected flags:"); ++ flags_out (ex_flags); ++ printf ("Got flags: "); ++ flags_out (flags); ++ printf ("z = "); ++ mpfr_dump (z); ++ exit (1); ++ } ++ } ++ mpfr_clear (z); ++ } /* zi */ ++ mpfr_nextabove (y); ++ } /* j */ ++ mpfr_clear (y); ++ } /* yi */ ++ mpfr_clear (x); ++ } /* xi */ ++ ++ set_emin (emin); ++ set_emax (emax); ++} ++ + int + main (int argc, char *argv[]) + { +@@ -1130,6 +1220,7 @@ + test_20070603 (); + test_20070628 (); + test_generic (2, 800, 50); ++ test_extreme (); + + tests_end_mpfr (); + return 0; +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2014-06-30 15:17:53.337268149 +0000 ++++ mpfr-3.1.2-b/PATCHES 2014-06-30 15:17:53.417270314 +0000 +@@ -0,0 +1 @@ ++vasprintf +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2014-06-30 15:17:53.337268149 +0000 ++++ mpfr-3.1.2-b/VERSION 2014-06-30 15:17:53.413270206 +0000 +@@ -1 +1 @@ +-3.1.2-p9 ++3.1.2-p10 +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2014-06-30 15:17:53.337268149 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2014-06-30 15:17:53.413270206 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p9" ++#define MPFR_VERSION_STRING "3.1.2-p10" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/vasprintf.c mpfr-3.1.2-b/src/vasprintf.c +--- mpfr-3.1.2-a/src/vasprintf.c 2013-11-15 00:51:49.267334408 +0000 ++++ mpfr-3.1.2-b/src/vasprintf.c 2014-06-30 15:17:53.377269231 +0000 +@@ -884,14 +884,18 @@ + first digit, we want the exponent for radix two and the decimal + point AFTER the first digit. */ + { +- MPFR_ASSERTN (exp > MPFR_EMIN_MIN /4); /* possible overflow */ ++ /* An integer overflow is normally not possible since MPFR_EXP_MIN ++ is twice as large as MPFR_EMIN_MIN. */ ++ MPFR_ASSERTN (exp > (MPFR_EXP_MIN + 3) / 4); + exp = (exp - 1) * 4; + } + else + /* EXP is the exponent for decimal point BEFORE the first digit, we + want the exponent for decimal point AFTER the first digit. */ + { +- MPFR_ASSERTN (exp > MPFR_EMIN_MIN); /* possible overflow */ ++ /* An integer overflow is normally not possible since MPFR_EXP_MIN ++ is twice as large as MPFR_EMIN_MIN. */ ++ MPFR_ASSERTN (exp > MPFR_EXP_MIN); + --exp; + } + } +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2014-06-30 15:17:53.337268149 +0000 ++++ mpfr-3.1.2-b/src/version.c 2014-06-30 15:17:53.413270206 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p9"; ++ return "3.1.2-p10"; + } +diff -Naurd mpfr-3.1.2-a/tests/tsprintf.c mpfr-3.1.2-b/tests/tsprintf.c +--- mpfr-3.1.2-a/tests/tsprintf.c 2013-11-15 00:51:49.267334408 +0000 ++++ mpfr-3.1.2-b/tests/tsprintf.c 2014-06-30 15:17:53.377269231 +0000 +@@ -1184,6 +1184,69 @@ + check_emax_aux (MPFR_EMAX_MAX); + } + ++static void ++check_emin_aux (mpfr_exp_t e) ++{ ++ mpfr_t x; ++ char *s1, s2[256]; ++ int i; ++ mpfr_exp_t emin; ++ mpz_t ee; ++ ++ MPFR_ASSERTN (e >= LONG_MIN); ++ emin = mpfr_get_emin (); ++ set_emin (e); ++ ++ mpfr_init2 (x, 16); ++ mpz_init (ee); ++ ++ mpfr_setmin (x, e); ++ mpz_set_si (ee, e); ++ mpz_sub_ui (ee, ee, 1); ++ ++ i = mpfr_asprintf (&s1, "%Ra", x); ++ MPFR_ASSERTN (i > 0); ++ ++ gmp_snprintf (s2, 256, "0x1p%Zd", ee); ++ ++ if (strcmp (s1, s2) != 0) ++ { ++ printf ("Error in check_emin_aux for emin = %ld\n", (long) e); ++ printf ("Expected %s\n", s2); ++ printf ("Got %s\n", s1); ++ exit (1); ++ } ++ ++ mpfr_free_str (s1); ++ ++ i = mpfr_asprintf (&s1, "%Rb", x); ++ MPFR_ASSERTN (i > 0); ++ ++ gmp_snprintf (s2, 256, "1p%Zd", ee); ++ ++ if (strcmp (s1, s2) != 0) ++ { ++ printf ("Error in check_emin_aux for emin = %ld\n", (long) e); ++ printf ("Expected %s\n", s2); ++ printf ("Got %s\n", s1); ++ exit (1); ++ } ++ ++ mpfr_free_str (s1); ++ ++ mpfr_clear (x); ++ mpz_clear (ee); ++ set_emin (emin); ++} ++ ++static void ++check_emin (void) ++{ ++ check_emin_aux (-15); ++ check_emin_aux (mpfr_get_emin ()); ++ check_emin_aux (MPFR_EMIN_MIN); ++} ++ + int + main (int argc, char **argv) + { +@@ -1203,6 +1266,7 @@ + decimal (); + mixed (); + check_emax (); ++ check_emin (); + + #if defined(HAVE_LOCALE_H) && defined(HAVE_SETLOCALE) + locale_da_DK (); +diff -Naurd mpfr-3.1.2-a/PATCHES mpfr-3.1.2-b/PATCHES +--- mpfr-3.1.2-a/PATCHES 2014-12-04 01:41:57.131789485 +0000 ++++ mpfr-3.1.2-b/PATCHES 2014-12-04 01:41:57.339791833 +0000 +@@ -0,0 +1 @@ ++strtofr +diff -Naurd mpfr-3.1.2-a/VERSION mpfr-3.1.2-b/VERSION +--- mpfr-3.1.2-a/VERSION 2014-12-04 01:41:57.127789443 +0000 ++++ mpfr-3.1.2-b/VERSION 2014-12-04 01:41:57.339791833 +0000 +@@ -1 +1 @@ +-3.1.2-p10 ++3.1.2-p11 +diff -Naurd mpfr-3.1.2-a/src/mpfr.h mpfr-3.1.2-b/src/mpfr.h +--- mpfr-3.1.2-a/src/mpfr.h 2014-12-04 01:41:57.127789443 +0000 ++++ mpfr-3.1.2-b/src/mpfr.h 2014-12-04 01:41:57.335791790 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 2 +-#define MPFR_VERSION_STRING "3.1.2-p10" ++#define MPFR_VERSION_STRING "3.1.2-p11" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.2-a/src/strtofr.c mpfr-3.1.2-b/src/strtofr.c +--- mpfr-3.1.2-a/src/strtofr.c 2013-03-13 15:37:32.000000000 +0000 ++++ mpfr-3.1.2-b/src/strtofr.c 2014-12-04 01:41:57.287791246 +0000 +@@ -473,8 +473,10 @@ + /* prec bits corresponds to ysize limbs */ + ysize_bits = ysize * GMP_NUMB_BITS; + /* and to ysize_bits >= prec > MPFR_PREC (x) bits */ +- y = MPFR_TMP_LIMBS_ALLOC (2 * ysize + 1); +- y += ysize; /* y has (ysize+1) allocated limbs */ ++ /* we need to allocate one more limb to work around bug ++ https://gmplib.org/list-archives/gmp-bugs/2013-December/003267.html */ ++ y = MPFR_TMP_LIMBS_ALLOC (2 * ysize + 2); ++ y += ysize; /* y has (ysize+2) allocated limbs */ + + /* pstr_size is the number of characters we read in pstr->mant + to have at least ysize full limbs. +diff -Naurd mpfr-3.1.2-a/src/version.c mpfr-3.1.2-b/src/version.c +--- mpfr-3.1.2-a/src/version.c 2014-12-04 01:41:57.131789485 +0000 ++++ mpfr-3.1.2-b/src/version.c 2014-12-04 01:41:57.339791833 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.2-p10"; ++ return "3.1.2-p11"; + } diff --git a/easybuild/easyconfigs/g/GCC/mpfr-3.1.3-allpatches-20150717.patch b/easybuild/easyconfigs/g/GCC/mpfr-3.1.3-allpatches-20150717.patch new file mode 100644 index 0000000000000000000000000000000000000000..779331605245842dba3b0acb4ba6535d88a2c3a9 --- /dev/null +++ b/easybuild/easyconfigs/g/GCC/mpfr-3.1.3-allpatches-20150717.patch @@ -0,0 +1,1699 @@ +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-02 10:49:23.950112879 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-02 10:49:24.042113845 +0000 +@@ -0,0 +1 @@ ++lngamma-and-doc +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-06-19 19:55:09.000000000 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-02 10:49:24.042113845 +0000 +@@ -1 +1 @@ +-3.1.3 ++3.1.3-p1 +diff -Naurd mpfr-3.1.3-a/doc/mpfr.texi mpfr-3.1.3-b/doc/mpfr.texi +--- mpfr-3.1.3-a/doc/mpfr.texi 2015-06-19 19:55:11.000000000 +0000 ++++ mpfr-3.1.3-b/doc/mpfr.texi 2015-07-02 10:49:24.018113593 +0000 +@@ -810,13 +810,17 @@ + When the input point is in the closure of the domain of the mathematical + function and an input argument is +0 (resp.@: @minus{}0), one considers + the limit when the corresponding argument approaches 0 from above +-(resp.@: below). If the limit is not defined (e.g., @code{mpfr_log} on +-@minus{}0), the behavior is specified in the description of the MPFR function. ++(resp.@: below), if possible. If the limit is not defined (e.g., ++@code{mpfr_sqrt} and @code{mpfr_log} on @minus{}0), the behavior is ++specified in the description of the MPFR function, but must be consistent ++with the rule from the above paragraph (e.g., @code{mpfr_log} on @pom{}0 ++gives @minus{}Inf). + + When the result is equal to 0, its sign is determined by considering the + limit as if the input point were not in the domain: If one approaches 0 + from above (resp.@: below), the result is +0 (resp.@: @minus{}0); +-for example, @code{mpfr_sin} on +0 gives +0. ++for example, @code{mpfr_sin} on @minus{}0 gives @minus{}0 and ++@code{mpfr_acos} on 1 gives +0 (in all rounding modes). + In the other cases, the sign is specified in the description of the MPFR + function; for example @code{mpfr_max} on @minus{}0 and +0 gives +0. + +@@ -832,8 +836,8 @@ + @c that advantages in practice), like for any bug fix. + Example: @code{mpfr_hypot} on (NaN,0) gives NaN, but @code{mpfr_hypot} + on (NaN,+Inf) gives +Inf (as specified in @ref{Special Functions}), +-since for any finite input @var{x}, @code{mpfr_hypot} on (@var{x},+Inf) +-gives +Inf. ++since for any finite or infinite input @var{x}, @code{mpfr_hypot} on ++(@var{x},+Inf) gives +Inf. + + @node Exceptions, Memory Handling, Floating-Point Values on Special Numbers, MPFR Basics + @comment node-name, next, previous, up +@@ -1581,7 +1585,8 @@ + @deftypefunx int mpfr_add_z (mpfr_t @var{rop}, mpfr_t @var{op1}, mpz_t @var{op2}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_add_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1} + @var{op2}} rounded in the direction +-@var{rnd}. For types having no signed zero, it is considered unsigned ++@var{rnd}. The IEEE-754 rules are used, in particular for signed zeros. ++But for types having no signed zeros, 0 is considered unsigned + (i.e., (+0) + 0 = (+0) and (@minus{}0) + 0 = (@minus{}0)). + The @code{mpfr_add_d} function assumes that the radix of the @code{double} type + is a power of 2, with a precision at most that declared by the C implementation +@@ -1599,7 +1604,8 @@ + @deftypefunx int mpfr_sub_z (mpfr_t @var{rop}, mpfr_t @var{op1}, mpz_t @var{op2}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_sub_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1} - @var{op2}} rounded in the direction +-@var{rnd}. For types having no signed zero, it is considered unsigned ++@var{rnd}. The IEEE-754 rules are used, in particular for signed zeros. ++But for types having no signed zeros, 0 is considered unsigned + (i.e., (+0) @minus{} 0 = (+0), (@minus{}0) @minus{} 0 = (@minus{}0), + 0 @minus{} (+0) = (@minus{}0) and 0 @minus{} (@minus{}0) = (+0)). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_d_sub} +@@ -1615,7 +1621,7 @@ + Set @var{rop} to @math{@var{op1} @GMPtimes{} @var{op2}} rounded in the + direction @var{rnd}. + When a result is zero, its sign is the product of the signs of the operands +-(for types having no signed zero, it is considered positive). ++(for types having no signed zeros, 0 is considered positive). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_mul_d}. + @end deftypefun + +@@ -1635,7 +1641,7 @@ + @deftypefunx int mpfr_div_q (mpfr_t @var{rop}, mpfr_t @var{op1}, mpq_t @var{op2}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{@var{op1}/@var{op2}} rounded in the direction @var{rnd}. + When a result is zero, its sign is the product of the signs of the operands +-(for types having no signed zero, it is considered positive). ++(for types having no signed zeros, 0 is considered positive). + The same restrictions than for @code{mpfr_add_d} apply to @code{mpfr_d_div} + and @code{mpfr_div_d}. + @end deftypefun +@@ -1643,15 +1649,18 @@ + @deftypefun int mpfr_sqrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + @deftypefunx int mpfr_sqrt_ui (mpfr_t @var{rop}, unsigned long int @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @m{\sqrt{@var{op}}, the square root of @var{op}} +-rounded in the direction @var{rnd} (set @var{rop} to @minus{}0 if @var{op} is +-@minus{}0, to be consistent with the IEEE 754 standard). ++rounded in the direction @var{rnd}. Set @var{rop} to @minus{}0 if ++@var{op} is @minus{}0, to be consistent with the IEEE 754 standard. + Set @var{rop} to NaN if @var{op} is negative. + @end deftypefun + + @deftypefun int mpfr_rec_sqrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @m{1/\sqrt{@var{op}}, the reciprocal square root of @var{op}} +-rounded in the direction @var{rnd}. Set @var{rop} to +Inf if @var{op} is +-@pom{}0, +0 if @var{op} is +Inf, and NaN if @var{op} is negative. ++rounded in the direction @var{rnd}. Set @var{rop} to +Inf if @var{op} is ++@pom{}0, +0 if @var{op} is +Inf, and NaN if @var{op} is negative. Warning! ++Therefore the result on @minus{}0 is different from the one of the rSqrt ++function recommended by the IEEE 754-2008 standard (Section 9.2.1), which ++is @minus{}Inf instead of +Inf. + @end deftypefun + + @deftypefun int mpfr_cbrt (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) +@@ -1832,7 +1841,9 @@ + @m{\log_2 @var{op}, log2(@var{op})} or + @m{\log_{10} @var{op}, log10(@var{op})}, respectively, + rounded in the direction @var{rnd}. +-Set @var{rop} to @minus{}Inf if @var{op} is @minus{}0 ++Set @var{rop} to +0 if @var{op} is 1 (in all rounding modes), ++for consistency with the ISO C99 and IEEE 754-2008 standards. ++Set @var{rop} to @minus{}Inf if @var{op} is @pom{}0 + (i.e., the sign of the zero has no influence on the result). + @end deftypefun + +@@ -2003,8 +2014,11 @@ + @deftypefun int mpfr_lngamma (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to the value of the logarithm of the Gamma function on @var{op}, + rounded in the direction @var{rnd}. +-When @math{@minus{}2@var{k}@minus{}1 @le{} @var{op} @le{} @minus{}2@var{k}}, +-@var{k} being a non-negative integer, @var{rop} is set to NaN. ++When @var{op} is 1 or 2, set @var{rop} to +0 (in all rounding modes). ++When @var{op} is an infinity or a nonpositive integer, set @var{rop} to +Inf, ++following the general rules on special values. ++When @math{@minus{}2@var{k}@minus{}1 < @var{op} < @minus{}2@var{k}}, ++@var{k} being a nonnegative integer, set @var{rop} to NaN@. + See also @code{mpfr_lgamma}. + @end deftypefun + +@@ -2012,10 +2026,11 @@ + Set @var{rop} to the value of the logarithm of the absolute value of the + Gamma function on @var{op}, rounded in the direction @var{rnd}. The sign + (1 or @minus{}1) of Gamma(@var{op}) is returned in the object pointed to +-by @var{signp}. When @var{op} is an infinity or a non-positive integer, set +-@var{rop} to +Inf. When @var{op} is NaN, @minus{}Inf or a negative integer, +-*@var{signp} is undefined, and when @var{op} is @pom{}0, *@var{signp} is +-the sign of the zero. ++by @var{signp}. ++When @var{op} is 1 or 2, set @var{rop} to +0 (in all rounding modes). ++When @var{op} is an infinity or a nonpositive integer, set @var{rop} to +Inf. ++When @var{op} is NaN, @minus{}Inf or a negative integer, *@var{signp} is ++undefined, and when @var{op} is @pom{}0, *@var{signp} is the sign of the zero. + @end deftypefun + + @deftypefun int mpfr_digamma (mpfr_t @var{rop}, mpfr_t @var{op}, mpfr_rnd_t @var{rnd}) +@@ -2064,7 +2079,10 @@ + @deftypefunx int mpfr_fms (mpfr_t @var{rop}, mpfr_t @var{op1}, mpfr_t @var{op2}, mpfr_t @var{op3}, mpfr_rnd_t @var{rnd}) + Set @var{rop} to @math{(@var{op1} @GMPtimes{} @var{op2}) + @var{op3}} + (resp.@: @math{(@var{op1} @GMPtimes{} @var{op2}) - @var{op3}}) +-rounded in the direction @var{rnd}. ++rounded in the direction @var{rnd}. Concerning special values (signed zeros, ++infinities, NaN), these functions behave like a multiplication followed by a ++separate addition or subtraction. That is, the fused operation matters only ++for rounding. + @end deftypefun + + @deftypefun int mpfr_agm (mpfr_t @var{rop}, mpfr_t @var{op1}, mpfr_t @var{op2}, mpfr_rnd_t @var{rnd}) +@@ -2089,8 +2107,8 @@ + i.e., $\sqrt{x^2+y^2}$, + @end tex + rounded in the direction @var{rnd}. +-Special values are handled as described in Section F.9.4.3 of +-the ISO C99 and IEEE 754-2008 standards: ++Special values are handled as described in the ISO C99 (Section F.9.4.3) ++and IEEE 754-2008 (Section 9.2.1) standards: + If @var{x} or @var{y} is an infinity, then +Inf is returned in @var{rop}, + even if the other number is NaN. + @end deftypefun +diff -Naurd mpfr-3.1.3-a/doc/mpfr.info mpfr-3.1.3-b/doc/mpfr.info +--- mpfr-3.1.3-a/doc/mpfr.info 2015-06-19 19:55:53.000000000 +0000 ++++ mpfr-3.1.3-b/doc/mpfr.info 2015-07-02 10:49:38.718267817 +0000 +@@ -1,4 +1,4 @@ +-This is mpfr.info, produced by makeinfo version 5.2 from mpfr.texi. ++This is mpfr.info, produced by makeinfo version 6.0 from mpfr.texi. + + This manual documents how to install and use the Multiple Precision + Floating-Point Reliable Library, version 3.1.3. +@@ -55,7 +55,7 @@ + MPFR Copying Conditions + *********************** + +-The GNU MPFR library (or MPFR for short) is "free"; this means that ++The GNU MPFR library (or MPFR for short) is “free”; this means that + everyone is free to use it and free to redistribute it on a free basis. + The library is not in the public domain; it is copyrighted and there are + restrictions on its distribution, but these restrictions are designed to +@@ -418,7 +418,7 @@ + 4.2 Nomenclature and Types + ========================== + +-A "floating-point number", or "float" for short, is an arbitrary ++A “floating-point number”, or “float” for short, is an arbitrary + precision significand (also called mantissa) with a limited precision + exponent. The C data type for such objects is ‘mpfr_t’ (internally + defined as a one-element array of a structure, and ‘mpfr_ptr’ is the C +@@ -432,7 +432,7 @@ + to the other functions supported by MPFR. Unless documented otherwise, + the sign bit of a NaN is unspecified. + +-The "precision" is the number of bits used to represent the significand ++The “precision” is the number of bits used to represent the significand + of a floating-point number; the corresponding C data type is + ‘mpfr_prec_t’. The precision can be any integer between ‘MPFR_PREC_MIN’ + and ‘MPFR_PREC_MAX’. In the current implementation, ‘MPFR_PREC_MIN’ is +@@ -446,7 +446,7 @@ + may abort, crash or have undefined behavior (depending on your C + implementation). + +-The "rounding mode" specifies the way to round the result of a ++The “rounding mode” specifies the way to round the result of a + floating-point operation, in case the exact result can not be + represented exactly in the destination significand; the corresponding C + data type is ‘mpfr_rnd_t’. +@@ -499,14 +499,14 @@ + representable numbers, it is rounded to the one with the least + significant bit set to zero. For example, the number 2.5, which is + represented by (10.1) in binary, is rounded to (10.0)=2 with a precision +-of two bits, and not to (11.0)=3. This rule avoids the "drift" ++of two bits, and not to (11.0)=3. This rule avoids the “drift” + phenomenon mentioned by Knuth in volume 2 of The Art of Computer + Programming (Section 4.2.2). + + Most MPFR functions take as first argument the destination variable, + as second and following arguments the input variables, as last argument + a rounding mode, and have a return value of type ‘int’, called the +-"ternary value". The value stored in the destination variable is ++“ternary value”. The value stored in the destination variable is + correctly rounded, i.e., MPFR behaves as if it computed the result with + an infinite precision, then rounded it to the precision of this + variable. The input variables are regarded as exact (in particular, +@@ -572,15 +572,18 @@ + When the input point is in the closure of the domain of the + mathematical function and an input argument is +0 (resp. −0), one + considers the limit when the corresponding argument approaches 0 from +-above (resp. below). If the limit is not defined (e.g., ‘mpfr_log’ on +-−0), the behavior is specified in the description of the MPFR function. ++above (resp. below), if possible. If the limit is not defined (e.g., ++‘mpfr_sqrt’ and ‘mpfr_log’ on −0), the behavior is specified in the ++description of the MPFR function, but must be consistent with the rule ++from the above paragraph (e.g., ‘mpfr_log’ on ±0 gives −Inf). + + When the result is equal to 0, its sign is determined by considering + the limit as if the input point were not in the domain: If one + approaches 0 from above (resp. below), the result is +0 (resp. −0); for +-example, ‘mpfr_sin’ on +0 gives +0. In the other cases, the sign is +-specified in the description of the MPFR function; for example +-‘mpfr_max’ on −0 and +0 gives +0. ++example, ‘mpfr_sin’ on −0 gives −0 and ‘mpfr_acos’ on 1 gives +0 (in all ++rounding modes). In the other cases, the sign is specified in the ++description of the MPFR function; for example ‘mpfr_max’ on −0 and +0 ++gives +0. + + When the input point is not in the closure of the domain of the + function, the result is NaN. Example: ‘mpfr_sqrt’ on −17 gives NaN. +@@ -590,8 +593,8 @@ + numbers; such a case is always explicitly specified in *note MPFR + Interface::. Example: ‘mpfr_hypot’ on (NaN,0) gives NaN, but + ‘mpfr_hypot’ on (NaN,+Inf) gives +Inf (as specified in *note Special +-Functions::), since for any finite input X, ‘mpfr_hypot’ on (X,+Inf) +-gives +Inf. ++Functions::), since for any finite or infinite input X, ‘mpfr_hypot’ on ++(X,+Inf) gives +Inf. + +  + File: mpfr.info, Node: Exceptions, Next: Memory Handling, Prev: Floating-Point Values on Special Numbers, Up: MPFR Basics +@@ -1253,8 +1256,9 @@ + mpfr_rnd_t RND) + -- Function: int mpfr_add_q (mpfr_t ROP, mpfr_t OP1, mpq_t OP2, + mpfr_rnd_t RND) +- Set ROP to OP1 + OP2 rounded in the direction RND. For types +- having no signed zero, it is considered unsigned (i.e., (+0) + 0 = ++ Set ROP to OP1 + OP2 rounded in the direction RND. The IEEE-754 ++ rules are used, in particular for signed zeros. But for types ++ having no signed zeros, 0 is considered unsigned (i.e., (+0) + 0 = + (+0) and (−0) + 0 = (−0)). The ‘mpfr_add_d’ function assumes that + the radix of the ‘double’ type is a power of 2, with a precision at + most that declared by the C implementation (macro +@@ -1280,8 +1284,9 @@ + mpfr_rnd_t RND) + -- Function: int mpfr_sub_q (mpfr_t ROP, mpfr_t OP1, mpq_t OP2, + mpfr_rnd_t RND) +- Set ROP to OP1 - OP2 rounded in the direction RND. For types +- having no signed zero, it is considered unsigned (i.e., (+0) − 0 = ++ Set ROP to OP1 - OP2 rounded in the direction RND. The IEEE-754 ++ rules are used, in particular for signed zeros. But for types ++ having no signed zeros, 0 is considered unsigned (i.e., (+0) − 0 = + (+0), (−0) − 0 = (−0), 0 − (+0) = (−0) and 0 − (−0) = (+0)). The + same restrictions than for ‘mpfr_add_d’ apply to ‘mpfr_d_sub’ and + ‘mpfr_sub_d’. +@@ -1300,7 +1305,7 @@ + mpfr_rnd_t RND) + Set ROP to OP1 times OP2 rounded in the direction RND. When a + result is zero, its sign is the product of the signs of the +- operands (for types having no signed zero, it is considered ++ operands (for types having no signed zeros, 0 is considered + positive). The same restrictions than for ‘mpfr_add_d’ apply to + ‘mpfr_mul_d’. + +@@ -1327,21 +1332,24 @@ + mpfr_rnd_t RND) + Set ROP to OP1/OP2 rounded in the direction RND. When a result is + zero, its sign is the product of the signs of the operands (for +- types having no signed zero, it is considered positive). The same ++ types having no signed zeros, 0 is considered positive). The same + restrictions than for ‘mpfr_add_d’ apply to ‘mpfr_d_div’ and + ‘mpfr_div_d’. + + -- Function: int mpfr_sqrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_sqrt_ui (mpfr_t ROP, unsigned long int OP, + mpfr_rnd_t RND) +- Set ROP to the square root of OP rounded in the direction RND (set +- ROP to −0 if OP is −0, to be consistent with the IEEE 754 +- standard). Set ROP to NaN if OP is negative. ++ Set ROP to the square root of OP rounded in the direction RND. Set ++ ROP to −0 if OP is −0, to be consistent with the IEEE 754 standard. ++ Set ROP to NaN if OP is negative. + + -- Function: int mpfr_rec_sqrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the reciprocal square root of OP rounded in the + direction RND. Set ROP to +Inf if OP is ±0, +0 if OP is +Inf, and +- NaN if OP is negative. ++ NaN if OP is negative. Warning! Therefore the result on −0 is ++ different from the one of the rSqrt function recommended by the ++ IEEE 754-2008 standard (Section 9.2.1), which is −Inf instead of ++ +Inf. + + -- Function: int mpfr_cbrt (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_root (mpfr_t ROP, mpfr_t OP, unsigned long int K, +@@ -1515,8 +1523,10 @@ + -- Function: int mpfr_log2 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_log10 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the natural logarithm of OP, log2(OP) or log10(OP), +- respectively, rounded in the direction RND. Set ROP to −Inf if OP +- is −0 (i.e., the sign of the zero has no influence on the result). ++ respectively, rounded in the direction RND. Set ROP to +0 if OP is ++ 1 (in all rounding modes), for consistency with the ISO C99 and ++ IEEE 754-2008 standards. Set ROP to −Inf if OP is ±0 (i.e., the ++ sign of the zero has no influence on the result). + + -- Function: int mpfr_exp (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + -- Function: int mpfr_exp2 (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) +@@ -1649,17 +1659,21 @@ + + -- Function: int mpfr_lngamma (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the value of the logarithm of the Gamma function on OP, +- rounded in the direction RND. When −2K−1 <= OP <= −2K, K being a +- non-negative integer, ROP is set to NaN. See also ‘mpfr_lgamma’. ++ rounded in the direction RND. When OP is 1 or 2, set ROP to +0 (in ++ all rounding modes). When OP is an infinity or a nonpositive ++ integer, set ROP to +Inf, following the general rules on special ++ values. When −2K−1 < OP < −2K, K being a nonnegative integer, set ++ ROP to NaN. See also ‘mpfr_lgamma’. + + -- Function: int mpfr_lgamma (mpfr_t ROP, int *SIGNP, mpfr_t OP, + mpfr_rnd_t RND) + Set ROP to the value of the logarithm of the absolute value of the + Gamma function on OP, rounded in the direction RND. The sign (1 or + −1) of Gamma(OP) is returned in the object pointed to by SIGNP. +- When OP is an infinity or a non-positive integer, set ROP to +Inf. +- When OP is NaN, −Inf or a negative integer, *SIGNP is undefined, +- and when OP is ±0, *SIGNP is the sign of the zero. ++ When OP is 1 or 2, set ROP to +0 (in all rounding modes). When OP ++ is an infinity or a nonpositive integer, set ROP to +Inf. When OP ++ is NaN, −Inf or a negative integer, *SIGNP is undefined, and when ++ OP is ±0, *SIGNP is the sign of the zero. + + -- Function: int mpfr_digamma (mpfr_t ROP, mpfr_t OP, mpfr_rnd_t RND) + Set ROP to the value of the Digamma (sometimes also called Psi) +@@ -1703,7 +1717,10 @@ + -- Function: int mpfr_fms (mpfr_t ROP, mpfr_t OP1, mpfr_t OP2, mpfr_t + OP3, mpfr_rnd_t RND) + Set ROP to (OP1 times OP2) + OP3 (resp. (OP1 times OP2) - OP3) +- rounded in the direction RND. ++ rounded in the direction RND. Concerning special values (signed ++ zeros, infinities, NaN), these functions behave like a ++ multiplication followed by a separate addition or subtraction. ++ That is, the fused operation matters only for rounding. + + -- Function: int mpfr_agm (mpfr_t ROP, mpfr_t OP1, mpfr_t OP2, + mpfr_rnd_t RND) +@@ -1717,9 +1734,10 @@ + RND) + Set ROP to the Euclidean norm of X and Y, i.e., the square root of + the sum of the squares of X and Y, rounded in the direction RND. +- Special values are handled as described in Section F.9.4.3 of the +- ISO C99 and IEEE 754-2008 standards: If X or Y is an infinity, then +- +Inf is returned in ROP, even if the other number is NaN. ++ Special values are handled as described in the ISO C99 (Section ++ F.9.4.3) and IEEE 754-2008 (Section 9.2.1) standards: If X or Y is ++ an infinity, then +Inf is returned in ROP, even if the other number ++ is NaN. + + -- Function: int mpfr_ai (mpfr_t ROP, mpfr_t X, mpfr_rnd_t RND) + Set ROP to the value of the Airy function Ai on X, rounded in the +@@ -2670,7 +2688,7 @@ + 5.16 Internals + ============== + +-A "limb" means the part of a multi-precision number that fits in a ++A “limb” means the part of a multi-precision number that fits in a + single word. Usually a limb contains 32 or 64 bits. The C data type + for a limb is ‘mp_limb_t’. + +@@ -3140,7 +3158,7 @@ + 0. PREAMBLE + + The purpose of this License is to make a manual, textbook, or other +- functional and useful document "free" in the sense of freedom: to ++ functional and useful document “free” in the sense of freedom: to + assure everyone the effective freedom to copy and redistribute it, + with or without modifying it, either commercially or + noncommercially. Secondarily, this License preserves for the +@@ -3655,9 +3673,9 @@ + * Menu: + + * mpfr_abs: Basic Arithmetic Functions. +- (line 160) +-* mpfr_acos: Special Functions. (line 51) +-* mpfr_acosh: Special Functions. (line 115) ++ (line 165) ++* mpfr_acos: Special Functions. (line 53) ++* mpfr_acosh: Special Functions. (line 117) + * mpfr_add: Basic Arithmetic Functions. + (line 6) + * mpfr_add_d: Basic Arithmetic Functions. +@@ -3670,15 +3688,15 @@ + (line 8) + * mpfr_add_z: Basic Arithmetic Functions. + (line 14) +-* mpfr_agm: Special Functions. (line 210) +-* mpfr_ai: Special Functions. (line 226) +-* mpfr_asin: Special Functions. (line 52) +-* mpfr_asinh: Special Functions. (line 116) ++* mpfr_agm: Special Functions. (line 219) ++* mpfr_ai: Special Functions. (line 236) ++* mpfr_asin: Special Functions. (line 54) ++* mpfr_asinh: Special Functions. (line 118) + * mpfr_asprintf: Formatted Output Functions. + (line 193) +-* mpfr_atan: Special Functions. (line 53) +-* mpfr_atan2: Special Functions. (line 63) +-* mpfr_atanh: Special Functions. (line 117) ++* mpfr_atan: Special Functions. (line 55) ++* mpfr_atan2: Special Functions. (line 65) ++* mpfr_atanh: Special Functions. (line 119) + * mpfr_buildopt_decimal_p: Miscellaneous Functions. + (line 162) + * mpfr_buildopt_gmpinternals_p: Miscellaneous Functions. +@@ -3690,7 +3708,7 @@ + * mpfr_can_round: Rounding Related Functions. + (line 39) + * mpfr_cbrt: Basic Arithmetic Functions. +- (line 108) ++ (line 113) + * mpfr_ceil: Integer Related Functions. + (line 7) + * mpfr_check_range: Exception Related Functions. +@@ -3735,18 +3753,18 @@ + (line 27) + * mpfr_cmp_z: Comparison Functions. + (line 11) +-* mpfr_const_catalan: Special Functions. (line 237) +-* mpfr_const_euler: Special Functions. (line 236) +-* mpfr_const_log2: Special Functions. (line 234) +-* mpfr_const_pi: Special Functions. (line 235) ++* mpfr_const_catalan: Special Functions. (line 247) ++* mpfr_const_euler: Special Functions. (line 246) ++* mpfr_const_log2: Special Functions. (line 244) ++* mpfr_const_pi: Special Functions. (line 245) + * mpfr_copysign: Miscellaneous Functions. + (line 109) +-* mpfr_cos: Special Functions. (line 29) +-* mpfr_cosh: Special Functions. (line 95) +-* mpfr_cot: Special Functions. (line 47) +-* mpfr_coth: Special Functions. (line 111) +-* mpfr_csc: Special Functions. (line 46) +-* mpfr_csch: Special Functions. (line 110) ++* mpfr_cos: Special Functions. (line 31) ++* mpfr_cosh: Special Functions. (line 97) ++* mpfr_cot: Special Functions. (line 49) ++* mpfr_coth: Special Functions. (line 113) ++* mpfr_csc: Special Functions. (line 48) ++* mpfr_csch: Special Functions. (line 112) + * mpfr_custom_get_exp: Custom Interface. (line 75) + * mpfr_custom_get_kind: Custom Interface. (line 65) + * mpfr_custom_get_significand: Custom Interface. (line 70) +@@ -3756,47 +3774,47 @@ + * mpfr_custom_move: Custom Interface. (line 82) + * MPFR_DECL_INIT: Initialization Functions. + (line 74) +-* mpfr_digamma: Special Functions. (line 166) ++* mpfr_digamma: Special Functions. (line 172) + * mpfr_dim: Basic Arithmetic Functions. +- (line 166) ++ (line 171) + * mpfr_div: Basic Arithmetic Functions. +- (line 72) ++ (line 74) + * mpfr_divby0_p: Exception Related Functions. + (line 134) + * mpfr_div_2exp: Compatibility with MPF. + (line 49) + * mpfr_div_2si: Basic Arithmetic Functions. +- (line 181) ++ (line 186) + * mpfr_div_2ui: Basic Arithmetic Functions. +- (line 179) ++ (line 184) + * mpfr_div_d: Basic Arithmetic Functions. +- (line 84) ++ (line 86) + * mpfr_div_q: Basic Arithmetic Functions. +- (line 88) ++ (line 90) + * mpfr_div_si: Basic Arithmetic Functions. +- (line 80) ++ (line 82) + * mpfr_div_ui: Basic Arithmetic Functions. +- (line 76) ++ (line 78) + * mpfr_div_z: Basic Arithmetic Functions. +- (line 86) ++ (line 88) + * mpfr_d_div: Basic Arithmetic Functions. +- (line 82) ++ (line 84) + * mpfr_d_sub: Basic Arithmetic Functions. +- (line 35) +-* mpfr_eint: Special Functions. (line 133) ++ (line 36) ++* mpfr_eint: Special Functions. (line 135) + * mpfr_eq: Compatibility with MPF. + (line 28) + * mpfr_equal_p: Comparison Functions. + (line 59) + * mpfr_erangeflag_p: Exception Related Functions. + (line 137) +-* mpfr_erf: Special Functions. (line 177) +-* mpfr_erfc: Special Functions. (line 178) +-* mpfr_exp: Special Functions. (line 23) +-* mpfr_exp10: Special Functions. (line 25) +-* mpfr_exp2: Special Functions. (line 24) +-* mpfr_expm1: Special Functions. (line 129) +-* mpfr_fac_ui: Special Functions. (line 121) ++* mpfr_erf: Special Functions. (line 183) ++* mpfr_erfc: Special Functions. (line 184) ++* mpfr_exp: Special Functions. (line 25) ++* mpfr_exp10: Special Functions. (line 27) ++* mpfr_exp2: Special Functions. (line 26) ++* mpfr_expm1: Special Functions. (line 131) ++* mpfr_fac_ui: Special Functions. (line 123) + * mpfr_fits_intmax_p: Conversion Functions. + (line 150) + * mpfr_fits_sint_p: Conversion Functions. +@@ -3815,20 +3833,20 @@ + (line 147) + * mpfr_floor: Integer Related Functions. + (line 8) +-* mpfr_fma: Special Functions. (line 203) ++* mpfr_fma: Special Functions. (line 209) + * mpfr_fmod: Integer Related Functions. + (line 92) +-* mpfr_fms: Special Functions. (line 205) ++* mpfr_fms: Special Functions. (line 211) + * mpfr_fprintf: Formatted Output Functions. + (line 157) + * mpfr_frac: Integer Related Functions. + (line 76) +-* mpfr_free_cache: Special Functions. (line 244) ++* mpfr_free_cache: Special Functions. (line 254) + * mpfr_free_str: Conversion Functions. + (line 137) + * mpfr_frexp: Conversion Functions. + (line 45) +-* mpfr_gamma: Special Functions. (line 148) ++* mpfr_gamma: Special Functions. (line 150) + * mpfr_get_d: Conversion Functions. + (line 7) + * mpfr_get_decimal64: Conversion Functions. +@@ -3887,7 +3905,7 @@ + (line 56) + * mpfr_greater_p: Comparison Functions. + (line 55) +-* mpfr_hypot: Special Functions. (line 218) ++* mpfr_hypot: Special Functions. (line 227) + * mpfr_inexflag_p: Exception Related Functions. + (line 136) + * mpfr_inf_p: Comparison Functions. +@@ -3922,21 +3940,21 @@ + (line 31) + * mpfr_integer_p: Integer Related Functions. + (line 119) +-* mpfr_j0: Special Functions. (line 182) +-* mpfr_j1: Special Functions. (line 183) +-* mpfr_jn: Special Functions. (line 184) ++* mpfr_j0: Special Functions. (line 188) ++* mpfr_j1: Special Functions. (line 189) ++* mpfr_jn: Special Functions. (line 190) + * mpfr_lessequal_p: Comparison Functions. + (line 58) + * mpfr_lessgreater_p: Comparison Functions. + (line 64) + * mpfr_less_p: Comparison Functions. + (line 57) +-* mpfr_lgamma: Special Functions. (line 157) +-* mpfr_li2: Special Functions. (line 143) +-* mpfr_lngamma: Special Functions. (line 152) ++* mpfr_lgamma: Special Functions. (line 162) ++* mpfr_li2: Special Functions. (line 145) ++* mpfr_lngamma: Special Functions. (line 154) + * mpfr_log: Special Functions. (line 16) + * mpfr_log10: Special Functions. (line 18) +-* mpfr_log1p: Special Functions. (line 125) ++* mpfr_log1p: Special Functions. (line 127) + * mpfr_log2: Special Functions. (line 17) + * mpfr_max: Miscellaneous Functions. + (line 22) +@@ -3947,29 +3965,29 @@ + * mpfr_modf: Integer Related Functions. + (line 82) + * mpfr_mul: Basic Arithmetic Functions. +- (line 51) ++ (line 53) + * mpfr_mul_2exp: Compatibility with MPF. + (line 47) + * mpfr_mul_2si: Basic Arithmetic Functions. +- (line 174) ++ (line 179) + * mpfr_mul_2ui: Basic Arithmetic Functions. +- (line 172) ++ (line 177) + * mpfr_mul_d: Basic Arithmetic Functions. +- (line 57) ++ (line 59) + * mpfr_mul_q: Basic Arithmetic Functions. +- (line 61) ++ (line 63) + * mpfr_mul_si: Basic Arithmetic Functions. +- (line 55) ++ (line 57) + * mpfr_mul_ui: Basic Arithmetic Functions. +- (line 53) ++ (line 55) + * mpfr_mul_z: Basic Arithmetic Functions. +- (line 59) ++ (line 61) + * mpfr_nanflag_p: Exception Related Functions. + (line 135) + * mpfr_nan_p: Comparison Functions. + (line 39) + * mpfr_neg: Basic Arithmetic Functions. +- (line 159) ++ (line 164) + * mpfr_nextabove: Miscellaneous Functions. + (line 15) + * mpfr_nextbelow: Miscellaneous Functions. +@@ -3983,13 +4001,13 @@ + * mpfr_overflow_p: Exception Related Functions. + (line 133) + * mpfr_pow: Basic Arithmetic Functions. +- (line 116) ++ (line 121) + * mpfr_pow_si: Basic Arithmetic Functions. +- (line 120) ++ (line 125) + * mpfr_pow_ui: Basic Arithmetic Functions. +- (line 118) ++ (line 123) + * mpfr_pow_z: Basic Arithmetic Functions. +- (line 122) ++ (line 127) + * mpfr_prec_round: Rounding Related Functions. + (line 13) + * ‘mpfr_prec_t’: Nomenclature and Types. +@@ -3999,7 +4017,7 @@ + * mpfr_print_rnd_mode: Rounding Related Functions. + (line 71) + * mpfr_rec_sqrt: Basic Arithmetic Functions. +- (line 103) ++ (line 105) + * mpfr_regular_p: Comparison Functions. + (line 43) + * mpfr_reldiff: Compatibility with MPF. +@@ -4021,11 +4039,11 @@ + * ‘mpfr_rnd_t’: Nomenclature and Types. + (line 34) + * mpfr_root: Basic Arithmetic Functions. +- (line 109) ++ (line 114) + * mpfr_round: Integer Related Functions. + (line 9) +-* mpfr_sec: Special Functions. (line 45) +-* mpfr_sech: Special Functions. (line 109) ++* mpfr_sec: Special Functions. (line 47) ++* mpfr_sech: Special Functions. (line 111) + * mpfr_set: Assignment Functions. + (line 9) + * mpfr_setsign: Miscellaneous Functions. +@@ -4100,57 +4118,57 @@ + (line 49) + * mpfr_signbit: Miscellaneous Functions. + (line 99) +-* mpfr_sin: Special Functions. (line 30) +-* mpfr_sinh: Special Functions. (line 96) +-* mpfr_sinh_cosh: Special Functions. (line 101) +-* mpfr_sin_cos: Special Functions. (line 35) ++* mpfr_sin: Special Functions. (line 32) ++* mpfr_sinh: Special Functions. (line 98) ++* mpfr_sinh_cosh: Special Functions. (line 103) ++* mpfr_sin_cos: Special Functions. (line 37) + * mpfr_si_div: Basic Arithmetic Functions. +- (line 78) ++ (line 80) + * mpfr_si_sub: Basic Arithmetic Functions. +- (line 31) ++ (line 32) + * mpfr_snprintf: Formatted Output Functions. + (line 180) + * mpfr_sprintf: Formatted Output Functions. + (line 170) + * mpfr_sqr: Basic Arithmetic Functions. +- (line 69) ++ (line 71) + * mpfr_sqrt: Basic Arithmetic Functions. +- (line 96) ++ (line 98) + * mpfr_sqrt_ui: Basic Arithmetic Functions. +- (line 97) ++ (line 99) + * mpfr_strtofr: Assignment Functions. + (line 80) + * mpfr_sub: Basic Arithmetic Functions. +- (line 25) ++ (line 26) + * mpfr_subnormalize: Exception Related Functions. + (line 60) + * mpfr_sub_d: Basic Arithmetic Functions. +- (line 37) ++ (line 38) + * mpfr_sub_q: Basic Arithmetic Functions. +- (line 43) ++ (line 44) + * mpfr_sub_si: Basic Arithmetic Functions. +- (line 33) ++ (line 34) + * mpfr_sub_ui: Basic Arithmetic Functions. +- (line 29) ++ (line 30) + * mpfr_sub_z: Basic Arithmetic Functions. +- (line 41) +-* mpfr_sum: Special Functions. (line 252) ++ (line 42) ++* mpfr_sum: Special Functions. (line 262) + * mpfr_swap: Assignment Functions. + (line 150) + * ‘mpfr_t’: Nomenclature and Types. + (line 6) +-* mpfr_tan: Special Functions. (line 31) +-* mpfr_tanh: Special Functions. (line 97) ++* mpfr_tan: Special Functions. (line 33) ++* mpfr_tanh: Special Functions. (line 99) + * mpfr_trunc: Integer Related Functions. + (line 10) + * mpfr_ui_div: Basic Arithmetic Functions. +- (line 74) ++ (line 76) + * mpfr_ui_pow: Basic Arithmetic Functions. +- (line 126) ++ (line 131) + * mpfr_ui_pow_ui: Basic Arithmetic Functions. +- (line 124) ++ (line 129) + * mpfr_ui_sub: Basic Arithmetic Functions. +- (line 27) ++ (line 28) + * mpfr_underflow_p: Exception Related Functions. + (line 132) + * mpfr_unordered_p: Comparison Functions. +@@ -4181,61 +4199,61 @@ + (line 182) + * mpfr_vsprintf: Formatted Output Functions. + (line 171) +-* mpfr_y0: Special Functions. (line 193) +-* mpfr_y1: Special Functions. (line 194) +-* mpfr_yn: Special Functions. (line 195) ++* mpfr_y0: Special Functions. (line 199) ++* mpfr_y1: Special Functions. (line 200) ++* mpfr_yn: Special Functions. (line 201) + * mpfr_zero_p: Comparison Functions. + (line 42) +-* mpfr_zeta: Special Functions. (line 171) +-* mpfr_zeta_ui: Special Functions. (line 172) ++* mpfr_zeta: Special Functions. (line 177) ++* mpfr_zeta_ui: Special Functions. (line 178) + * mpfr_z_sub: Basic Arithmetic Functions. +- (line 39) ++ (line 40) + + +  + Tag Table: + Node: Top775 + Node: Copying2007 +-Node: Introduction to MPFR3766 +-Node: Installing MPFR5880 +-Node: Reporting Bugs11323 +-Node: MPFR Basics13353 +-Node: Headers and Libraries13669 +-Node: Nomenclature and Types16828 +-Node: MPFR Variable Conventions18874 +-Node: Rounding Modes20418 +-Ref: ternary value21544 +-Node: Floating-Point Values on Special Numbers23526 +-Node: Exceptions26572 +-Node: Memory Handling29749 +-Node: MPFR Interface30894 +-Node: Initialization Functions33008 +-Node: Assignment Functions40318 +-Node: Combined Initialization and Assignment Functions49673 +-Node: Conversion Functions50974 +-Node: Basic Arithmetic Functions60035 +-Node: Comparison Functions69200 +-Node: Special Functions72687 +-Node: Input and Output Functions86672 +-Node: Formatted Output Functions88644 +-Node: Integer Related Functions98431 +-Node: Rounding Related Functions105051 +-Node: Miscellaneous Functions108888 +-Node: Exception Related Functions117568 +-Node: Compatibility with MPF124386 +-Node: Custom Interface127127 +-Node: Internals131526 +-Node: API Compatibility133066 +-Node: Type and Macro Changes134995 +-Node: Added Functions137844 +-Node: Changed Functions141132 +-Node: Removed Functions145545 +-Node: Other Changes145973 +-Node: Contributors147576 +-Node: References150219 +-Node: GNU Free Documentation License151973 +-Node: Concept Index174562 +-Node: Function and Type Index180659 ++Node: Introduction to MPFR3770 ++Node: Installing MPFR5884 ++Node: Reporting Bugs11327 ++Node: MPFR Basics13357 ++Node: Headers and Libraries13673 ++Node: Nomenclature and Types16832 ++Node: MPFR Variable Conventions18894 ++Node: Rounding Modes20438 ++Ref: ternary value21568 ++Node: Floating-Point Values on Special Numbers23554 ++Node: Exceptions26813 ++Node: Memory Handling29990 ++Node: MPFR Interface31135 ++Node: Initialization Functions33249 ++Node: Assignment Functions40559 ++Node: Combined Initialization and Assignment Functions49914 ++Node: Conversion Functions51215 ++Node: Basic Arithmetic Functions60276 ++Node: Comparison Functions69777 ++Node: Special Functions73264 ++Node: Input and Output Functions87862 ++Node: Formatted Output Functions89834 ++Node: Integer Related Functions99621 ++Node: Rounding Related Functions106241 ++Node: Miscellaneous Functions110078 ++Node: Exception Related Functions118758 ++Node: Compatibility with MPF125576 ++Node: Custom Interface128317 ++Node: Internals132716 ++Node: API Compatibility134260 ++Node: Type and Macro Changes136189 ++Node: Added Functions139038 ++Node: Changed Functions142326 ++Node: Removed Functions146739 ++Node: Other Changes147167 ++Node: Contributors148770 ++Node: References151413 ++Node: GNU Free Documentation License153167 ++Node: Concept Index175760 ++Node: Function and Type Index181857 +  + End Tag Table + +diff -Naurd mpfr-3.1.3-a/src/lngamma.c mpfr-3.1.3-b/src/lngamma.c +--- mpfr-3.1.3-a/src/lngamma.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/lngamma.c 2015-07-02 10:49:24.018113593 +0000 +@@ -603,16 +603,17 @@ + mpfr_get_prec (y), mpfr_log_prec, y, inex)); + + /* special cases */ +- if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x))) ++ if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x) || ++ (MPFR_IS_NEG (x) && mpfr_integer_p (x)))) + { +- if (MPFR_IS_NAN (x) || MPFR_IS_NEG (x)) ++ if (MPFR_IS_NAN (x)) + { + MPFR_SET_NAN (y); + MPFR_RET_NAN; + } +- else /* lngamma(+Inf) = lngamma(+0) = +Inf */ ++ else /* lngamma(+/-Inf) = lngamma(nonpositive integer) = +Inf */ + { +- if (MPFR_IS_ZERO (x)) ++ if (!MPFR_IS_INF (x)) + mpfr_set_divby0 (); + MPFR_SET_INF (y); + MPFR_SET_POS (y); +@@ -620,8 +621,8 @@ + } + } + +- /* if x < 0 and -2k-1 <= x <= -2k, then lngamma(x) = NaN */ +- if (MPFR_IS_NEG (x) && (unit_bit (x) == 0 || mpfr_integer_p (x))) ++ /* if -2k-1 < x < -2k <= 0, then lngamma(x) = NaN */ ++ if (MPFR_IS_NEG (x) && unit_bit (x) == 0) + { + MPFR_SET_NAN (y); + MPFR_RET_NAN; +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-02 10:49:24.038113803 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3" ++#define MPFR_VERSION_STRING "3.1.3-p1" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-02 10:49:24.042113845 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3"; ++ return "3.1.3-p1"; + } +diff -Naurd mpfr-3.1.3-a/tests/tlngamma.c mpfr-3.1.3-b/tests/tlngamma.c +--- mpfr-3.1.3-a/tests/tlngamma.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/tests/tlngamma.c 2015-07-02 10:49:24.018113593 +0000 +@@ -33,7 +33,7 @@ + special (void) + { + mpfr_t x, y; +- int inex; ++ int i, inex; + + mpfr_init (x); + mpfr_init (y); +@@ -46,25 +46,29 @@ + exit (1); + } + +- mpfr_set_inf (x, -1); ++ mpfr_set_inf (x, 1); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || __gmpfr_flags != 0) + { +- printf ("Error for lngamma(-Inf)\n"); ++ printf ("Error for lngamma(+Inf)\n"); + exit (1); + } + +- mpfr_set_inf (x, 1); ++ mpfr_set_inf (x, -1); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || __gmpfr_flags != 0) + { +- printf ("Error for lngamma(+Inf)\n"); ++ printf ("Error for lngamma(-Inf)\n"); + exit (1); + } + + mpfr_set_ui (x, 0, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) + { + printf ("Error for lngamma(+0)\n"); + exit (1); +@@ -72,32 +76,58 @@ + + mpfr_set_ui (x, 0, MPFR_RNDN); + mpfr_neg (x, x, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) + { + printf ("Error for lngamma(-0)\n"); + exit (1); + } + + mpfr_set_ui (x, 1, MPFR_RNDN); ++ mpfr_clear_flags (); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp_ui (y, 0) || MPFR_IS_NEG (y)) ++ if (mpfr_cmp_ui0 (y, 0) || MPFR_IS_NEG (y)) + { + printf ("Error for lngamma(1)\n"); + exit (1); + } + +- mpfr_set_si (x, -1, MPFR_RNDN); +- mpfr_lngamma (y, x, MPFR_RNDN); +- if (!mpfr_nan_p (y)) ++ for (i = 1; i <= 5; i++) + { +- printf ("Error for lngamma(-1)\n"); +- exit (1); ++ int c; ++ ++ mpfr_set_si (x, -i, MPFR_RNDN); ++ mpfr_clear_flags (); ++ mpfr_lngamma (y, x, MPFR_RNDN); ++ if (!mpfr_inf_p (y) || mpfr_sgn (y) < 0 || ++ __gmpfr_flags != MPFR_FLAGS_DIVBY0) ++ { ++ printf ("Error for lngamma(-%d)\n", i); ++ exit (1); ++ } ++ if (i & 1) ++ { ++ mpfr_nextabove (x); ++ c = '+'; ++ } ++ else ++ { ++ mpfr_nextbelow (x); ++ c = '-'; ++ } ++ mpfr_lngamma (y, x, MPFR_RNDN); ++ if (!mpfr_nan_p (y)) ++ { ++ printf ("Error for lngamma(-%d%cepsilon)\n", i, c); ++ exit (1); ++ } + } + + mpfr_set_ui (x, 2, MPFR_RNDN); + mpfr_lngamma (y, x, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp_ui (y, 0) || MPFR_IS_NEG (y)) ++ if (mpfr_cmp_ui0 (y, 0) || MPFR_IS_NEG (y)) + { + printf ("Error for lngamma(2)\n"); + exit (1); +@@ -127,7 +157,7 @@ + mpfr_set_str (x, CHECK_X2, 10, MPFR_RNDN); + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_str (x, CHECK_Y2, 10, MPFR_RNDN); +- if (MPFR_IS_NAN (y) || mpfr_cmp (y, x)) ++ if (mpfr_cmp0 (y, x)) + { + printf ("mpfr_lngamma("CHECK_X2") is wrong:\n" + "expected "); +@@ -143,7 +173,7 @@ + mpfr_lngamma (y, x, MPFR_RNDU); + mpfr_set_prec (x, 175); + mpfr_set_str_binary (x, "0.1010001100011101101011001101110010100001000001000001110011000001101100001111001001000101011011100100010101011110100111110101010100010011010010000101010111001100011000101111E7"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (1)\n"); + exit (1); +@@ -155,7 +185,7 @@ + mpfr_lngamma (x, y, MPFR_RNDZ); + mpfr_set_prec (y, 21); + mpfr_set_str_binary (y, "0.111000101000001100101E9"); +- if (MPFR_IS_NAN (x) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (120)\n"); + printf ("Expected "); mpfr_print_binary (y); puts (""); +@@ -169,7 +199,7 @@ + inex = mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_prec (x, 206); + mpfr_set_str_binary (x, "0.10000111011000000011100010101001100110001110000111100011000100100110110010001011011110101001111011110110000001010100111011010000000011100110110101100111000111010011110010000100010111101010001101000110101001E13"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error in mpfr_lngamma (768)\n"); + exit (1); +@@ -185,7 +215,7 @@ + mpfr_set_str_binary (x, "0.1100E-66"); + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_str_binary (x, "0.1100E6"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error for lngamma(0.1100E-66)\n"); + exit (1); +@@ -199,7 +229,7 @@ + mpfr_lngamma (y, x, MPFR_RNDN); + mpfr_set_prec (x, 32); + mpfr_set_str_binary (x, "-0.10001000111011111011000010100010E207"); +- if (MPFR_IS_NAN (y) || mpfr_cmp (x, y)) ++ if (mpfr_cmp0 (x, y)) + { + printf ("Error for lngamma(-2^199+0.5)\n"); + printf ("Got "); +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-02 10:50:08.046573308 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-02 10:50:08.126574142 +0000 +@@ -0,0 +1 @@ ++muldiv-2exp-overflow +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-07-02 10:49:24.042113845 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-02 10:50:08.126574142 +0000 +@@ -1 +1 @@ +-3.1.3-p1 ++3.1.3-p2 +diff -Naurd mpfr-3.1.3-a/src/div_2si.c mpfr-3.1.3-b/src/div_2si.c +--- mpfr-3.1.3-a/src/div_2si.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/div_2si.c 2015-07-02 10:50:08.106573933 +0000 +@@ -49,7 +49,7 @@ + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +- else if (MPFR_UNLIKELY(n < 0 && (__gmpfr_emax < MPFR_EMIN_MIN - n || ++ else if (MPFR_UNLIKELY(n <= 0 && (__gmpfr_emax < MPFR_EMIN_MIN - n || + exp > __gmpfr_emax + n)) ) + return mpfr_overflow (y, rnd_mode, MPFR_SIGN(y)); + +diff -Naurd mpfr-3.1.3-a/src/div_2ui.c mpfr-3.1.3-b/src/div_2ui.c +--- mpfr-3.1.3-a/src/div_2ui.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/div_2ui.c 2015-07-02 10:50:08.106573933 +0000 +@@ -32,7 +32,7 @@ + rnd_mode), + ("y[%Pu]=%.*Rg inexact=%d", mpfr_get_prec(y), mpfr_log_prec, y, inexact)); + +- if (MPFR_UNLIKELY (MPFR_IS_SINGULAR (x))) ++ if (MPFR_UNLIKELY (n == 0 || MPFR_IS_SINGULAR (x))) + return mpfr_set (y, x, rnd_mode); + else + { +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-07-02 10:49:24.038113803 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-02 10:50:08.126574142 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3-p1" ++#define MPFR_VERSION_STRING "3.1.3-p2" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/mul_2si.c mpfr-3.1.3-b/src/mul_2si.c +--- mpfr-3.1.3-a/src/mul_2si.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/src/mul_2si.c 2015-07-02 10:50:08.106573933 +0000 +@@ -39,7 +39,7 @@ + { + mpfr_exp_t exp = MPFR_GET_EXP (x); + MPFR_SETRAW (inexact, y, x, exp, rnd_mode); +- if (MPFR_UNLIKELY( n > 0 && (__gmpfr_emax < MPFR_EMIN_MIN + n || ++ if (MPFR_UNLIKELY(n >= 0 && (__gmpfr_emax < MPFR_EMIN_MIN + n || + exp > __gmpfr_emax - n))) + return mpfr_overflow (y, rnd_mode, MPFR_SIGN(y)); + else if (MPFR_UNLIKELY(n < 0 && (__gmpfr_emin > MPFR_EMAX_MAX + n || +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-07-02 10:49:24.042113845 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-02 10:50:08.126574142 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3-p1"; ++ return "3.1.3-p2"; + } +diff -Naurd mpfr-3.1.3-a/tests/tmul_2exp.c mpfr-3.1.3-b/tests/tmul_2exp.c +--- mpfr-3.1.3-a/tests/tmul_2exp.c 2015-06-19 19:55:10.000000000 +0000 ++++ mpfr-3.1.3-b/tests/tmul_2exp.c 2015-07-02 10:50:08.106573933 +0000 +@@ -242,6 +242,76 @@ + large (MPFR_EMAX_MAX); + } + ++/* Cases where the function overflows on n = 0 when rounding is like ++ away from zero. */ ++static void ++overflow0 (mpfr_exp_t emax) ++{ ++ mpfr_exp_t old_emax; ++ mpfr_t x, y1, y2; ++ int neg, r, op; ++ static char *sop[4] = { "mul_2ui", "mul_2si", "div_2ui", "div_2si" }; ++ ++ old_emax = mpfr_get_emax (); ++ set_emax (emax); ++ ++ mpfr_init2 (x, 8); ++ mpfr_inits2 (6, y1, y2, (mpfr_ptr) 0); ++ ++ mpfr_set_inf (x, 1); ++ mpfr_nextbelow (x); ++ ++ for (neg = 0; neg <= 1; neg++) ++ { ++ RND_LOOP (r) ++ { ++ int inex1, inex2; ++ unsigned int flags1, flags2; ++ ++ /* Even if there isn't an overflow (rounding ~ toward zero), ++ the result is the same as the one of an overflow. */ ++ inex1 = mpfr_overflow (y1, (mpfr_rnd_t) r, neg ? -1 : 1); ++ flags1 = MPFR_FLAGS_INEXACT; ++ if (mpfr_inf_p (y1)) ++ flags1 |= MPFR_FLAGS_OVERFLOW; ++ for (op = 0; op < 4; op++) ++ { ++ mpfr_clear_flags (); ++ inex2 = ++ op == 0 ? mpfr_mul_2ui (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 1 ? mpfr_mul_2si (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 2 ? mpfr_div_2ui (y2, x, 0, (mpfr_rnd_t) r) : ++ op == 3 ? mpfr_div_2si (y2, x, 0, (mpfr_rnd_t) r) : ++ (MPFR_ASSERTN (0), 0); ++ flags2 = __gmpfr_flags; ++ if (!(mpfr_equal_p (y1, y2) && ++ SAME_SIGN (inex1, inex2) && ++ flags1 == flags2)) ++ { ++ printf ("Error in overflow0 for %s, mpfr_%s, emax = %" ++ MPFR_EXP_FSPEC "d,\nx = ", ++ mpfr_print_rnd_mode ((mpfr_rnd_t) r), sop[op], ++ (mpfr_eexp_t) emax); ++ mpfr_dump (x); ++ printf ("Expected "); ++ mpfr_dump (y1); ++ printf (" with inex = %d, flags =", inex1); ++ flags_out (flags1); ++ printf ("Got "); ++ mpfr_dump (y2); ++ printf (" with inex = %d, flags =", inex2); ++ flags_out (flags2); ++ exit (1); ++ } ++ } ++ } ++ mpfr_neg (x, x, MPFR_RNDN); ++ } ++ ++ mpfr_clears (x, y1, y2, (mpfr_ptr) 0); ++ set_emax (old_emax); ++} ++ + int + main (int argc, char *argv[]) + { +@@ -334,6 +404,11 @@ + underflow0 (); + large0 (); + ++ if (mpfr_get_emax () != MPFR_EMAX_MAX) ++ overflow0 (mpfr_get_emax ()); ++ overflow0 (MPFR_EMAX_MAX); ++ overflow0 (-1); ++ + tests_end_mpfr (); + return 0; + } +diff -Naurd mpfr-3.1.3-a/PATCHES mpfr-3.1.3-b/PATCHES +--- mpfr-3.1.3-a/PATCHES 2015-07-17 08:54:48.592799981 +0000 ++++ mpfr-3.1.3-b/PATCHES 2015-07-17 08:54:48.616811495 +0000 +@@ -0,0 +1 @@ ++muldiv-2exp-underflow +diff -Naurd mpfr-3.1.3-a/VERSION mpfr-3.1.3-b/VERSION +--- mpfr-3.1.3-a/VERSION 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/VERSION 2015-07-17 08:54:48.616811495 +0000 +@@ -1 +1 @@ +-3.1.3-p2 ++3.1.3-p3 +diff -Naurd mpfr-3.1.3-a/src/div_2si.c mpfr-3.1.3-b/src/div_2si.c +--- mpfr-3.1.3-a/src/div_2si.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/div_2si.c 2015-07-17 08:54:48.608807656 +0000 +@@ -45,7 +45,8 @@ + if (rnd_mode == MPFR_RNDN && + (__gmpfr_emin > MPFR_EMAX_MAX - (n - 1) || + exp < __gmpfr_emin + (n - 1) || +- (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +diff -Naurd mpfr-3.1.3-a/src/div_2ui.c mpfr-3.1.3-b/src/div_2ui.c +--- mpfr-3.1.3-a/src/div_2ui.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/div_2ui.c 2015-07-17 08:54:48.608807656 +0000 +@@ -44,7 +44,9 @@ + if (MPFR_UNLIKELY (n >= diffexp)) /* exp - n <= emin - 1 */ + { + if (rnd_mode == MPFR_RNDN && +- (n > diffexp || (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ (n > diffexp || ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN (y)); + } +diff -Naurd mpfr-3.1.3-a/src/mpfr.h mpfr-3.1.3-b/src/mpfr.h +--- mpfr-3.1.3-a/src/mpfr.h 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/src/mpfr.h 2015-07-17 08:54:48.616811495 +0000 +@@ -27,7 +27,7 @@ + #define MPFR_VERSION_MAJOR 3 + #define MPFR_VERSION_MINOR 1 + #define MPFR_VERSION_PATCHLEVEL 3 +-#define MPFR_VERSION_STRING "3.1.3-p2" ++#define MPFR_VERSION_STRING "3.1.3-p3" + + /* Macros dealing with MPFR VERSION */ + #define MPFR_VERSION_NUM(a,b,c) (((a) << 16L) | ((b) << 8) | (c)) +diff -Naurd mpfr-3.1.3-a/src/mul_2si.c mpfr-3.1.3-b/src/mul_2si.c +--- mpfr-3.1.3-a/src/mul_2si.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/src/mul_2si.c 2015-07-17 08:54:48.608807656 +0000 +@@ -48,7 +48,8 @@ + if (rnd_mode == MPFR_RNDN && + (__gmpfr_emin > MPFR_EMAX_MAX + (n + 1) || + exp < __gmpfr_emin - (n + 1) || +- (inexact >= 0 && mpfr_powerof2_raw (y)))) ++ ((MPFR_IS_NEG (y) ? inexact <= 0 : inexact >= 0) && ++ mpfr_powerof2_raw (y)))) + rnd_mode = MPFR_RNDZ; + return mpfr_underflow (y, rnd_mode, MPFR_SIGN(y)); + } +diff -Naurd mpfr-3.1.3-a/src/version.c mpfr-3.1.3-b/src/version.c +--- mpfr-3.1.3-a/src/version.c 2015-07-02 10:50:08.126574142 +0000 ++++ mpfr-3.1.3-b/src/version.c 2015-07-17 08:54:48.616811495 +0000 +@@ -25,5 +25,5 @@ + const char * + mpfr_get_version (void) + { +- return "3.1.3-p2"; ++ return "3.1.3-p3"; + } +diff -Naurd mpfr-3.1.3-a/tests/tmul_2exp.c mpfr-3.1.3-b/tests/tmul_2exp.c +--- mpfr-3.1.3-a/tests/tmul_2exp.c 2015-07-02 10:50:08.106573933 +0000 ++++ mpfr-3.1.3-b/tests/tmul_2exp.c 2015-07-17 08:54:48.608807656 +0000 +@@ -50,77 +50,82 @@ + { + mpfr_t x, y, z1, z2; + mpfr_exp_t emin; +- int i, k; ++ int i, k, s; + int prec; + int rnd; + int div; + int inex1, inex2; + unsigned int flags1, flags2; + +- /* Test mul_2si(x, e - k), div_2si(x, k - e) and div_2ui(x, k - e) +- * with emin = e, x = 1 + i/16, i in { -1, 0, 1 }, and k = 1 to 4, +- * by comparing the result with the one of a simple division. ++ /* Test mul_2si(x, e - k), div_2si(x, k - e) and div_2ui(x, k - e) with ++ * emin = e, x = s * (1 + i/16), i in { -1, 0, 1 }, s in { -1, 1 }, and ++ * k = 1 to 4, by comparing the result with the one of a simple division. + */ + emin = mpfr_get_emin (); + set_emin (e); + mpfr_inits2 (8, x, y, (mpfr_ptr) 0); + for (i = 15; i <= 17; i++) +- { +- inex1 = mpfr_set_ui_2exp (x, i, -4, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- for (prec = 6; prec >= 3; prec -= 3) +- { +- mpfr_inits2 (prec, z1, z2, (mpfr_ptr) 0); +- RND_LOOP (rnd) +- for (k = 1; k <= 4; k++) +- { +- /* The following one is assumed to be correct. */ +- inex1 = mpfr_mul_2si (y, x, e, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- inex1 = mpfr_set_ui (z1, 1 << k, MPFR_RNDN); +- MPFR_ASSERTN (inex1 == 0); +- mpfr_clear_flags (); +- /* Do not use mpfr_div_ui to avoid the optimization +- by mpfr_div_2si. */ +- inex1 = mpfr_div (z1, y, z1, (mpfr_rnd_t) rnd); +- flags1 = __gmpfr_flags; +- +- for (div = 0; div <= 2; div++) ++ for (s = 1; s >= -1; s -= 2) ++ { ++ inex1 = mpfr_set_si_2exp (x, s * i, -4, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); ++ for (prec = 6; prec >= 3; prec -= 3) ++ { ++ mpfr_inits2 (prec, z1, z2, (mpfr_ptr) 0); ++ RND_LOOP (rnd) ++ for (k = 1; k <= 4; k++) + { ++ /* The following one is assumed to be correct. */ ++ inex1 = mpfr_mul_2si (y, x, e, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); ++ inex1 = mpfr_set_ui (z1, 1 << k, MPFR_RNDN); ++ MPFR_ASSERTN (inex1 == 0); + mpfr_clear_flags (); +- inex2 = div == 0 ? +- mpfr_mul_2si (z2, x, e - k, (mpfr_rnd_t) rnd) : div == 1 ? +- mpfr_div_2si (z2, x, k - e, (mpfr_rnd_t) rnd) : +- mpfr_div_2ui (z2, x, k - e, (mpfr_rnd_t) rnd); +- flags2 = __gmpfr_flags; +- if (flags1 == flags2 && SAME_SIGN (inex1, inex2) && +- mpfr_equal_p (z1, z2)) +- continue; +- printf ("Error in underflow("); +- if (e == MPFR_EMIN_MIN) +- printf ("MPFR_EMIN_MIN"); +- else if (e == emin) +- printf ("default emin"); +- else if (e >= LONG_MIN) +- printf ("%ld", (long) e); +- else +- printf ("= LONG_MIN) ++ printf ("%ld", (long) e); ++ else ++ printf (", 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 = '4.6.7' +versionsuffix = '-mpi' + +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': '5.1.29'} +toolchainopts = {'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, + 'regressiontests-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.eb new file mode 100644 index 0000000000000000000000000000000000000000..4a945e2af83e2f8fca76dfada72081751d67909e --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.25-mpi.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 / 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 = '4.6.7' +versionsuffix = '-mpi' + +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': '5.2.25'} +toolchainopts = {'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, + 'regressiontests-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.eb new file mode 100644 index 0000000000000000000000000000000000000000..239ea564c88a384d882352de22a415a280772b31 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-4.6.7-CrayGNU-5.2.40-mpi.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 / 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 = '4.6.7' +versionsuffix = '-mpi' + +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': '5.2.40'} +toolchainopts = {'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, + 'regressiontests-%(version)s.tar.gz', +] + +builddependencies = [('CMake', '3.2.2')] + +runtest = False + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.eb new file mode 100644 index 0000000000000000000000000000000000000000..b6b649c1ecd135e8afc5c5d206f659fffebf49ca --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.2-ictce-7.1.2-mt.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 = '5.0.2' +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': 'ictce', 'version': '7.1.2'} +toolchainopts = {'openmp': True, 'usempi': False} + +source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '2.8.12'), + ('libxml2', '2.9.1') +] + +dependencies = [('Boost', '1.55.0', '-Python-2.7.8')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-hybrid.eb new file mode 100644 index 0000000000000000000000000000000000000000..0914af5ffd815e91143a287a1abd34f961e81a31 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-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 = '5.0.4' +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': '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-5.0.4-intel-2015a-mt.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.eb new file mode 100644 index 0000000000000000000000000000000000000000..f0da8f6053684f7d374eb64e64ba63dba439904c --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.4-intel-2015a-mt.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 = '5.0.4' +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': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True, 'usempi': False} + +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-5.0.5-intel-2015a-hybrid.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-intel-2015a-hybrid.eb new file mode 100644 index 0000000000000000000000000000000000000000..c7e0273a3e5ed97fdbeb84f1d2307bda240829c5 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-5.0.5-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 = '5.0.5' +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/Geant4/Geant4-10.01.p01-intel-2015a.eb b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..412c19225c040f5f5683c04e7a060fc2f3994e44 --- /dev/null +++ b/easybuild/easyconfigs/g/Geant4/Geant4-10.01.p01-intel-2015a.eb @@ -0,0 +1,24 @@ +name = 'Geant4' +version = '10.01.p01' + +homepage = 'http://geant4.cern.ch/' +description = """Geant4 is a toolkit for the simulation of the passage of particles through matter. + Its areas of application include high energy, nuclear and accelerator physics, + as well as studies in medical and space science.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://geant4.cern.ch/support/source'] +sources = ['%(namelower)s.%(version)s.tar.gz'] + +dependencies = [ + ('expat', '2.1.0'), + ('CLHEP', '2.2.0.5'), +] + +builddependencies = [('CMake', '3.2.2')] + +configopts = "-DEXPAT_LIBRARY=$EBROOTEXPAT/lib/libexpat.so -DEXPAT_INCLUDE_DIR=$EBROOTEXPAT/include" +configopts += "-DGEANT4_INSTALL_DATA=OFF" + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb new file mode 100644 index 0000000000000000000000000000000000000000..0fa0ab2a82059ddfd643b9cd7fadd2967e62876a --- /dev/null +++ b/easybuild/easyconfigs/g/GenotypeHarmonizer/GenotypeHarmonizer-1.4.14-Java-1.7.0_80.eb @@ -0,0 +1,27 @@ +easyblock = 'PackedBinary' + +name = 'GenotypeHarmonizer' +version = '1.4.14' + +homepage = 'https://github.com/molgenis/systemsgenetics/wiki/Genotype-Harmonizer' +description = """The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data + stored using different file formats with different and potentially unknown strands.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) +dependencies = [(java, javaver)] + +source_urls = ['http://www.molgenis.org/downloads/GenotypeHarmonizer/'] +sources = ['GenotypeHarmonizer-%(version)s-dist.tar.gz' ] + +checksums = ['0a7b041efdd7a5d7ced0ae48eb4a9e06'] + +sanity_check_paths = { + 'files': ['GenotypeHarmonizer.jar', 'GenotypeHarmonizer.sh'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..a7968a49296d9a3db1e0254de9f021dda3f3e338 --- /dev/null +++ b/easybuild/easyconfigs/g/GraphViz/GraphViz-2.18-intel-2014b-Perl-5.20.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PerlModule' + +name = 'GraphViz' +version = '2.18' + +homepage = 'https://metacpan.org/pod/GraphViz' +description = """This module provides a Perl interface to the amazing Graphviz, +an open source graph visualization tool from AT&T.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = ['http://cpan.metacpan.org/authors/id/R/RS/RSAVAGE/'] +sources = [SOURCE_TGZ] + +perl = 'Perl' +perlver = '5.20.0' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ("Graphviz", "2.38.0"), +] + + +options = {'modulename': 'GraphViz'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.6.eb index 757c5d4553c302b5de823106b6db9739e251b302..4d3d248af6c309c38457f3c9537231d5dca4438a 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-0.4.2-ictce-5.5.0-Python-2.7.6.eb @@ -13,8 +13,8 @@ scheduling; coroutines, in other words. This is useful when you want to control toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['http://pypi.python.org/packages/source/g/greenlet/'] -sources = ['%s-%s.zip' % (name.lower(), version)] +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_ZIP] python = "Python" pythonversion = '2.7.6' diff --git a/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb b/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..342cbc03cbd9888948dd832ac52cc340ea4f3483 --- /dev/null +++ b/easybuild/easyconfigs/g/g2log/g2log-1.0-foss-2014b.eb @@ -0,0 +1,28 @@ +name = 'g2log' +version = '1.0' +easyblock = 'CMakeMake' + +homepage = 'https://sites.google.com/site/kjellhedstrom2//g2log-efficient-background-io-processign-with-c11' +description = """g2log, efficient asynchronous logger using C++11""" + +toolchain = {'name': 'foss', 'version': '2014b'} + +source_urls = ['https://bitbucket.org/KjellKod/g2log/get/'] +sources = ['version-%(version)s.tar.gz'] + +preconfigopts = 'unzip ../3rdParty/gtest/gtest-1.6.0__stripped.zip -d ../3rdParty/gtest/ &&' +preinstallopts = 'mkdir %(installdir)s/lib && cp lib*.a %(installdir)s/lib ||' + +builddependencies = [ + ('CMake', '3.0.0'), +] + +start_dir = 'g2log' +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/liblib_g2logger.a', 'lib/liblib_activeobject.a'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gensim/gensim-0.11.1-1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/g/gensim/gensim-0.11.1-1-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..f497f885414f3605533ae38350e095ce8f31f5fe --- /dev/null +++ b/easybuild/easyconfigs/g/gensim/gensim-0.11.1-1-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'gensim' +version = '0.11.1-1' + +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': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.10' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..bf0165977fd0e4b19b1e716276f789167a5a41c8 --- /dev/null +++ b/easybuild/easyconfigs/g/getdp/getdp-2.5.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'getdp' +version = '2.5.0' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://geuz.org/getdp' +description = """GetDP is an open source finite element solver using mixed elements to discretize de Rham-type + complexes in one, two and three dimensions.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://geuz.org/getdp/src/'] +sources = ['%(name)s-%(version)s-source.tgz'] + +builddependencies = [('CMake', '3.2.2')] + +dependencies = [ + ('GSL', '1.16'), + ('PETSc', '3.5.3', versionsuffix), + ('SLEPc', '3.5.3', versionsuffix), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/getdp'], + 'dirs': ['share'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..b9b28dda44512de1295192445b2a890d43073bb4 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-goolf-1.7.20.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.2' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may + build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools + and documentation""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..238843b2065100579acf3cd7e19c1d8bea53a8a2 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.2-intel-2014.06.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.19.2' + +homepage = 'http://www.gnu.org/software/gettext/' +description = """GNU `gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +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': '2014.06'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..51c244d3eff5c7d5b62da4103211813b817abde1 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.19.4-foss-2015a.eb @@ -0,0 +1,18 @@ +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""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = '--without-emacs' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb index 48bda49ebe43fce3f118dbe803b088fc00933a2a..6a03e95dbafbc41d59d61b0dbcd5508c4488d4e6 100644 --- a/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/g/git/git-2.2.2-GCC-4.9.2.eb @@ -25,18 +25,19 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/git/git/archive'] -preconfigopts = 'make configure && ' - -# Work around git build system bug. If LIBS contains -lpthread, then configure -# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. -configopts = "--enable-pthreads='-lpthread'" - dependencies = [ ('cURL', '7.40.0'), ('expat', '2.1.0'), ('gettext', '0.19.4'), + ('Perl', '5.20.1', '-bare'), ] +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBPERLROOT} --enable-pthreads='-lpthread'" + sanity_check_paths = { 'files': ['bin/git'], 'dirs': [], diff --git a/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb b/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..ec7ac4488bbd61fefb6b589c0f6a1b799a480feb --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.4.1-GCC-4.9.2.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 +# Authors:: Dmitri Gribenko +# 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 = 'git' +version = '2.4.1' + +homepage = 'http://git-scm.com/' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/git/git/archive'] + +dependencies = [ + ('cURL', '7.40.0'), + ('expat', '2.1.0'), + ('gettext', '0.19.4'), + ('Perl', '5.20.1', '-bare'), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gmsh/gmsh-2.9.1-intel-2015a.eb b/easybuild/easyconfigs/g/gmsh/gmsh-2.9.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..40e96ab54bf184ff41973d1762bbbb4e84470260 --- /dev/null +++ b/easybuild/easyconfigs/g/gmsh/gmsh-2.9.1-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'gmsh' +version = '2.9.1' + +homepage = 'http://geuz.org/gmsh' +description = """Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://geuz.org/gmsh/src/'] +sources = ['%(name)s-%(version)s-source.tgz'] + +builddependencies = [('CMake', '3.2.2')] + +separate_build_dir = True + +configopts = '-DENABLE_FLTK=0' + +sanity_check_paths = { + 'files': ['bin/gmsh'], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..e30d4a22d3964442fee4dead1790dd0cf9d8e671 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2014b.eb @@ -0,0 +1,35 @@ +## +# 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 = '5.0.0' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.12.18'), + ('libjpeg-turbo', '1.3.1'), +] + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8f7d80279e437e7a1061d89c9f493698a37a23b3 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-5.0.0-intel-2015a.eb @@ -0,0 +1,35 @@ +## +# 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 = '5.0.0' + +homepage = 'http://gnuplot.sourceforge.net/' +description = """Portable interactive, function plotting utility""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')] + +dependencies = [ + ('cairo', '1.12.18'), + ('libjpeg-turbo', '1.4.0'), +] + +sanity_check_paths = { + 'files': ['bin/gnuplot'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2015.05.eb b/easybuild/easyconfigs/g/gompi/gompi-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..a9acbdd507e79aba4f5d0d88848625e39aa1e7f6 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2015.05.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'gompi' +version = '2015.05' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '4.9.2' +binutilsver = '2.25' +tcver = '%s-binutils-%s' % (gccver, binutilsver) + +# compiler toolchain dependencies +dependencies = [ + ('GCC', gccver, '-binutils-%s' % binutilsver), + ('binutils', binutilsver, '', ('GCC', tcver)), + ('OpenMPI', '1.8.5', '', ('GNU', '%s-%s' % (gccver, binutilsver))), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/goolf/goolf-1.5.16.eb b/easybuild/easyconfigs/g/goolf/goolf-1.5.16.eb new file mode 100644 index 0000000000000000000000000000000000000000..e9cea8d51bb4850f6be1200de796b81ca2744336 --- /dev/null +++ b/easybuild/easyconfigs/g/goolf/goolf-1.5.16.eb @@ -0,0 +1,37 @@ +easyblock = "Toolchain" + +name = 'goolf' +version = '1.5.16' + +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'} + +comp_name = 'GCC' +comp_version = '4.8.3' +comp = (comp_name, comp_version) + +blaslib = 'OpenBLAS' +blasver = '0.2.13' +blas = '%s-%s' % (blaslib, blasver) +blas_suff = '-LAPACK-3.5.0' + +# toolchain used to build goolf dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc_ver = "%s" % version +comp_mpi_tc = (comp_mpi_tc_name, comp_mpi_tc_ver) + +# compiler toolchain dependencies +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preperation functions +dependencies = [ + comp, + ('OpenMPI', '1.6.5', '', comp), # part of gompi-1.5.16 + (blaslib, blasver, blas_suff, comp_mpi_tc), + ('FFTW', '3.3.4', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s%s' % (blas, blas_suff), comp_mpi_tc) +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..d44084ea5c696190de421111735b187edcc519a4 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2014b.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': '2014b'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2015a.eb b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..03d48cbdf1cf69f7f17b3ff896b85515b8f3e7c8 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.0.4-intel-2015a.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': '2015a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/grace/grace-5.1.23-intel-2015a.eb b/easybuild/easyconfigs/g/grace/grace-5.1.23-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..208d216f7b30a3d511bb388a67e252a94a82fe26 --- /dev/null +++ b/easybuild/easyconfigs/g/grace/grace-5.1.23-intel-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'grace' +version = '5.1.23' + +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': 'intel', 'version': '2015a'} + +dependencies = [ + ('motif', '2.3.4', '-libX11-1.6.3'), + ('netCDF', '4.3.2'), +] + +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/guile/guile-1.8.8-intel-2015a.eb b/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d66e7cf11837a739f0a6cd0d3c38ebb1938643f2 --- /dev/null +++ b/easybuild/easyconfigs/g/guile/guile-1.8.8-intel-2015a.eb @@ -0,0 +1,31 @@ +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libtool', '2.4.2'), + ('GMP', '5.0.5'), + ('libunistring', '0.9.3'), + ('pkg-config', '0.27.1'), + ('libffi', '3.0.13'), + ('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/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb index 5cdf92f035541cfe3317133e862ce009ca817810..fa154ada7f7a483362f151230d9465406a9b1432 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goalf-1.1.0-no-OFED.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb index 49d7098c878710ad31eacf34082f1ecc8471bef2..558ae70b7fead833a82eff5cee73a0dea7c48c41 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-goolf-1.4.10.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb index 6de0d3d8d3aa53bd540fda7d95c5c72477842d89..0464a3968b9daadd5fce2e177691289c0a8dca31 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-3.2.2.u3.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb index 46c998562cdf1cbeb1ca1f786e6891ca86f453f4..c9298da39e098f68203b0399ec5b37e8d4571972 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.7-patch1-ictce-5.3.0.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb index b955c4abf7a5b35cd2dcf579c2cda40df6723523..8d4de54b7a9cc467b0c988b9426d0e7b12dea352 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-4.1.13.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%s/src/' % version.split('-')[0]] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb index c9f730872f6f4006d0b4d05cb59a1318add4d337..fa2a08d015f88a23d2d45730b000606a4e9d4f28 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-ictce-5.3.0.eb @@ -18,7 +18,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb index 6866cddf63e8649a6b3e3d333e96f67e9fdc88d9..fa449b6641226d1b6bcc631c9c99d29cad57952d 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.8-iqacml-3.7.3.eb @@ -20,7 +20,7 @@ dependencies = [ sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] -configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/hdf" +configopts = "--with-szlib=$EBROOTSZIP --includedir=%(installdir)s/include/%(namelower)s" sanity_check_paths = { 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb new file mode 100755 index 0000000000000000000000000000000000000000..1b265145240d6ea7e0f89738ff56a01b6db7755e --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-5.3.0-gpfs-zlib-1.2.5.eb @@ -0,0 +1,31 @@ +name = 'HDF5' +version = '1.8.10' +versionsuffix = "-gpfs" + +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5_%(version)s_configure_ictce.patch', + 'HDF5-%(version)s_mpi-includes_order_fix.patch' +] + +zlib = 'zlib' +zlibver = '1.2.5' +versionsuffix += '-%s-%s' % (zlib, zlibver) + +dependencies = [ + (zlib, zlibver), + ('Szip', '2.1'), +] + +configopts = "--enable-gpfs" + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb new file mode 100644 index 0000000000000000000000000000000000000000..caf75ce765720f6717d7c9c969ed3dca67c459c6 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.10-ictce-6.1.5-gpfs.eb @@ -0,0 +1,27 @@ +name = 'HDF5' +version = '1.8.10' +versionsuffix = "-gpfs" + +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': 'ictce', 'version': '6.1.5'} +toolchainopts = {'optarch': True, 'usempi': True, 'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'HDF5_%(version)s_configure_ictce.patch', + 'HDF5-%(version)s_mpi-includes_order_fix.patch' +] + +dependencies = [ + ('zlib', '1.2.7'), + ('Szip', '2.1'), +] + +configopts = "--enable-gpfs" + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2014b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..2af8e449bf044a78d309b97dc0aef326b903e3d6 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2014b.eb @@ -0,0 +1,21 @@ +name = 'HDF5' +version = '1.8.13' + +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': '2014b'} +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'] + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f79d365b61b675b858b3a5ff607c123d7ae398ce --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.13-foss-2015a.eb @@ -0,0 +1,25 @@ +name = 'HDF5' +version = '1.8.13' + +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': '2015a'} +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="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..35077bfe35b1c7586ed630324ffed3b37be0a40b --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-foss-2015a.eb @@ -0,0 +1,26 @@ +# Built with EasyBuild version 2.2.0dev on 2015-06-16_11-02-41 +name = 'HDF5' +version = "1.8.14" + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = [ + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-gpfs.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb similarity index 92% rename from easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-gpfs.eb rename to easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb index 081c94297ddd33ad48811872beb4006d5af52e9b..2b7af38374dd2b305c787158d6b82bcd54e5aaa6 100644 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a-gpfs.eb +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.14-intel-2015a.eb @@ -1,6 +1,5 @@ name = 'HDF5' version = '1.8.14' -versionsuffix = '-gpfs' homepage = 'http://www.hdfgroup.org/HDF5/' description = """HDF5 is a unique technology suite that makes possible the management of @@ -17,7 +16,6 @@ patches = [ 'configure_libtool.patch', ] -configopts = "--enable-gpfs" buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' dependencies = [ diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..ef7549e98750a39c283e048d38a0641d2b1e02c7 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-foss-2015a.eb @@ -0,0 +1,23 @@ +name = 'HDF5' +version = '1.8.15' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9b028b25b80993ead6d4eed8d6aeb7b7a0e9f432 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-intel-2015a.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.15' + +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': '2015a'} +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 = [ + 'HDF5-%(version)s_configure_intel.patch', + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a9ec210198beb82aa7b7f62a359dbeb28d19e940 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-foss-2015a.eb @@ -0,0 +1,23 @@ +name = 'HDF5' +version = '1.8.15-patch1' + +homepage = 'http://www.hdfgroup.org/HDF5/' +description = """HDF5 is a unique technology suite that makes possible the management of + extremely large and complex data collections.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True, 'usempi': True} + +source_urls = ['http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['configure_libtool.patch'] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..ec9b5d3a8a312b650c67e1dbcbf0e7e6d5698017 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15-patch1-intel-2015a.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +version = '1.8.15-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': '2015a'} +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 = [ + 'HDF5-1.8.15_configure_intel.patch', + 'configure_libtool.patch', +] + +buildopts = 'CXXFLAGS="$CXXFLAGS -DMPICH_IGNORE_CXX_SEEK"' + +dependencies = [ + ('zlib', '1.2.8'), + ('Szip', '2.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15_configure_intel.patch b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15_configure_intel.patch new file mode 100644 index 0000000000000000000000000000000000000000..b74e70593eec71c6a79ec650a4f1419b6af1683f --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.8.15_configure_intel.patch @@ -0,0 +1,95 @@ +--- hdf5-1.8.15/configure.orig 2015-05-01 20:56:59.000000000 +0200 ++++ hdf5-1.8.15/configure 2015-06-02 15:04:26.757168623 +0200 +@@ -5190,7 +5190,7 @@ + ac_link='$FC -o conftest$ac_exeext $FCFLAGS $LDFLAGS $ac_fcflags_srcext conftest.$ac_ext $LIBS >&5' + ac_compiler_gnu=$ac_cv_fc_compiler_gnu + if test -n "$ac_tool_prefix"; then +- for ac_prog in gfortran g95 xlf95 f95 fort ifort ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 ++ for ac_prog in gfortran g95 xlf95 f95 fort ifort mpif77 mpif90 ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 + do + # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. + set dummy $ac_tool_prefix$ac_prog; ac_word=$2 +@@ -5234,7 +5234,7 @@ + fi + if test -z "$FC"; then + ac_ct_FC=$FC +- for ac_prog in gfortran g95 xlf95 f95 fort ifort ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 ++ for ac_prog in gfortran g95 xlf95 f95 fort ifort mpif77 mpif90 ifc efc pgfortran pgf95 lf95 ftn nagfor xlf90 f90 pgf90 pghpf epcf90 g77 xlf f77 frt pgf77 cf77 fort77 fl32 af77 + do + # Extract the first word of "$ac_prog", so it can be a program name with args. + set dummy $ac_prog; ac_word=$2 +@@ -11993,7 +11993,7 @@ + ;; + # icc used to be incompatible with GCC. + # ICC 10 doesn't accept -KPIC any more. +- icc* | ifort*) ++ icc* | mpicc*| ifort* | mpif77* | mpif90*) + lt_prog_compiler_wl='-Wl,' + lt_prog_compiler_pic='-fPIC' + lt_prog_compiler_static='-static' +@@ -12629,11 +12629,11 @@ + # Portland Group f77 and f90 compilers + whole_archive_flag_spec='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive' + tmp_addflag=' $pic_flag -Mnomain' ;; +- ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64 ++ ecc*,ia64* | icc*,ia64* | mpicc*,ia64*) # Intel C compiler on ia64 + tmp_addflag=' -i_dynamic' ;; +- efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64 ++ efc*,ia64* | ifort*,ia64* | mpif77*,ia64* | mpif90*,ia64*) # Intel Fortran compiler on ia64 + tmp_addflag=' -i_dynamic -nofor_main' ;; +- ifc* | ifort*) # Intel Fortran compiler ++ ifc* | ifort* | mpif77* | mpif90*) # Intel Fortran compiler + tmp_addflag=' -nofor_main' ;; + lf95*) # Lahey Fortran 8.1 + whole_archive_flag_spec= +@@ -13115,7 +13115,7 @@ + link_all_deplibs=yes + allow_undefined_flag="$_lt_dar_allow_undefined" + case $cc_basename in +- ifort*) _lt_dar_can_shared=yes ;; ++ ifort* | mpif77* | mpif90*) _lt_dar_can_shared=yes ;; + *) _lt_dar_can_shared=$GCC ;; + esac + if test "$_lt_dar_can_shared" = "yes"; then +@@ -16113,7 +16113,7 @@ + link_all_deplibs_CXX=yes + allow_undefined_flag_CXX="$_lt_dar_allow_undefined" + case $cc_basename in +- ifort*) _lt_dar_can_shared=yes ;; ++ ifort* | mpif77* | mpif90*) _lt_dar_can_shared=yes ;; + *) _lt_dar_can_shared=$GCC ;; + esac + if test "$_lt_dar_can_shared" = "yes"; then +@@ -19024,7 +19024,7 @@ + ;; + # icc used to be incompatible with GCC. + # ICC 10 doesn't accept -KPIC any more. +- icc* | ifort*) ++ icc* | mpicc* | ifort* | mpif77* | mpif90*) + lt_prog_compiler_wl_FC='-Wl,' + lt_prog_compiler_pic_FC='-fPIC' + lt_prog_compiler_static_FC='-static' +@@ -19645,11 +19645,11 @@ + # Portland Group f77 and f90 compilers + whole_archive_flag_spec_FC='${wl}--whole-archive`for conv in $convenience\"\"; do test -n \"$conv\" && new_convenience=\"$new_convenience,$conv\"; done; func_echo_all \"$new_convenience\"` ${wl}--no-whole-archive' + tmp_addflag=' $pic_flag -Mnomain' ;; +- ecc*,ia64* | icc*,ia64*) # Intel C compiler on ia64 ++ ecc*,ia64* | icc*,ia64* | mpicc*,ia64*) # Intel C compiler on ia64 + tmp_addflag=' -i_dynamic' ;; +- efc*,ia64* | ifort*,ia64*) # Intel Fortran compiler on ia64 ++ efc*,ia64* | ifort*,ia64* | mpif77*,ia64* | mpif90*,ia64*) # Intel Fortran compiler on ia64 + tmp_addflag=' -i_dynamic -nofor_main' ;; +- ifc* | ifort*) # Intel Fortran compiler ++ ifc* | ifort* | mpif77* | mpif90*) # Intel Fortran compiler + tmp_addflag=' -nofor_main' ;; + lf95*) # Lahey Fortran 8.1 + whole_archive_flag_spec_FC= +@@ -20103,7 +20103,7 @@ + link_all_deplibs_FC=yes + allow_undefined_flag_FC="$_lt_dar_allow_undefined" + case $cc_basename in +- ifort*) _lt_dar_can_shared=yes ;; ++ ifort* | mpif77* | mpif90*) _lt_dar_can_shared=yes ;; + *) _lt_dar_can_shared=$GCC ;; + esac + if test "$_lt_dar_can_shared" = "yes"; then diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5255f85ddcd37709b77b7063e1420b3759793394 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.1b2-intel-2015a.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.1b2' + +homepage = 'http://hmmer.janelia.org/' +description = """HMMER is used for searching sequence databases for homologs of protein sequences, + and for making protein sequence alignments. It implements methods using probabilistic models + called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other + sequence alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote homologs + because of the strength of its underlying mathematical models. In the past, this strength + came at significant computational expense, but in the new HMMER3 project, HMMER is now + essentially as fast as BLAST.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +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' + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["hmmemit", "hmmsearch", "hmmscan", + "esl-alimap", "esl-cluster", "esl-mask"]], + 'dirs': [] +} + +runtest = 'check' + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb b/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb new file mode 100644 index 0000000000000000000000000000000000000000..d327bfbbab7013ccee166bd90ec9adf6eac5309b --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.0-goolf-1.5.16.eb @@ -0,0 +1,18 @@ +name = 'HPL' +version = '2.0' + +homepage = 'http://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic +on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the +High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'goolf', 'version': '1.5.16'} +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-CrayCCE-5.1.29.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..a7abc8534e34afb8081bfa5007baef3af27ba083 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.1.29.eb @@ -0,0 +1,22 @@ +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': 'CrayCCE', 'version': '5.1.29'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +patches = [ + # fix Make dependencies, so parallel build also works + 'HPL_parallel-make.patch', + 'HPL-2.1_LINKER-ld.patch', +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.25.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..109c7ddafc5bc64b7cd9ae15da082863cb2930fe --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.25.eb @@ -0,0 +1,22 @@ +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': 'CrayCCE', 'version': '5.2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +patches = [ + # fix Make dependencies, so parallel build also works + 'HPL_parallel-make.patch', + 'HPL-2.1_LINKER-ld.patch', +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..b91a1eb4990f64887a63a6fd07aa9af228ad401c --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayCCE-5.2.40.eb @@ -0,0 +1,22 @@ +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': 'CrayCCE', 'version': '5.2.40'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.netlib.org/benchmark/%(namelower)s'] + +patches = [ + # fix Make dependencies, so parallel build also works + 'HPL_parallel-make.patch', + 'HPL-2.1_LINKER-ld.patch', +] + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..806d976659065169b36f0fdb31fb8e353981bd83 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.1.29.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': '5.1.29'} +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-5.2.25.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..b4acf0c1bcaf70031d31fe2d2fb00c7d83e08a27 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.25.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': '5.2.25'} +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-5.2.40.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..dcfcc5ca6e5847bd5738fc11a2fadc254bf327ce --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayGNU-5.2.40.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': '5.2.40'} +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-5.1.29.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..c8cac688c8e6e2a9df5e1c5bd75dfd2ec190f568 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.1.29.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': '5.1.29'} +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-5.2.25.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..0344d227a57c76d8bdf6e263263d106c3127ec63 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.25.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': '5.2.25'} +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-5.2.40.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..8a33b68ad9dcb2f756de287cb4479082304842d9 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-CrayIntel-5.2.40.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': '5.2.40'} +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-2015.05.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..6e7b16eb218b302a6066f2eab752b6be2c3b27d1 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-foss-2015.05.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': '2015.05'} +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-ictce-7.3.5.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..55ab924d7d736c777533b724e480ba84428cbd6a --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-ictce-7.3.5.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': 'ictce', 'version': '7.3.5'} +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-2014.06.eb b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..38c3e337e3c2d694f19b28444f9e4692600440f8 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1-intel-2014.06.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': 'intel', 'version': '2014.06'} +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_LINKER-ld.patch b/easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch new file mode 100644 index 0000000000000000000000000000000000000000..799444d4e257fc8078ffd2d5e923e2a399bf924e --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.1_LINKER-ld.patch @@ -0,0 +1,13 @@ +Cray compiler don't like having $LINKER set to a non-absolute path +author: Kenneth Hoste (HPC-UGent) +--- hpl-2.1/makes/Make.ptest.orig 2015-04-25 13:46:18.668624435 +0200 ++++ hpl-2.1/makes/Make.ptest 2015-04-25 13:47:20.958060830 +0200 +@@ -73,7 +73,7 @@ + ( $(CP) ../HPL.dat $(BINdir) ) + # + dexe.grd: $(HPL_pteobj) $(HPLlib) +- $(LINKER) $(LINKFLAGS) -o $(xhpl) $(HPL_pteobj) $(HPL_LIBS) ++ LINKER=`which ld` $(LINKER) $(LINKFLAGS) -o $(xhpl) $(HPL_pteobj) $(HPL_LIBS) + $(MAKE) $(BINdir)/HPL.dat + $(TOUCH) dexe.grd + # diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.3.eb index 467ed7ee6db74041aa08bb4930e1c6c79717b708..e1391aa56bfbbf6bf5d7d411cb8f851b6be01822 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-goolf-1.4.10-Python-2.7.3.eb @@ -8,7 +8,7 @@ description = """A framework to process and analyze data from high-throughput se toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.3.0-Python-2.7.3.eb index d593001ecd35d0a68ecf2c69b8abc8071bc713ce..285c21b3f76d2a81c9ef7b242e417fb648367d89 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.3.0-Python-2.7.3.eb @@ -8,7 +8,7 @@ description = """A framework to process and analyze data from high-throughput se toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.5.0-Python-2.7.6.eb index 478d636658657b704604d1f9679d56f9b21f0909..411df518d3c7fd50a466d518198d8a860d9ec771 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.5.4p5-ictce-5.5.0-Python-2.7.6.eb @@ -8,7 +8,7 @@ description = """A framework to process and analyze data from high-throughput se toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['https://pypi.python.org/packages/source/H/HTSeq/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..0118dd4b321394c81e947a4e24d53643924d98ea --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.6.1p1-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'HTSeq' +version = '0.6.1p1' + +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': '2014b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.8' +pyshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) +eggname = '%%(name)s-%%(version)s-py%s-linux-x86_64.egg' % pyshortver + +dependencies = [ + (python, pythonver), + ('matplotlib', '1.3.1', versionsuffix), +] + +sanity_check_paths = { + 'files': ["bin/htseq-count", "bin/htseq-qa"], + 'dirs': ["lib/python%s/site-packages/%s" % (pyshortver, eggname)], +} + +options = {'modulename': '%(name)s'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb index fea9291ff726a03922154f42c2567644117aab0e..0b189ca56d3f4dec1c9633a205696176c2ae5459 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.5.0-cdh5.3.1-native.eb @@ -19,12 +19,15 @@ builddependencies = [ ('Maven', '3.2.3'), ('protobuf', '2.5.0'), ('CMake', '3.1.3'), + ('snappy', '1.1.2', '', ('GCC', '4.9.2')), ] dependencies = [(java, javaver)] build_native_libs = True +extra_native_libs = [('snappy', 'lib/libsnappy.so*')] + parallel = 1 moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..8b0afc7b1f5b7f0bd19946111382bf1df8603d53 --- /dev/null +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.4-intel-2015a.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': 'intel', 'version': '2015a'} +toolchainopts = {'opt': True, 'unroll': True, 'optarch': True, 'pic': True, 'cstd': 'c99'} + +source_urls = ['http://ab-initio.mit.edu/harminv/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --with-blas=mkl_em64t --with-lapack=mkl_em64t --enable-shared" + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/h/Hypre/Hypre-2.10.0b-intel-2015a.eb b/easybuild/easyconfigs/h/Hypre/Hypre-2.10.0b-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..160c06dcb805f610bc2ce81604905da9b5bacb4e --- /dev/null +++ b/easybuild/easyconfigs/h/Hypre/Hypre-2.10.0b-intel-2015a.eb @@ -0,0 +1,22 @@ +name = 'Hypre' +version = '2.10.0b' + +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': '2015a'} +toolchainopts = {'pic': True} + +# download via https://computation.llnl.gov/project/linear_solvers/download/hypre-2.10.0b_reg.php +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-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..f4b587afd4aa2054301c87265af5847f3def6a25 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-2.5.0-intel-2015a-Python-2.7.9.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': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +# to really use mpi enabled hdf5 we now seem to need a configure step +prebuildopts = ' python setup.py configure --mpi --hdf5=$EBROOTHDF5 && ' + +dependencies = [ + (python, pyver), + ('HDF5', '1.8.14'), +] + +sanity_check_paths = { + 'files': ['lib/python%(pv)s/site-packages/%%(name)s-%%(version)s-py%(pv)s-linux-x86_64.egg' % {'pv': pyshortver}], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..241e630c3511382a15e91c6a4591d50c9f813062 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'hanythingondemand' +version = '2.2.1' + +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': '2015a'} + +source_urls = [ + 'https://github.com/hpcugent/hanythingondemand/archive/' +] +sources = ['%s.tar.gz' % version] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +dependencies = [ + (python, pythonver), + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), + ('netifaces', '0.10.4', versionsuffix), + ('netaddr', '0.7.14', versionsuffix), +] + +options = {'modulename': 'hod'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..f6063d9ec35a143e9b23bae2bc733ae1d1949d8f --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.2-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'hanythingondemand' +version = '2.2.2' + +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': '2015a'} + +source_urls = [ + 'https://github.com/hpcugent/hanythingondemand/archive/' +] +sources = ['%s.tar.gz' % version] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +dependencies = [ + (python, pythonver), + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), + ('netifaces', '0.10.4', versionsuffix), + ('netaddr', '0.7.14', versionsuffix), +] + +options = {'modulename': 'hod'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..9182229d2c9e1f13e0d42aaf6cd73d6df89c6bc2 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.3-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'hanythingondemand' +version = '2.2.3' + +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': '2015a'} + +source_urls = [ + 'https://github.com/hpcugent/hanythingondemand/archive/' +] +sources = ['%s.tar.gz' % version] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +dependencies = [ + (python, pythonver), + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), + ('netifaces', '0.10.4', versionsuffix), + ('netaddr', '0.7.14', versionsuffix), +] + +options = {'modulename': 'hod'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..73433b308159d427ef171befba8b28610014dbe4 --- /dev/null +++ b/easybuild/easyconfigs/h/hanythingondemand/hanythingondemand-2.2.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'hanythingondemand' +version = '2.2.4' + +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': '2015a'} + +source_urls = [ + 'https://github.com/hpcugent/hanythingondemand/archive/' +] +sources = ['%s.tar.gz' % version] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +# a Python version with mpi4py and pbs_python (vsc.fancylogger) is required at runtime +dependencies = [ + (python, pythonver), + ('pbs_python', '4.6.0', versionsuffix), + ('vsc-mympirun', '3.4.2', '', True), + ('vsc-base', '2.1.2', '', True), + ('netifaces', '0.10.4', versionsuffix), + ('netaddr', '0.7.14', versionsuffix), +] + +options = {'modulename': 'hod'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb b/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..bd8c70bf67223e9464b03585ce21bfc46b274acd --- /dev/null +++ b/easybuild/easyconfigs/h/hisat/hisat-0.1.5-beta-goolf-1.7.20.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'hisat' +version = '0.1.5-beta' + +homepage = 'http://ccb.jhu.edu/software/hisat/index.shtml' +description = """HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. In addition to one + global FM index that represents a whole genome, HISAT uses a large set of small FM indexes that collectively cover + the whole genome (each index represents a genomic region of ~64,000 bp and ~48,000 indexes are needed to cover the + human genome). These small indexes (called local indexes) combined with several alignment strategies enable effective + alignment of RNA-seq reads, in particular, reads spanning multiple exons. The memory footprint of HISAT is relatively + low (~4.3GB for the human genome). We have developed HISAT based on the Bowtie2 implementation to handle most of the + operations on the FM index. """ + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sources = ['%(name)s-%(version)s-source.zip'] +source_urls = ['http://ccb.jhu.edu/software/hisat/downloads/'] + +checksums = ['9524a0170d85c5b560b51e0087f4cf46'] + +executables = [name, 'hisat-build', 'hisat-inspect', 'hisat-build-s', 'hisat-inspect-s', 'hisat-align-s', + 'hisat-build-l', 'hisat-inspect-l', 'hisat-align-l'] +files_to_copy = [(executables, 'bin')] + + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..33b2aeafd6639d9f349403cd6d394393a9c0af3c --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.10.1-GNU-4.9.2-2.25.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.10.1' + +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': 'GNU', 'version': '4.9.2-2.25'} + +dependencies = [('numactl', '2.0.10')] + +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-1.7.2-ictce-5.5.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..1f891126fda663c4c5aebf6d38c3e68af3503871 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.7.2-ictce-5.5.0.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = "1.7.2" + +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': 'ictce', 'version': '5.5.0'} + +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/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..0ee4a4f74034fad3f36869481aeeec6c9b721695 --- /dev/null +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.1-goolf-1.4.10.eb @@ -0,0 +1,41 @@ +# 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 + +# "make install" doesnt copy all the compiled binaries so we use the "MakeCp" easyblock +# to be sure everything is copied and we run ./configure in premakeopts +easyblock = 'MakeCp' + +name = 'IDBA-UD' +version = '1.1.1' + +homepage = 'http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/' +description = """ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads + Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. + IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth + contigs are removed iteratively with cutoff threshold from low to high to reduce the errors + in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled + locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD + can iterate k value of de Bruijn graph to a very large value with less gaps and less branches + to form long contigs in both low-depth and high-depth regions.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://hku-idba.googlecode.com/files/'] +sources = ['idba-%(version)s.tar.gz'] + +prebuildopts = './configure && ' + +# we delete every .o file which is left in bin folder +buildopts = ' && rm -fr bin/*.o && rm -fr bin/Makefile*' + +files_to_copy = ["bin", "script", "README", "ChangeLog", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["idba", "idba_hybrid", "idba_tran", + "idba_ud", "parallel_blat", "idba_tran_test"]], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb new file mode 100644 index 0000000000000000000000000000000000000000..0c2d1cc059f006bddc7a05b94fb798a5367e0932 --- /dev/null +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_dynamic.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'IMPUTE2' +version = '2.3.0' +versionsuffix = '_x86_64_dynamic' + +homepage = 'http://mathgen.stats.ox.ac.uk/impute/impute_v2.html' +description = """ IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation + and haplotype phasing program based on ideas from Howie et al. 2009 """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://mathgen.stats.ox.ac.uk/impute/'] +sources = ['%s_v%s%s.tgz' % (name.lower().rstrip('2'), version, versionsuffix)] + +sanity_check_paths = { + 'files': ["impute2"], + 'dirs': ["Example"] +} + +# add the top dir to PATH +modextrapaths = { + 'PATH': '' +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb new file mode 100644 index 0000000000000000000000000000000000000000..0fb795f7ebb564400e36a11a7e35d953cd58f5a7 --- /dev/null +++ b/easybuild/easyconfigs/i/IMPUTE2/IMPUTE2-2.3.0_x86_64_static.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = "Tarball" + +name = 'IMPUTE2' +version = '2.3.0' +versionsuffix = '_x86_64_static' + +homepage = 'http://mathgen.stats.ox.ac.uk/impute/impute_v2.html' +description = """ IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation + and haplotype phasing program based on ideas from Howie et al. 2009 """ + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://mathgen.stats.ox.ac.uk/impute/'] +sources = ['%s_v%s%s.tgz' % (name.lower().rstrip('2'), version, versionsuffix)] + +sanity_check_paths = { + 'files': ["impute2"], + 'dirs': ["Example"] +} + +# add the top dir to PATH +modextrapaths = { + 'PATH': '' +} + +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-goolf-1.4.10.eb new file mode 100755 index 0000000000000000000000000000000000000000..690d220498ad0ff3898c804498cf8d4ef8983efe --- /dev/null +++ b/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-goolf-1.4.10.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': 'goolf', 'version': '1.4.10'} + +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/IMa2/IMa2-8.27.12-ictce-5.5.0.eb b/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-ictce-5.5.0.eb new file mode 100755 index 0000000000000000000000000000000000000000..a3ed62f5d6aa488d3e79a67e80fa2d071732178d --- /dev/null +++ b/easybuild/easyconfigs/i/IMa2/IMa2-8.27.12-ictce-5.5.0.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': 'ictce', 'version': '5.5.0'} + +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/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb index 3c52ea836c798912cb345632a59c5f5ce2a91da5..92f605169bdefe0d13a2793776b66062185261b6 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-1.1.0-goolf-1.4.10-Python-2.7.3.eb @@ -14,11 +14,14 @@ description = """IPython provides a rich architecture for interactive computing toolchain = {'name': 'goolf', 'version': '1.4.10'} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://archive.ipython.org/release/%(version)s/'] +source_urls = [ + PYPI_LOWER_SOURCE, + 'http://archive.ipython.org/release/%(version)s/', +] python = 'Python' pyver = '2.7.3' -pyshortver = '2.7' +pyshortver = '.'.join(pyver.split('.')[:2]) versionsuffix = '-%s-%s' % (python, pyver) dependencies = [ diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..4ddce0d14217ddea9252339d3f412bfbf3096dc5 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.1.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,45 @@ +easyblock = "PythonPackage" + +name = 'IPython' +version = '3.1.0' + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + PYPI_LOWER_SOURCE, + 'http://archive.ipython.org/release/%(version)s/', +] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('pysqlite', '2.6.3', versionsuffix), + ('PyZMQ', '14.6.0', '%s-zmq3' % versionsuffix), + ('requests', '2.6.2', versionsuffix), + ('Pygments', '2.0.2', versionsuffix), +] + +# override extensions sanity check, default filter that imports a Python module doesn't work here +exts_filter = ('ipython -h', "") + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], +} + +sanity_check_commands = [('iptest','')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..ca831cfe277d6b150831f9d9ed43addffeb5ac45 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,45 @@ +easyblock = "PythonPackage" + +name = 'IPython' +version = '3.2.0' + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + PYPI_LOWER_SOURCE, + 'http://archive.ipython.org/release/%(version)s/', +] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('pysqlite', '2.6.3', versionsuffix), + ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), + ('requests', '2.7.0', versionsuffix), + ('Pygments', '2.0.2', versionsuffix), +] + +# override extensions sanity check, default filter that imports a Python module doesn't work here +exts_filter = ('ipython -h', '') + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], +} + +sanity_check_commands = [('iptest','')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..5b0893e10be373866c73d86d2eb56554615bc7b7 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-3.2.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,45 @@ +easyblock = "PythonPackage" + +name = 'IPython' +version = '3.2.0' + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + PYPI_LOWER_SOURCE, + 'http://archive.ipython.org/release/%(version)s/', +] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('pysqlite', '2.6.3', versionsuffix), + ('PyZMQ', '14.7.0', '%s-zmq3' % versionsuffix), + ('requests', '2.7.0', versionsuffix), + ('Pygments', '2.0.2', versionsuffix), +] + +# override extensions sanity check, default filter that imports a Python module doesn't work here +exts_filter = ('ipython -h', '') + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/IPython' % pyshortver], +} + +sanity_check_commands = [('iptest','')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb index 3ba25676db502ead45b181e724635c338a3bc3a4..f6423e5d6eb43d9926048ed3846f1c38e871353e 100644 --- a/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/i/ISL/ISL-0.14-GCC-4.9.2.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} source_urls = ['http://isl.gforge.inria.fr/'] sources = [SOURCELOWER_TAR_BZ2] -dependencies = [('GMP', '6.0.0')] +dependencies = [('GMP', '6.0.0a')] sanity_check_paths = { 'files': ['lib/libisl.so', 'lib/libisl.a'], diff --git a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb index 1ed83c45264e9253c0289137d110911f75f3673e..7dc3787320bc598d08a264e33b4b08762faf3e69 100644 --- a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-goolf-1.4.10.eb @@ -32,7 +32,7 @@ with_configure = True graphlib_version = '0.3' preconfigopts = "cd ../graphlib-%s && ./configure && make && " % graphlib_version # build isoinfer, make sure we can link to libgraph.a -preconfigopts += "cd ../isoinfer-%(version)s && " +preconfigopts += "cd ../%(namelower)s-%(version)s && " preconfigopts += 'export LDFLAGS="$LDFLAGS -L%%(builddir)s/graphlib-%s/src" && ' % graphlib_version files_to_copy = [ diff --git a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb index 3f65089c099e3b915fbbf0507c318aff46d4c66f..436dd9a680a2451f2d7f6ce26212a76346e6fe97 100644 --- a/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/i/IsoInfer/IsoInfer-0.9.1-ictce-6.2.5.eb @@ -32,7 +32,7 @@ with_configure = True graphlib_version = '0.3' preconfigopts = "cd ../graphlib-%s && ./configure && make && " % graphlib_version # build isoinfer, make sure we can link to libgraph.a -preconfigopts += "cd ../isoinfer-%(version)s && " +preconfigopts += "cd ../%(namelower)s-%(version)s && " preconfigopts += 'export LDFLAGS="$LDFLAGS -L%%(builddir)s/graphlib-%s/src" && ' % graphlib_version files_to_copy = [ diff --git a/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb new file mode 100644 index 0000000000000000000000000000000000000000..55dec91be55769f4d5b613c34fd41901c312f15c --- /dev/null +++ b/easybuild/easyconfigs/i/icc/icc-2015.3.187.eb @@ -0,0 +1,17 @@ +name = 'icc' +version = '2015.3.187' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "C and C++ compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_ccompxe_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb new file mode 100644 index 0000000000000000000000000000000000000000..8387432380faa1b66b676bf56a488f1a29294895 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifort/iccifort-2015.3.187.eb @@ -0,0 +1,16 @@ +easyblock = "Toolchain" + +name = 'iccifort' +version = '2015.3.187' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C,C++ and fortran compilers, Intel MPI and Intel MKL""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +dependencies = [ + ('icc', version), + ('ifort', version), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb b/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..6190ed29063cb5fa8e792ec610c143be93114617 --- /dev/null +++ b/easybuild/easyconfigs/i/ictce/ictce-7.3.5.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'ictce' +version = '7.3.5' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +suff = '3.187' +compver = '2015.%s' % suff + +dependencies = [ # version/released + ('icc', compver), # Apr 13th 2015 + ('ifort', compver), # Apr 13th 2015 + ('impi', '5.0.3.048', '', ('iccifort', compver)), # Feb 10th 2015 + ('imkl', '11.2.%s' % suff, '', ('iimpi', version)), # Apr 13th 2015 +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb new file mode 100644 index 0000000000000000000000000000000000000000..8253a3390bf1b285389443b8f083d2d3d9c46fee --- /dev/null +++ b/easybuild/easyconfigs/i/ifort/ifort-2015.3.187.eb @@ -0,0 +1,17 @@ +name = 'ifort' +version = '2015.3.187' + +homepage = 'http://software.intel.com/en-us/intel-compilers/' +description = "Fortran compiler from Intel" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['l_fcompxe_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-5.5.0-GCC-4.8.3.eb b/easybuild/easyconfigs/i/iimpi/iimpi-5.5.0-GCC-4.8.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..692710542886fd83bb6da54dc777288a36717082 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-5.5.0-GCC-4.8.3.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'iimpi' +version = '5.5.0' +versionsuffix = '-GCC-4.8.3' + +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'} + +suff = '5.192' +compver = '2013.%s' % suff + +dependencies = [ # version/released + ('icc', compver, versionsuffix), # 28 Apr 2014 + ('ifort', compver, versionsuffix), # 28 Apr 2014 + ('impi', '4.1.1.036', '', ('iccifort', '%s%s' % (compver, versionsuffix))), # 06 Mar 2014 +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..b0fe67cb26eafd431e86a5f22653622865fd9ad2 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-7.3.5.eb @@ -0,0 +1,18 @@ +easyblock = "Toolchain" + +name = 'iimpi' +version = '7.3.5' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +compver = '2015.3.187' +dependencies = [ + ('icc', compver), + ('ifort', compver), + ('impi', '5.0.3.048', '', ('iccifort', compver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..e04b1511363de673517ff592f95da214d23ca8a9 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.0.5.192-iimpi-5.5.0-GCC-4.8.3.eb @@ -0,0 +1,22 @@ +name = 'imkl' +version = '11.0.5.192' + +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': '5.5.0-GCC-4.8.3'} + +sources = ['l_mkl_%(version)s.tgz'] + +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-11.2.3.187-iimpi-7.3.5.eb b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..807b5f200467b8fe766651769e26fb2dc0398db1 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-11.2.3.187-iimpi-7.3.5.eb @@ -0,0 +1,22 @@ +name = 'imkl' +version = '11.2.3.187' + +homepage = 'http://software.intel.com/en-us/intel-mkl/' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpi', 'version': '7.3.5'} + +sources = ['l_mkl_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +interfaces = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..00ee030d34f072ef17e780e76da6632a82eea431 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-4.1.1.036-iccifort-2013.5.192-GCC-4.8.3.eb @@ -0,0 +1,19 @@ +name = 'impi' +version = '4.1.1.036' + +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': '2013.5.192-GCC-4.8.3'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb new file mode 100644 index 0000000000000000000000000000000000000000..5e0972d8f3ef5fbe04aa75c53478eb9144f08cdd --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.0.3.048-iccifort-2015.3.187.eb @@ -0,0 +1,19 @@ +name = 'impi' +version = '5.0.3.048' + +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': '2015.3.187'} + +sources = ['l_mpi_p_%(version)s.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb new file mode 100644 index 0000000000000000000000000000000000000000..fb7853e6f59371ef26225e73f45155111ab886a8 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-5.1.0.079-iccifort-2015.3.187.eb @@ -0,0 +1,20 @@ +name = 'impi' +version = '5.1.0.079' + +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': '2015.3.187'} + +# source tarball doesn't match actual version?! +sources = ['l_mpi_p_5.1.0.038.tgz'] + +dontcreateinstalldir = 'True' + +# license file +import os +license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic") + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0437a042dbb3891fc9d8440e099ce18063758faa --- /dev/null +++ b/easybuild/easyconfigs/i/inputproto/inputproto-2.3-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'inputproto' +version = '2.3' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org InputProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +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-2014.06.eb b/easybuild/easyconfigs/i/intel/intel-2014.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..57c2903c5774d8af57b1288fe7268e3dc8431e69 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2014.06.eb @@ -0,0 +1,23 @@ +easyblock = "Toolchain" + +name = 'intel' +version = '2014.06' + +homepage = 'http://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +suff = '5.192' +compver = '2013.%s' % suff + +gccsuff = '-GCC-4.8.3' + +dependencies = [ + ('icc', compver, gccsuff), + ('ifort', compver, gccsuff), + ('impi', '4.1.1.036', '', ('iccifort', '%s%s' % (compver, gccsuff))), + ('imkl', '11.0.5.192', '', ('iimpi', '5.5.0%s' % gccsuff)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..903be570eba76b8d092434cb05f7d7991af2b900 --- /dev/null +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.3.eb @@ -0,0 +1,23 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'JUBE' +version = '2.0.3' + +homepage = "http://www.fz-juelich.de/jsc/jube" +description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, + run those sets on different computer systems and evaluate the results.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] +sources = [SOURCE_TAR_GZ] +checksums = ['8afc5e3959752e7541f5f59b07fd1e1c'] + +options = {'modulename': 'jube2'} + +sanity_check_paths = { + 'files': ['bin/jube'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..545b5785eada40b34061adf8097d4741040ecd91 --- /dev/null +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.4.eb @@ -0,0 +1,23 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'JUBE' +version = '2.0.4' + +homepage = "http://www.fz-juelich.de/jsc/jube" +description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, + run those sets on different computer systems and evaluate the results.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] +sources = [SOURCE_TAR_GZ] +checksums = ['96a7946d38d678b25ba4bbd539482a14'] + +options = {'modulename': 'jube2'} + +sanity_check_paths = { + 'files': ['bin/jube'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..b270f53d57e3e3d997743f6207a0f4a5e01843dd --- /dev/null +++ b/easybuild/easyconfigs/j/JUBE/JUBE-2.0.5.eb @@ -0,0 +1,23 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'JUBE' +version = '2.0.5' + +homepage = "http://www.fz-juelich.de/jsc/jube" +description = """The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, + run those sets on different computer systems and evaluate the results.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://apps.fz-juelich.de/jsc/jube/jube2/download.php?file='] +sources = [SOURCE_TAR_GZ] +checksums = ['f506e9f39898af3d7456890ba219ab90'] + +options = {'modulename': 'jube2'} + +sanity_check_paths = { + 'files': ['bin/jube'], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_79.eb b/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_79.eb new file mode 100644 index 0000000000000000000000000000000000000000..4c4751893b45d2ac36d4cf571a163b3a04e515f2 --- /dev/null +++ b/easybuild/easyconfigs/j/JUnit/JUnit-4.11-Java-1.7.0_79.eb @@ -0,0 +1,25 @@ +easyblock = 'JAR' + +name = 'JUnit' +version = '4.11' + +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/'] + +java = 'Java' +javaver = '1.7.0_79' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': sources, + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..feca7c584a414ef52eb3b8880a6fd04cf646dc54 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.1.29.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': 'CrayGNU', 'version': '5.1.29'} +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-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..606c94876ce68c925106b0330656cf55463dd8ca --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.25.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': 'CrayGNU', 'version': '5.2.25'} +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-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..cef32fd43d8333a8283e01e55c21ce7eeeff8cb1 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-CrayGNU-5.2.40.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': 'CrayGNU', 'version': '5.2.40'} +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-foss-2015a.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..02cb1d4f4c8f76a6dec82b0400463ea2d02d393b --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-foss-2015a.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': '2015a'} +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-2014.06.eb b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2014.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..41dba8410ee56cdde0cffbb59ff8c861a5391533 --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-1.900.1-intel-2014.06.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': '2014.06'} +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-1.7.0_79.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_79.eb new file mode 100644 index 0000000000000000000000000000000000000000..d7b280abb2396474be7ce210ac24bd3709629c0e --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_79.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.7.0_79' + +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-1.7.0_80.eb b/easybuild/easyconfigs/j/Java/Java-1.7.0_80.eb new file mode 100644 index 0000000000000000000000000000000000000000..9acb602fa14a87a41d79211cea08804bd43118db --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.7.0_80.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.7.0_80' + +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_45.eb b/easybuild/easyconfigs/j/Java/Java-1.8.0_45.eb new file mode 100644 index 0000000000000000000000000000000000000000..50a687a0505c8706344f43480761d4e8ac222c6d --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8.0_45.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8.0_45' + +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-2.1.3-foss-2014b.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..bd77b8e773e08f359083cb4fae7603cc6e9b2004 --- /dev/null +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-foss-2014b.eb @@ -0,0 +1,28 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +easyblock = 'ConfigureMake' + +name = 'Jellyfish' +version = '2.1.3' + +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': 'foss', 'version': '2014b'} + +source_urls = ['ftp://ftp.genome.umd.edu/pub/jellyfish/'] +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*'" + +sanity_check_paths = { + 'files': ['bin/jellyfish'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb index 595bb566df9266eb5e928cd0dd4ddb07d4ca7954..e874c0503026a44dbee2ecc595f8b54b422f12c6 100644 --- a/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/j/Jellyfish/Jellyfish-2.1.3-goolf-1.4.10.eb @@ -18,7 +18,8 @@ sources = [SOURCELOWER_TAR_GZ] parallel = 1 -runtest = "check" +# 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*'" sanity_check_paths = { 'files': ['bin/jellyfish'], diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb index f06323716c59cec7de19ea4fd5f221ba8257aae0..46c4f977e8c60159001cb4a9dc1ecdf5084be5f3 100644 --- a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "Jinja2" version = "2.6" -homepage = "http://pypi.python.org/pypi/Jinja2" +homepage = "https://pypi.python.org/pypi/Jinja2" description = """Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.""" diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb index 88fdc36fa58fb47e5f339a14f5d34baf4e246f36..e37ffbc4e200b2442519fcfb932711f027575f65 100644 --- a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-goolf-1.4.10-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "Jinja2" version = "2.6" -homepage = "http://pypi.python.org/pypi/Jinja2" +homepage = "https://pypi.python.org/pypi/Jinja2" description = """Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb index 47071467089e8054d952068481557ca0ad5f1e07..191856a900b64cc36bb0f071978369ac2e9650a3 100644 --- a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-4.0.6-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "Jinja2" version = "2.6" -homepage = "http://pypi.python.org/pypi/Jinja2" +homepage = "https://pypi.python.org/pypi/Jinja2" description = """Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.""" diff --git a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb index a801441c8b62cf7c086d613b1037114c4dfc874a..9711dba080d22d65d1138b2658f583a361ec302e 100644 --- a/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/j/Jinja2/Jinja2-2.6-ictce-5.3.0-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "Jinja2" version = "2.6" -homepage = "http://pypi.python.org/pypi/Jinja2" +homepage = "https://pypi.python.org/pypi/Jinja2" description = """Jinja2 is a template engine written in pure Python. It provides a Django inspired non-XML syntax but supports inline expressions and an optional sandboxed environment.""" diff --git a/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..62923f260f75b2e09b1850a3cba8f59e1c2c4838 --- /dev/null +++ b/easybuild/easyconfigs/k/kbproto/kbproto-1.0.7-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'kbproto' +version = '1.0.7' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X.org KBProto protocol headers.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files': ['include/X11/extensions/%s' % x for x in ['XKBgeom.h', 'XKB.h', 'XKBproto.h', 'XKBsrv.h', 'XKBstr.h']], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0-headless.eb b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0-headless.eb new file mode 100644 index 0000000000000000000000000000000000000000..d4e5cc4292a396e45f6841e909438acb44ef6f8a --- /dev/null +++ b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9-ictce-5.5.0-headless.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'LAMARC' +version = '2.1.9' +versionsuffix = '-headless' + +homepage = 'http://evolution.genetics.washington.edu/lamarc/' +description = """LAMARC is a program which estimates population-genetic parameters such as population size, + population growth rate, recombination rate, and migration rates.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +source_urls = ['http://evolution.genetics.washington.edu/lamarc/download/'] +sources = ['%(namelower)s-%(version)s-src.tgz'] + +patches = ['LAMARC-2.1.9_Makefile-fix.patch'] + +configopts = "--disable-converter --disable-gui" + +sanity_check_paths = { + 'files': ["bin/lamarc"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9_Makefile-fix.patch b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9_Makefile-fix.patch new file mode 100644 index 0000000000000000000000000000000000000000..74db39ff1cb9940d4fc4ecadde6a029acbdf6878 --- /dev/null +++ b/easybuild/easyconfigs/l/LAMARC/LAMARC-2.1.9_Makefile-fix.patch @@ -0,0 +1,10 @@ +--- lamarc/Makefile.in.orig 2014-03-19 14:25:08.261820031 +0100 ++++ lamarc/Makefile.in 2014-03-19 14:25:15.382031107 +0100 +@@ -1810,7 +1810,6 @@ + doc/html/genotype.html \ + doc/html/glossary.html \ + doc/html/growthmenu.html \ +- doc/html/forces.html \ + doc/html/index.html \ + doc/html/insumfile.2reg3rep.html \ + doc/html/insumfile.2reg3rep.xml \ diff --git a/easybuild/easyconfigs/l/LAPACK/LAPACK-3.5.0-gompi-1.5.16.eb b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.5.0-gompi-1.5.16.eb new file mode 100644 index 0000000000000000000000000000000000000000..0027dce752ccee40cb092e3037f1b84b9411ea54 --- /dev/null +++ b/easybuild/easyconfigs/l/LAPACK/LAPACK-3.5.0-gompi-1.5.16.eb @@ -0,0 +1,15 @@ +name = 'LAPACK' +version = "3.5.0" + +homepage = 'http://www.netlib.org/lapack/' +description = """LAPACK is written in Fortran90 and provides routines for solving systems of + simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue + problems, and singular value problems.""" + +toolchain = {'name': 'gompi', 'version': '1.5.16'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TGZ] +source_urls = [homepage] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..46a3c3ee49fd8d5df3ad41acd37397ff284c70fb --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.0.3' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..e29ed51d54a3e8d8fa6a052963032a210439e63c --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.3-intel-2014.06.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 = 'LibTIFF' +version = '4.0.3' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +toolchain = {'name': 'intel', 'version': '2014.06'} + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..70578c5f23ecd7eae1d286fe27ec6f9160d09924 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-foss-2015a.eb @@ -0,0 +1,34 @@ +# Built with EasyBuild version 2.2.0dev on 2015-06-16_10-51-42 +## +# 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 = 'LibTIFF' +version = '4.0.4' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'foss', 'version': '2015a'} + +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-4.0.4-intel-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6b0d237d173faa8e8c9cbc79a3d8ab1c2d8af7fe --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4-intel-2015a.eb @@ -0,0 +1,34 @@ +# Built with EasyBuild version 2.2.0dev on 2015-06-16_10-51-42 +## +# 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 = 'LibTIFF' +version = '4.0.4' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'intel', 'version': '2015a'} + +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-4.0.4beta-foss-2015a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..accbb2bb0a71dcbc746fb52a30f151707c1e2fcc --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.4beta-foss-2015a.eb @@ -0,0 +1,35 @@ +# Built with EasyBuild version 2.2.0dev on 2015-06-16_10-51-42 +## +# 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 = 'LibTIFF' +# misleading name, this is a 'stable' release +version = '4.0.4beta' + +homepage = 'http://www.remotesensing.org/libtiff/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +source_urls = [ + 'http://download.osgeo.org/libtiff/', + 'ftp://ftp.remotesensing.org/pub/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] + +toolchain = {'name': 'foss', 'version': '2015a'} + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..7d4d9128c9401b9150ee0ccf2d47274e571349f3 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.1.29.eb @@ -0,0 +1,24 @@ +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': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'opt': True, '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.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..e7bca79f1d79fda628bdc5418373ca92cf68ef98 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.25.eb @@ -0,0 +1,24 @@ +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': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'opt': True, '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.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..4f2df4435212a833351fb15915b6d8d3f2c1320f --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-1.1.4-CrayGNU-5.2.40.eb @@ -0,0 +1,24 @@ +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': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'opt': True, '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.a' % x for x in ['deriv', 'int', 'r12']] + + ['lib/lib%s.so' % x for x in ['deriv', 'int', 'r12']], + 'dirs':[], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..57f6a9f4e3f631531f27facbf86040b16e92fdf6 --- /dev/null +++ b/easybuild/easyconfigs/l/libICE/libICE-1.0.9-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libICE' +version = '1.0.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Inter-Client Exchange library for freedesktop.org""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('xtrans', '1.3.5'), +] + +builddependencies = [ + ('xproto', '7.0.27'), +] + +sanity_check_paths = { + 'files' : ['include/X11/ICE/ICE%s.h' % x for x in ['', 'conn', 'lib', 'msg', 'proto', 'util']], + 'dirs' : [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7d8fcfe61addb4eda143576e468742909975f991 --- /dev/null +++ b/easybuild/easyconfigs/l/libSM/libSM-1.2.2-intel-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libSM' +version = '1.2.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 Session Management library, which allows for applications to both manage sessions, + and make use of session managers to save and restore their state for later use.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/lib/'] + +dependencies = [ + ('libICE', '1.0.9'), +] +builddependencies = [ + ('xproto', '7.0.27'), + ('xtrans', '1.3.5'), +] + +sanity_check_paths = { + 'files' : ['include/X11/SM/%s' % x for x in ['SM.h', 'SMlib.h', 'SMproto.h']], + 'dirs' : [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libXScrnSaver/libXScrnSaver-1.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libXScrnSaver/libXScrnSaver-1.2.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0889930509402b0b32bc7a0bd8de6ba4c9cfdf34 --- /dev/null +++ b/easybuild/easyconfigs/l/libXScrnSaver/libXScrnSaver-1.2.2-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libXScrnSaver' +version = '1.2.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 Screen Saver extension client library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('libX11', '1.6.3', '-Python-2.7.9'), + ('libXext', '1.3.3') +] + +sanity_check_paths = { + 'files': ['lib/libXss.a', 'lib/libXss.so', 'include/X11/extensions/scrnsaver.h'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2015a.eb b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3129ec62b114c097d13f74a946cd86458666f6f6 --- /dev/null +++ b/easybuild/easyconfigs/l/libXfixes/libXfixes-5.0.1-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libXfixes' +version = '5.0.1' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X Fixes extension library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('fixesproto', '5.0'), + ('xextproto', '7.3.0'), +] + +sanity_check_paths = { + 'files' : ['include/X11/extensions/Xfixes.h', 'lib/libXfixes.a', 'lib/libXfixes.so'], + 'dirs' : [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..65123b2fae75491d544f2a8225532a30c136786d --- /dev/null +++ b/easybuild/easyconfigs/l/libXft/libXft-2.3.2-intel-2015a-libX11-1.6.3.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'libXft' +version = '2.3.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.6'), + ('renderproto', '0.11'), +] + +libx11ver = '1.6.3' +versionsuffix = '-libX11-%s' % libx11ver + +dependencies = [ + ('libX11', libx11ver, '-Python-2.7.9'), + ('libXrender', '0.9.9'), + ('freetype', '2.5.5'), + ('fontconfig', '2.11.93'), +] + +sanity_check_paths = { + 'files': ['lib/libXft.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..20988d4e6e69b2efc0e0d25e070b2e45710d4e18 --- /dev/null +++ b/easybuild/easyconfigs/l/libXi/libXi-1.7.4-intel-2015a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' +name = 'libXi' +version = '1.7.4' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """LibXi provides an X Window System client interface to the XINPUT extension to the X protocol.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +dependencies = [ + ('xproto', '7.0.27'), + ('xextproto', '7.3.0'), + ('libXext', '1.3.3'), + ('inputproto', '2.3'), + ('libXfixes', '5.0.1'), +] + +sanity_check_paths = { + 'files' : ['include/X11/extensions/XInput.h', 'include/X11/extensions/XInput2.h', 'lib/libXi.so', 'lib/libXi.a'], + 'dirs' : [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb index 778cd1670cc7f85fc419bb7b4c592dd8c77df7b9..cea866f2b70edc72597ed741ce9f067862012f5b 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-foss-2014b.eb @@ -12,11 +12,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('kbproto', '1.0.6'), ('renderproto', '0.11'), ] dependencies = [ - ('kbproto', '1.0.6'), ('libX11', '1.6.2', '-Python-2.7.8'), ] diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb index fe8ecdca33913919ab4509674cd319a77c345d67..80e0f6ea245a0d1779817f08d5d5a1bd2730d8f2 100644 --- a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.8-intel-2014b.eb @@ -12,11 +12,11 @@ sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] builddependencies = [ + ('kbproto', '1.0.6'), ('renderproto', '0.11'), ] dependencies = [ - ('kbproto', '1.0.6'), ('libX11', '1.6.2', '-Python-2.7.8'), ] diff --git a/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..52e06388f33af85749323d1f1fcd9f3305e6a94e --- /dev/null +++ b/easybuild/easyconfigs/l/libXrender/libXrender-0.9.9-intel-2015a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libXrender' +version = '0.9.9' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """X11 client-side library""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('kbproto', '1.0.7'), + ('renderproto', '0.11'), +] + +dependencies = [ + ('libX11', '1.6.3', '-Python-2.7.9'), +] + +sanity_check_paths = { + 'files': ['lib/libXrender.a'], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2015a-libX11-1.6.3.eb b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2015a-libX11-1.6.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..507c378340f0f54124909e8297dd53ea7202c3dc --- /dev/null +++ b/easybuild/easyconfigs/l/libXt/libXt-1.1.4-intel-2015a-libX11-1.6.3.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'libXt' +version = '1.1.4' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are + based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation).""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +libx11ver = '1.6.3' +versionsuffix = '-libX11-%s' % libx11ver +dependencies = [ + ('libSM', '1.2.2'), + ('libICE', '1.0.9'), + ('libX11', libx11ver, '-Python-2.7.9'), +] + +builddependencies = [ + ('xproto', '7.0.27'), + ('kbproto', '1.0.6'), +] + +sanity_check_paths = { + 'files' : ['include/X11/%s' % x for x in [ + 'CallbackI.h', 'CompositeP.h', 'Constraint.h', 'Core.h', 'CreateI.h', 'HookObjI.h', 'Intrinsic.h', + 'IntrinsicP.h', 'ObjectP.h', 'RectObj.h', 'ResConfigP.h', 'SelectionI.h', 'ShellI.h', 'StringDefs.h', + 'TranslateI.h', 'Vendor.h', 'Xtos.h', 'Composite.h', 'ConstrainP.h', 'ConvertI.h', 'CoreP.h', 'EventI.h', + 'InitialI.h', 'IntrinsicI.h', 'Object.h', 'PassivGraI.h', 'RectObjP.h', 'ResourceI.h', 'Shell.h', 'ShellP.h', + 'ThreadsI.h', 'VarargsI.h', 'VendorP.h', + ] + ], + 'dirs' : [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libbeef/libbeef-0.1.1-intel-2015a.eb b/easybuild/easyconfigs/l/libbeef/libbeef-0.1.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d5d17f503c50987e0f186439d0326cb118897bee --- /dev/null +++ b/easybuild/easyconfigs/l/libbeef/libbeef-0.1.1-intel-2015a.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libbeef' +version = '0.1.1' + +homepage = 'https://confluence.slac.stanford.edu/display/SUNCAT/BEEF+Functional+Software' +description = """libbeef is a package providing the class of BEEF-vdW functionals and + Bayesian error estimates to Fortran- or C-based DFT codes.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['https://confluence.slac.stanford.edu/download/attachments/146704476'] +sources = [SOURCE_TAR_GZ] + +configopts = 'CC="$CC"' + +sanity_check_paths = { + 'files': ['bin/bee', 'lib/libbeef.a'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libctl/libctl-3.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libctl/libctl-3.2.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0de2f0bd938d65de14493ce42034937df366cd65 --- /dev/null +++ b/easybuild/easyconfigs/l/libctl/libctl-3.2.2-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'libctl' +version = '3.2.2' + +homepage = 'http://ab-initio.mit.edu/libctl' +description = """libctl is a free Guile-based library implementing flexible control files for scientific simulations.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +source_urls = ['http://ab-initio.mit.edu/libctl/'] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('guile', '1.8.8')] + +# fix for guile-config being broken because shebang line contains full path to bin/guile +configopts = 'GUILE_CONFIG="$EBROOTGUILE/bin/guile -e main -s $EBROOTGUILE/bin/guile-config"' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..1a559500ae13e01c3e5af469244b9ce9d1703fb0 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.0.13-intel-2015a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.0.13' + +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': '2015a'} + +source_urls = [ + 'ftp://sourceware.org/pub/libffi/', + 'http://www.mirrorservice.org/sites/sourceware.org/pub/libffi/', +] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['libffi-%(version)s_include-xmmintrin.patch'] + +sanity_check_paths = { + 'files': ['lib/libffi.%s' % SHLIB_EXT, 'lib/libffi.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..ba1db82dae7639a1c9c100a2084f49d0f4fcae5e --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.1-goolf-1.7.20.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.1' + +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': 'goolf', 'version': '1.7.20'} + +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-3.1-intel-2014.06.eb b/easybuild/easyconfigs/l/libffi/libffi-3.1-intel-2014.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..4f8e9bd62b334150de5fd1ec78219b2b388e4653 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.1-intel-2014.06.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.1' + +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': '2014.06'} + +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-2015a.eb b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..17a9f263e81c3fa579796c73b5cc0c9727d802a1 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.2.1-foss-2015a.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': '2015a'} + +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/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..b5f853d5af4fcb0651cb8fceb9c37f813438c254 --- /dev/null +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-goolf-1.7.20.eb @@ -0,0 +1,32 @@ +## +# 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 = 'libgtextutils' +version = '0.6.1' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['http://hannonlab.cshl.edu/fastx_toolkit'] + +sanity_check_paths = { + 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..16d490f92bf2bccaa322f74f12cf17471598c078 --- /dev/null +++ b/easybuild/easyconfigs/l/libgtextutils/libgtextutils-0.6.1-intel-2015a.eb @@ -0,0 +1,32 @@ +## +# 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 = 'libgtextutils' +version = '0.6.1' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCE_TAR_BZ2] +source_urls = ['http://hannonlab.cshl.edu/fastx_toolkit'] + +sanity_check_paths = { + 'files': ['lib/libgtextutils.so', 'lib/libgtextutils.a'], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..d2b54d01ffffcd7378cc4f9c50b53ab0222acd4d --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-goolf-1.7.20.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.3.1' + +homepage = 'http://sourceforge.net/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': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.05'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014.06.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..c76e470179f8b40856715ca806c15b5e4250563a --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.3.1-intel-2014.06.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.3.1' + +homepage = 'http://sourceforge.net/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': '2014.06'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.05'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..4197b7c6358b2d6621a0b6789dee75b0a9fe7fd9 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-goolf-1.7.20.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.0' + +homepage = 'http://sourceforge.net/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': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.06'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-ictce-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..24b1cf1a07384678a528f0a37f68701277867390 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.0-ictce-7.3.5.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.0' + +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': 'ictce', 'version': '7.3.5'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.06'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015a.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..3f922516d94cf412d1116db53cd2f7f811bdac65 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-1.4.1-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'libjpeg-turbo' +version = '1.4.1' + +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': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('NASM', '2.11.08'), +] + +configopts = "--with-jpeg8" +runtest = "test" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.12-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.12-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..11dd528148faed80e5058bef5b735a55be0a49e4 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.12-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.12' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.12-intel-2014.06.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.12-intel-2014.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..e5160148db2487960dfa0f1f6210778803612259 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.12-intel-2014.06.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.12' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.16-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..4132ab6f671a25ee0058afadd1226c5e99f3d5c8 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.16-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.16' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-foss-2015a.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..2519d4c46d1772a87a99234d478a912b7c6764ad --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-foss-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.17' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..8e90204af6ff2d543a03b28a3758e03c9fcd4640 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.17' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..fd641ddebc59bcdb3310a0de75cad47a92c4265c --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-ictce-7.3.5.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.17' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.17-intel-2015a.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..afab7cb441a1a3693c08d421a35f30320c59b432 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.17-intel-2015a.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.17' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('zlib', '1.2.8')] + +configopts = "--with-pic" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..8b8b71eae5aa103546d338536e46e5fa21e4f327 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.1.29.eb @@ -0,0 +1,27 @@ +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': '5.1.29'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +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-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..6078f8b7e2eb38e5b1a72c3c1ee129ede11294f3 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.25.eb @@ -0,0 +1,27 @@ +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': '5.2.25'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +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-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..7264a9260eca0536022e45b5d543f7c3dac5b825 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-CrayGNU-5.2.40.eb @@ -0,0 +1,27 @@ +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': '5.2.40'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +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-2015.05.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..c23d9ba71113a7bd731c278228c714475ecfe121 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-foss-2015.05.eb @@ -0,0 +1,27 @@ +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': '2015.05'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +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-goolf-1.7.20.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..5449121e0bf0f18175068282421ae692526d3150 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-goolf-1.7.20.eb @@ -0,0 +1,27 @@ +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': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +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-ictce-7.3.5.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..34ea8a516d62e173e32ccd411b57632f66a3e2f4 --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-ictce-7.3.5.eb @@ -0,0 +1,29 @@ +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': 'ictce', 'version': '7.3.5'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +preconfigopts = " LDFLAGS='-ltinfo' " + +dependencies = [('ncurses', '5.9')] + +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-2014.06.eb b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..7154c323baca6a8f1fef0bf324e9573ee2a81c3e --- /dev/null +++ b/easybuild/easyconfigs/l/libreadline/libreadline-6.3-intel-2014.06.eb @@ -0,0 +1,27 @@ +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': '2014.06'} +toolchainopts = {'pic': True} + +sources = ['readline-%(version)s.tar.gz'] +source_urls = ['http://ftp.gnu.org/gnu/readline'] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files' : ['lib/libreadline.a', 'lib/libhistory.a'] + + ['include/readline/%s' % x for x in ['chardefs.h', 'history.h', 'keymaps.h', 'readline.h', 'rlconf.h', + 'rlstdc.h', 'rltypedefs.h', 'tilde.h']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.2-intel-2015a.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..eddb4ada023ccb617fc0e265082cfc4c4066b58c --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.2-intel-2015a.eb @@ -0,0 +1,15 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.2' + +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 = ['http://ftp.gnu.org/gnu/%s' % name.lower()] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..f29d89e1c6f27074975fbcf3d6237f7ba5adeab4 --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-4.9.2-2.25.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': 'GNU', 'version': '4.9.2-2.25'} + +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-GNU-5.1.0-2.25.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-5.1.0-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..33c6f3867ed98f6470bff34307768d7b5e142edf --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GNU-5.1.0-2.25.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': 'GNU', 'version': '5.1.0-2.25'} + +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-intel-2015a.eb b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..93d202fc27ca2dba90dbe2d4ae26f4556d8c439c --- /dev/null +++ b/easybuild/easyconfigs/l/libunistring/libunistring-0.9.3-intel-2015a.eb @@ -0,0 +1,26 @@ +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': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +patches = ['libunistring_icc_builtin_nan-inf.patch'] + +parallel = 1 + +sanity_check_paths = { + 'files' : ['lib/libunistring.a', 'lib/libunistring.so', 'include/unistring'] + + ['include/uni%s.h' % x for x in ['case', 'conv', 'ctype', 'lbrk', 'name', 'norm', + 'stdio', 'str', 'types', 'wbrk', 'width']], + 'dirs' : [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..548d650cdec042864a888f6c499ef7f144e45117 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.1.29.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.1' + +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': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' + +# 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.a'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..79002b6ce40019a04ee94162628105170c9b3a69 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.25.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.1' + +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': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' + +# 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.a'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..80df7f4320457430fd61b9f13027831a3c6212fe --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.1-CrayGNU-5.2.40.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.1' + +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': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS"' + +# 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.a'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..25c12f798e5de9a8b1f4c2961dabb2520d5d2d31 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-2.2.2-intel-2015a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libxc' +version = '2.2.2' + +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': '2015a'} +toolchainopts = {'opt': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://www.tddft.org/programs/octopus/down.php?file=libxc/'] + +configopts = 'FC="$F77" FCFLAGS="$FFLAGS" --enable-shared' + +# 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.a', 'lib/libxc.so'], + 'dirs': ['include'], +} + +parallel = 1 + +moduleclass = 'chem' 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/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb index aaf4c869fd8f2d510c16bc6d43fa64475688df26..254704e224a733d5360d3ccd029f11d5897528d4 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -24,4 +24,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb index c67963ba182bd282643c30a3259cc5b7dac66901..3d078ed6cff185ff284c1db2c78b60b87287ef44 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-goalf-1.1.0-no-OFED.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' 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 d6a8666d27dfe2d7b0e4bd388fe8625e3cf37551..33c6ee44e228daa6f9d864b48eba51ee4099db2a 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 @@ -23,4 +23,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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 3d1f3f2077131d745835dfdb2acbfb98e789657a..d35a5afd09eab750a3747278ecf1ca78f38d17b0 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 @@ -18,4 +18,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb index ddf8c959891d1b635637e624fa2a5d22d8f1a3f4..2cbd068791c0ceaf7508d0a9f1b3a8354c10a66e 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6-Python-2.7.3.eb @@ -24,4 +24,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb index c92bb71719aa1a28deec72a2a8efa3a33d999bb9..111dd07ee9a426c069c70949ae0f86cf404e6909 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.0.6.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb index e56d2ad35387bc1da3b636f7aaf3b49f168c8d13..2e200ff7477aa49c008b58fb1f67df839ef658be 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.8.0-ictce-4.1.13-Python-2.7.3.eb @@ -24,4 +24,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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 e014507e31ff21bd5329ef731e5912d3e04388ba..2e16511fc4134ef18a1dda4a441c85eb226d9e5d 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 @@ -24,4 +24,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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 1a06b1ab67e14d975baab04f8ebef8a709750d2a..8718a3c0cd0dc8c381241e107cd658b9af6d6a6e 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 @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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 833381d4b24b18d167a600acdf6d91a2dc8161cf..dd8fbb563c35fac6353c7b4ca714454c02eb48a4 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 @@ -24,4 +24,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb index 1babda58a00c8a770d4edc83e454656b694791f1..5f8aa9158f8f9208b22432487f2800cec0732925 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-goalf-1.1.0-no-OFED.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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 9c2538dce193148c178766bd2a60e2c1e0f1aa96..df4be8cc115d73bb126241e846fbbe25a8d9497f 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 @@ -18,4 +18,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb index 34aa5f2ec628855c40cd45e53aee9079e941176d..ddb04fedc974f73bb115fe12d46dff980042a92b 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.0.6.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb index 59de5c01a760075da72be964b215f9a9943466f1..2d7551a78aca5c47bd7e9c1c84fbacb0c909fdbd 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.0-ictce-4.1.13.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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 5618053aba929a71e04c9a5492e21bded5a6abec..f6b392b5e3866c3ec971ae33c1059410b44e7f07 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 @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..528265c88b6702bb58c8ba953ee0492d17f0170b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gmpolf-1.4.8.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +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': 'gmpolf', 'version': '1.4.8'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb index 0d54f03977331560d8edf3b64ef7972fbb0a2289..d743e7f4c4e67d45d7087f793d35060bda84f4f3 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.1.0-no-OFED.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb index 2145f1ccf3642751064d553c446ec9a92bc61f18..824084e03ab8693a5175cbe5dc94e445e2b80091 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goalf-1.5.12-no-OFED.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb new file mode 100644 index 0000000000000000000000000000000000000000..96f39c944c7fb4cf1db0801012c53407d75c80af --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-gompi-1.4.12-no-OFED.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +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': 'gompi', 'version': '1.4.12-no-OFED'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +moduleclass = 'lib' 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 b46d67c8c8252d034aeeb50bdb636ee30ffd1e1b..35fadff4ea583b7f674df3a03d5a418395699622 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 @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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 new file mode 100644 index 0000000000000000000000000000000000000000..a36d6bdb322648c36263e53a1839df41d676e62b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-goolf-1.5.14.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +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': '1.5.14'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb index 02c5f8e418e1939158f4168b88c62f3c0705ff83..51cf5a1ff902b6188ef913b6152ca8d74b4c2215 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.0.6.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb index b3eac90a5135fc738be54f4dd7e99e44fc6869e9..28520b4f811e8aed1183407445464179ebbcff81 100644 --- a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-4.1.13.eb @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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 new file mode 100644 index 0000000000000000000000000000000000000000..0c0ab111ee37ad5deab11536e028a2c86c99013b --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.1-ictce-5.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxml2' +version = '2.9.1' + +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': 'ictce', 'version': '5.2.0'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.7')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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 e18bbcef3bbe722866f0425285e25dfa7a6ceef1..d80e534ea6b09e64cfa592ef95587661e9d71739 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 @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.7')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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 ef442f4bb59b2ad3581e62c7593b6e643358c012..69506204a7f201b65ba5402050e21976f61adb51 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 @@ -24,4 +24,9 @@ dependencies = [ ('Python', pythonver), ] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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 5c7f304740e63f95bf22fb48d9d0b3a6aed8d297..69319cf49abdb7b987b64a398a2abd1b81cbd2e9 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 @@ -19,4 +19,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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 3194637d11d4b6021ff32f38c77d4469f1d361ca..cd4bbd99a0a32fbdbe54751e642cc8116b02d7b9 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 @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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 102c2914dbfbed3a7a942047bc970703f0db36be..3a42235cf92efc5bc8821f7c1cbfa2ffada60bee 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 @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + 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 25967be1173d9792dd44e3f95f615e9c4e74dc37..d446d4e3c6ad570a4f2b7fedbac3cf7888df5a4b 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 @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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 12454bc9c490647eeffee3f3707f9803095c0854..fa340e7e8573ac053b3fd5e7539b0c2b029133a8 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 @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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 new file mode 100644 index 0000000000000000000000000000000000000000..ae743268436b33a75442a9bfab36a81e127754df --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.5.14.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +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': 'goolf', 'version': '1.5.14'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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 new file mode 100644 index 0000000000000000000000000000000000000000..906e3a297c17c1b90b07da688d1c0cdcc24e3ae6 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-goolf-1.7.20.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +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': 'goolf', 'version': '1.7.20'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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 new file mode 100644 index 0000000000000000000000000000000000000000..94f3df39bebd584702184ffda89925106324d74e --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014.06.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +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': 'intel', 'version': '2014.06'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + '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 new file mode 100644 index 0000000000000000000000000000000000000000..215198c95aaa8773a53ba744c97604cf22becd3c --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.2-intel-2014b.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +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': 'intel', 'version': '2014b'} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' + +dependencies = [('zlib', '1.2.8')] + +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + +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 84a2d133c68d3ed02c317d55937dbc20880915a5..2857dd4e54295fbb523a42a1e77474ac3d8ff9b5 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 @@ -20,4 +20,9 @@ configopts = 'CC="$CC" CXX="$CXX" --with-pic --without-python' dependencies = [('zlib', '1.2.8')] +sanity_check_paths = { + 'files': [('lib/libxml2.a', 'lib64/libxml2.a'), ('lib/libxml2.so', 'lib64/libxml2.so')], + 'dirs': ['bin', 'include/libxml2/libxml'], +} + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015a.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7b42e2d0837cd106981a9343e87aa2e9cbb42c1b --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.1.6-intel-2015a.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': '2015a'} + +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.so"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-6.1.5.eb b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-6.1.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..062e490de1ec9700d054e4168e374334cc701f3a --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.16-ictce-6.1.5.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'M4' +version = '1.4.16' + +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': 'ictce', 'version': '6.1.5'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +patches = ['M4-%(version)s-no-gets.patch'] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..de4b32575675f1b9c1329f556ee86245512acba5 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.1.29.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': 'CrayGNU', 'version': '5.1.29'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..06f80557f1dfc8dfa1c1183e832f05cbc2b892de --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.25.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': 'CrayGNU', 'version': '5.2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..d1ac7167dc7a06ffaae85125f2b049841401a091 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-CrayGNU-5.2.40.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': 'CrayGNU', 'version': '5.2.40'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +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 new file mode 100644 index 0000000000000000000000000000000000000000..e2764250bf50989e531d962b75283e395d30600f --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-4.9.2-2.25.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': 'GNU', 'version': '4.9.2-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000000000000000000000000000000000..e83b261924d4a2783a0f5e6aa1151bd2864ee363 --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-GNU-5.1.0-2.25.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': 'GNU', 'version': '5.1.0-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000000000000000000000000000000000..94ec58056bd19a15fe6fe924516739ca49f4cb6e --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2014b.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': 'foss', 'version': '2014b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +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 new file mode 100644 index 0000000000000000000000000000000000000000..411820a76bb3e8fef73e6da7d5917889be8273ee --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17-foss-2015a.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': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +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 new file mode 100644 index 0000000000000000000000000000000000000000..3f396ce26b1f9699142abde0d13df234d7552e9a --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.17.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': 'dummy', 'version': 'dummy'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +configopts = "--enable-cxx" + +sanity_check_paths = { + 'files': ["bin/m4"], + 'dirs': [], +} + +moduleclass = 'devel' 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 new file mode 100644 index 0000000000000000000000000000000000000000..79d3f53e5ad6a9edbab99b0717ef9196c15d60ff --- /dev/null +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.2-goolf-1.4.10.eb @@ -0,0 +1,24 @@ +## +# 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 = 'MATIO' +version = '1.5.2' + +homepage = 'http://sourceforge.net/projects/matio/' +description = """matio is an C library for reading and writing Matlab MAT files.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_ZIP] + +dependencies = [('zlib','1.2.7')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..cea8ae91c9928a6987cef0b4a93bb741b94e87d8 --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-intel-2015a.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': 'intel', 'version': '2015a'} +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', +] + +patches = ['METIS_IDXTYPEWIDTH.patch'] + +builddependencies = [('CMake', '3.2.1')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..e1bdcca9dabfb8311dc35e8b4260cd99e9eb028b --- /dev/null +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.0.2.eb @@ -0,0 +1,14 @@ +name = 'Mathematica' +version = '10.0.2' + +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' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..0093f6a4c2b4df7f3ac50fb06ca3c6713b42498d --- /dev/null +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-10.1.0.eb @@ -0,0 +1,14 @@ +name = 'Mathematica' +version = '10.1.0' + +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' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/Mathematica/Mathematica-9.0.1.eb b/easybuild/easyconfigs/m/Mathematica/Mathematica-9.0.1.eb index 2d148e7a750c874a5a62ad389d6d03831613f828..aafd02cf83cfc50c4c0be0582f67297f1b065781 100644 --- a/easybuild/easyconfigs/m/Mathematica/Mathematica-9.0.1.eb +++ b/easybuild/easyconfigs/m/Mathematica/Mathematica-9.0.1.eb @@ -7,7 +7,7 @@ and computing fields.""" toolchain = {'name': 'dummy', 'version': 'dummy'} -sources = ['Mathematica_%s_LINUX.sh' % version] +sources = ['Mathematica_%(version)s_LINUX.sh'] license_server = 'license.example.com' diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb b/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb index 99b133b3f5ba3174290b537490f01ef299f4e1ba..15da01ed14e117a304d5c65055e367cc896ce186 100644 --- a/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/m/Meep/Meep-1.2-ictce-4.0.6.eb @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -patches = ['Meep-%s_version-string-without-spaces.patch' % version] +patches = ['Meep-%(version)s_version-string-without-spaces.patch'] dependencies = [ ('Harminv', '1.3.1'), 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 67e5d881fbc1d1eda6a3d2af898beb923b115efb..475c5f321c7a187e89e19bf1bb2594257723e056 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 @@ -16,7 +16,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -patches = ['Meep-%s_version-string-without-spaces.patch' % version] +patches = ['Meep-%(version)s_version-string-without-spaces.patch'] dependencies = [ ('Harminv', '1.3.1'), diff --git a/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..baee3155cfdb2c7e519d33b9cc6bccc97c15aa35 --- /dev/null +++ b/easybuild/easyconfigs/m/Meep/Meep-1.3-intel-2015a.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': 'intel', 'version': '2015a'} +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', '1.8.14'), + ('libctl', '3.2.2'), + ('GSL', '1.16'), + ('FFTW', '3.3.4') +] + +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_version-string-without-spaces.patch b/easybuild/easyconfigs/m/Meep/Meep-1.3_version-string-without-spaces.patch new file mode 100644 index 0000000000000000000000000000000000000000..90cebc985995ac97e04a2c5eb44609aae0c51d74 --- /dev/null +++ b/easybuild/easyconfigs/m/Meep/Meep-1.3_version-string-without-spaces.patch @@ -0,0 +1,11 @@ +--- meep-1.3/libctl/Makefile.in.orig 2015-03-31 17:47:53.000000000 +0200 ++++ meep-1.3/libctl/Makefile.in 2015-04-08 13:23:54.206192661 +0200 +@@ -369,7 +369,7 @@ + ############################################################################## + + # what is printed out when invoking your program with --version: +-VERSION_STRING = "Meep @VERSION@, Copyright (C) 2005-2015 Massachusetts Insitute of Technology." ++VERSION_STRING = "Meep_@VERSION@,_Copyright_(C)_2005-2015_Massachusetts_Insitute_of_Technology." + MY_DEFS = -DHAVE_CTL_HOOKS=1 -DHAVE_CTL_EXPORT_HOOK=1 + PROGRAM_NAME = meep + SPECIFICATION_FILE = $(PROGRAM_NAME).scm 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 new file mode 100644 index 0000000000000000000000000000000000000000..5836ec7f0f8b87018de0211084f1546aa60dcdce --- /dev/null +++ b/easybuild/easyconfigs/m/MrBayes/MrBayes-3.2.5-intel-2015a.eb @@ -0,0 +1,18 @@ +name = 'MrBayes' +version = '3.2.5' + +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} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ["http://downloads.sourceforge.net/project/mrbayes/mrbayes/%(version)s"] + +dependencies = [ + ('beagle-lib', '20141202'), + ('libreadline', '6.3'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.eb new file mode 100644 index 0000000000000000000000000000000000000000..afe163b841159ca2b65c40ae7fabd895702189dc --- /dev/null +++ b/easybuild/easyconfigs/m/MuTect/MuTect-1.1.4-Java-1.7.0_76.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 = 'Tarball' + +name = 'MuTect' +version = '1.1.4' + +homepage = 'http://www.broadinstitute.org/cancer/cga/mutect' +description = """ MuTect is a method developed at the Broad Institute for the reliable + and accurate identification of somatic point mutations in next generation sequencing + data of cancer genomes. """ + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.broadinstitute.org/cancer/cga/sites/default/files/data/tools/mutect/'] +sources = ['muTect-%(version)s-bin.zip'] + +java = 'Java' +javaver = '1.7.0_76' +versionsuffix = '-%s-%s' % (java, javaver) + +dependencies = [(java, javaver)] + +sanity_check_paths = { + 'files': ["muTect-%(version)s.jar"], + 'dirs': [], +} + +modloadmsg = """ +to execute: java -jar \\$EBROOTMUTECT/muTect-%(version)s.jar +""" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..080aad8636fe87fb99761a076cee7d48f1692260 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.2.1' + +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': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.10' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..959081d6a063e88f758756f942dcc3fa4453c214 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.2.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.2.1' + +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': '2015a'} + +source_urls = ['http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('zlib', '1.2.8'), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/matplotlib' % pythonshortversion], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb index d97e421867e7c179adc274a909a85bfc27b93a3b..6a25c33b0cbe780a0f0297b9f49afbfd19e6f774 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-4.1.13-Python-2.7.6.eb @@ -26,7 +26,6 @@ dependencies = [ ('libpng', '1.6.6'), ] -# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? pyprefix = 'lib/python%s/site-packages' % pyshortver eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.6.eb index 0e33120d408354f7f3116731bd3af1347d74ea14..0397044feaa20dcd6cb68e5db4774a398cc06883 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-ictce-5.5.0-Python-2.7.6.eb @@ -26,7 +26,6 @@ dependencies = [ ('libpng', '1.6.9'), ] -# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? pyprefix = 'lib/python%s/site-packages' % pyshortver eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..765f86a131a7f3bcf20cf09eb927b6db81eee965 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.3.1-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,37 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.3.1' + +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': '2014b'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.8' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('zlib', '1.2.8'), + ('freetype', '2.5.3'), + ('libpng', '1.6.12'), +] + +# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb index da065319219e3c960849d9f9b32ab8a168b4f30d..8072aaea0f4c6bbf2448032ed8444cc1221088cd 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-foss-2015a-Python-2.7.9.eb @@ -25,7 +25,6 @@ dependencies = [ ('libpng', '1.6.16'), ] -# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? pyprefix = 'lib/python%s/site-packages' % pyshortver eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb index 3a24c2da815cfe90a8f325d5eedbafe92c293926..25762ccdf762f36a7fdbab7372778c8fd29b84f5 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-2.7.9.eb @@ -27,7 +27,6 @@ dependencies = [ ('libpng', '1.6.16'), ] -# is this actually needed? the PythonPackage will check if import matplotlib succeeds, which is as good as this? pyprefix = 'lib/python%s/site-packages' % pyshortver eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver sanity_check_paths = { diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..5849d559f78cb5a1ee14232e011a56c115827759 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-1.4.3-intel-2015a-Python-3.4.3.eb @@ -0,0 +1,37 @@ +easyblock = "PythonPackage" + +name = 'matplotlib' +version = '1.4.3' + +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': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = [('matplotlib-%(version)s_Qhull-intel-fix.patch')] + +python = "Python" +pythonversion = '3.4.3' +pyshortver = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('freetype', '2.5.5'), + ('libpng', '1.6.16'), +] + +pyprefix = 'lib/python%s/site-packages' % pyshortver +eggname = 'matplotlib-%%(version)s-py%s-linux-x86_64.egg' % pyshortver +sanity_check_paths = { + 'files': [], + 'dirs': [('%s/%%(name)s' % pyprefix, '%s/%s' % (pyprefix, eggname))], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..5d19338ab330d70960ae54b3f6d6f8abb6792cf9 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.10.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'molmod' +version = '1.0' + +homepage = 'http://molmod.github.io/molmod/' +description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://users.ugent.be/~tovrstra/molmod'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.10' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.2.1', versionsuffix), +] + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/molmod' % pythonshortversion], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..b6703cee3099afdb0d973de768d2723f09f54be8 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = 'molmod' +version = '1.0' + +homepage = 'http://molmod.github.io/molmod/' +description = """MolMod is a Python library with many compoments that are useful to write molecular modeling programs.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://users.ugent.be/~tovrstra/molmod'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.2.1', versionsuffix), +] + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'python setup.py build_ext -i; nosetests -v' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/molmod' % pythonshortversion], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb new file mode 100644 index 0000000000000000000000000000000000000000..d4224bd978c6af068b0fd89f1059c1032d7dbfd4 --- /dev/null +++ b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9-gmatteo-20150325.eb @@ -0,0 +1,39 @@ +easyblock = "PythonPackage" + +name = 'monty' +version = '0.6.4' + +homepage = 'https://pypi.python.org/pypi/monty/' +description = """Monty implements supplementary useful functions for Python that are not part of the standard library. + Examples include useful utilities like transparent support for zipped files, useful design patterns such as singleton + and cached_class, and many more.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +commit = '3152d41' +extrasuff = 'gmatteo-20150325' + +source_urls = ['https://github.com/gmatteo/monty/archive/%s.tar.gz#' % commit] +sources = ['%%(name)s-%%(version)s-%s.tar.gz' % extrasuff] +checksums = ['d8afe0556fd29191e66babb31750b7c4'] + +python = 'Python' +pythonversion = '2.7.9' + +versionsuffix = '-%s-%s-%s' % (python, pythonversion, extrasuff) + +dependencies = [ + (python, pythonversion), + ('PyYAML', '3.11', '-%s-%s' % (python, pythonversion)), +] + +py_short_ver = '.'.join(pythonversion.split('.')[0:2]) +pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) + +sanity_check_paths = { + 'files': [("%s-%%(version)s-py%s.egg" % (pylibdir, py_short_ver), + "%s-%%(version)s-py%s-linux-x86_64.egg" % (pylibdir, py_short_ver))], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..58d8cae9eec262a4ba714966e303e2cfb3070115 --- /dev/null +++ b/easybuild/easyconfigs/m/monty/monty-0.6.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'monty' +version = '0.6.4' + +homepage = 'https://pypi.python.org/pypi/monty/' +description = """Monty implements supplementary useful functions for Python that are not part of the standard library. + Examples include useful utilities like transparent support for zipped files, useful design patterns such as singleton + and cached_class, and many more.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('PyYAML', '3.11', versionsuffix), +] + +py_short_ver = ".".join(pythonversion.split(".")[0:2]) +pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) + +sanity_check_paths = { + 'files': [("%s-%%(version)s-py%s.egg" % (pylibdir, py_short_ver), + "%s-%%(version)s-py%s-linux-x86_64.egg" % (pylibdir, py_short_ver))], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb b/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..3197280c4387112407c72b4a682519c14c89bea2 --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.4-intel-2015a-libX11-1.6.3.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.4' + +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': 'intel', 'version': '2015a'} +# use -O1 to dance around icc segfaulting +toolchainopts = {'lowopt': True} + +sources = ['%(name)s-%(version)s-src.tgz'] +source_urls = [SOURCEFORGE_SOURCE] + +libx11ver = '1.6.3' +versionsuffix = '-libX11-%s' % libx11ver +dependencies = [ + ('libXt', '1.1.4', versionsuffix), + ('libXau', '1.0.8'), + ('libX11', libx11ver, '-Python-2.7.9'), + ('libXext', '1.3.3'), + ('libXdmcp', '1.1.2'), + ('libpng', '1.6.16'), + ('xbitmaps', '1.1.1'), + ('freetype', '2.5.5'), + ('libjpeg-turbo', '1.4.0'), + ('bzip2', '1.0.6'), +] +builddependencies = [ + ('Autotools', '20150119', '', ('GCC', '4.9.2')), + ('flex', '2.5.39', '', ('GCC', '4.9.2')), + ('Bison', '3.0.4', '', ('GCC', '4.9.2')), + ('util-linux', '2.26.1'), +] + +preconfigopts = "./autogen.sh && " + +# 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' diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..f3694ef966292c5d751238f9a1640194530fb628 --- /dev/null +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-1.3-goolf-1.4.10-Python-3.2.3.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'mpi4py' +version = '1.3' + +homepage = 'https://code.google.com/p/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': 'goolf', 'version': '1.4.10'} + +source_urls = [ + BITBUCKET_DOWNLOADS, + GOOGLECODE_SOURCE, +] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '3.2.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-goolf-1.7.20.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..61250ef0ab190312acd0bd996109c6b7efb7a30c --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-goolf-1.7.20.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 +# 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 = '2.11.05' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..8eacf467e7158b7f34d04ac0afd9b8a3bd847e63 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.05-intel-2014.06.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 +# 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 = '2.11.05' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] + +toolchain = {'name': 'intel', 'version': '2014.06'} + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.11.06-goolf-1.7.20.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..8ece8f5082134c1c09b8167d3f0e6ce132d4630f --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-goolf-1.7.20.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 +# 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 = '2.11.06' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +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-2.11.06-ictce-7.3.5.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-ictce-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..d2c0dab761544f931fca8e6b3d552c1b29c0576d --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.06-ictce-7.3.5.eb @@ -0,0 +1,19 @@ +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.11.06' + +homepage = 'http://www.nasm.us/' +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} + +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-2.11.08-intel-2015a.eb b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..77ceaa2d9a8cb9485589e5d6aa8467335b855b98 --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.11.08-intel-2015a.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': 'intel', 'version': '2015a'} + +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/NEMO/NEMO-3.4-r5541-ictce-6.1.5-IC3.eb b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5-IC3.eb new file mode 100644 index 0000000000000000000000000000000000000000..3f22d894436ef0799bd9c4092a0c7e13cebe953f --- /dev/null +++ b/easybuild/easyconfigs/n/NEMO/NEMO-3.4-r5541-ictce-6.1.5-IC3.eb @@ -0,0 +1,29 @@ +name = 'NEMO' +version = '3.4-r5541' +versionsuffix = '-IC3' + +homepage = 'http://www.nemo-ocean.eu/' +description = """NEMO (Nucleus for European Modelling of the Ocean) is a state-of-the-art modeling framework for + oceanographic research, operational oceanography seasonal forecast and climate studies.""" + +toolchain = {'name': 'ictce','version': '6.1.5'} +toolchainopts = {'opt': False, 'optarch': False} + +# authenticated SVN access required +# svn --username 'login' co http://forge.ipsl.jussieu.fr/nemo/svn/branches/2012/dev_v3_4_STABLE_2012 +# tar cfvz NEMO-3.4-r.tar.gz dev_v3_4_STABLE_2012 +sources = [SOURCE_TAR_GZ] + +dependencies = [('netCDF-Fortran', '4.2')] + +# setting specific to IC3 +# enable ocean model and Louvain-la-Neuve sea-ice model +# see http://www.nemo-ocean.eu/About-NEMO +with_components = ['OPA_SRC', 'LIM_SRC_3'] +# enable LIM3, MPI, IOM, global ORCA config at 1 degree resolution (& more) +# disable LIM2, global ORCA config at 2 degree resolution, tides induced vertical mixing +# see http://www.nemo-ocean.eu/About-NEMO, http://www.nemo-ocean.eu/Using-NEMO/User-Guides/Basics/cpp-keys-v3_4 +add_keys = ['key_dtasal', 'key_dtatem', 'key_lim3', 'key_iomput', 'key_mpp_mpi', 'key_orca_r1=75', 'key_tradmp'] +del_keys = ['key_lim2', 'key_orca_r2', 'key_zdftmx'] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..2eefc9a7f35a4bb722e574829d36ffd5702995fb --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-intel-2014b-2014-09-10-Python-2.7.8.eb @@ -0,0 +1,31 @@ +name = 'NWChem' +version = '6.5.revision26243' + +homepage = 'http://www.nwchem-sw.org' +description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in + their ability to treat large scientific computational chemistry problems efficiently, and in their use of available + parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. + NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all + combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties + and relativity.""" + +toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'i8': True} + +source_urls = [ 'http://www.nwchem-sw.org/download.php?f='] +verdate = '2014-09-10' +sources = ['Nwchem-%s-src.%s.tar.bz2' % (version, verdate)] + +patches = [ + 'NWChem_fix-date.patch', + 'NWChem-%(version)s-parallelbuild.patch', +] + +python = 'Python' +pyver = '2.7.8' +versionsuffix = '-%s-%s-%s' % (verdate, python, pyver) +dependencies = [(python, pyver)] + +modules = 'all python' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch new file mode 100644 index 0000000000000000000000000000000000000000..c3a7a329824e6bdd5e084025e8f42ab5892e1945 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-6.5.revision26243-parallelbuild.patch @@ -0,0 +1,92 @@ +# corrected parallel builds, no debug info and no vec reports +# B. Hajgato Nov 13 2014 +--- src/config/makefile.h.orig 2014-09-10 20:08:39.000000000 +0200 ++++ src/config/makefile.h 2014-11-12 11:33:06.449137413 +0100 +@@ -1231,7 +1231,7 @@ + _FC=ifort + #ifort 9.1 + # LINK.f = ifort $(LDFLAGS) +- FOPTIONS += -align -mp1 -w -g -vec-report1 ++ FOPTIONS += -align -mp1 -w + ifdef USE_GPROF + FOPTIONS += -qp + endif +@@ -1394,7 +1394,7 @@ + CORE_SUBDIRS_EXTRA = blas lapack + CC = gcc + RANLIB = ranlib +- MAKEFLAGS = -j 1 --no-print-directory ++ MAKEFLAGS = -j 8 --no-print-directory + INSTALL = @echo $@ is built + CPP = gcc -E -nostdinc -undef -P + FCONVERT = (/bin/cp $< /tmp/$$$$.c; \ +@@ -1527,7 +1527,7 @@ + DEFINES += -DGFORTRAN + endif + ifeq ($(_FC),ifc) +- FOPTIONS = -align -mp1 -w -g -vec-report1 ++ FOPTIONS = -align -mp1 -w + ifdef USE_GPROF + FOPTIONS += -qp + endif +@@ -1602,7 +1602,7 @@ + endif + + ifeq ($(CC),icc) +- COPTIONS = -mp1 -w -g -vec-report1 ++ COPTIONS = -mp1 -w + COPTIMIZE = -O3 -unroll + ifeq ($(_CPU),i586) + COPTIMIZE += -tpp5 -xi # this are for PentiumII +@@ -1814,7 +1814,7 @@ + endif + endif + DEFINES += -DEXT_INT +- MAKEFLAGS = -j 1 --no-print-directory ++ MAKEFLAGS = -j 8 --no-print-directory + _CPU = $(shell uname -m ) + ifeq ($(BLAS_LIB),) + CORE_SUBDIRS_EXTRA += blas +@@ -1923,7 +1923,7 @@ + endif # end of ia32 bit + ifeq ($(_CPU),x86_64) + # +- MAKEFLAGS = -j 2 --no-print-directory ++ MAKEFLAGS = -j 8 --no-print-directory + COPTIMIZE = -O1 + ifeq ($(NWCHEM_TARGET),CATAMOUNT) + FC=pgf90 +@@ -1959,19 +1959,17 @@ + ifeq ($(_IFCV15ORNEWER), Y) + FOPTIONS += -qopt-report-file=stderr + ifdef USE_OPTREPORT +- FOPTIONS += -qopt-report=1 -qopt-report-phase=vec ++ FOPTIONS += -qopt-report=0 -qopt-report-phase=vec + endif + ifdef USE_OPENMP + FOPTIONS += -qopenmp +- FOPTIONS += -qopt-report-phase=openmp + COPTIONS += -qopenmp + DEFINES+= -DUSE_OPENMP + endif + else +- FOPTIONS += -vec-report6 ++ FOPTIONS += -vec-report0 + ifdef USE_OPENMP + FOPTIONS += -openmp +- FOPTIONS += -openmp-report2 + COPTIONS += -openmp + DEFINES+= -DUSE_OPENMP + endif +@@ -2086,9 +2084,9 @@ + ICCV15ORNEWER=$(shell icc -V 2>&1|egrep "Version "|head -n 1 | sed 's/.*Version \([0-9][0-9]\).*/\1/' | awk '{if ($$1 >= 15) {print "Y";exit}}') + COPTIONS += -xHOST -ftz + ifeq ($(ICCV15ORNEWER), Y) +- COPTIONS += -qopt-report-phase:openmp -vec-report=1 ++ COPTIONS += -qopt-report-phase:openmp + else +- COPTIONS += -openmp-report=2 -vec-report=1 ++ COPTIONS += -openmp-report0 + endif + #old COPTIMIZE = -O3 -hlo -mP2OPT_hlo_level=2 + COPTIMIZE = -O3 diff --git a/easybuild/easyconfigs/n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb b/easybuild/easyconfigs/n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..a5891cb70a547174b22bddc89266f01c2385fd8c --- /dev/null +++ b/easybuild/easyconfigs/n/ncdf/ncdf-1.6.6-ictce-5.3.0-R-2.15.3.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'ncdf' +version = '1.6.6' + +homepage = 'http://cran.r-project.org/web/packages/ncdf4' +description = """This package provides a high-level R interface to data files written using Unidata's netCDF library + (version 4 or earlier), which are binary data files that are portable across platforms and include metadata + information in addition to the data sets.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = [ + 'http://cran.freestatistics.org/src/contrib', + 'http://cran.r-project.org/src/contrib/Archive/ncdf', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +r = 'R' +rver = '2.15.3' + +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [ + (r, rver), + ('netCDF', '4.2.1.1', '-zlib-1.2.5'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..dc58f15fe280dd47db246f4d73f22cbf1dd57063 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.10-ictce-5.3.0-R-2.15.3.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'ncdf4' +version = '1.10' + +homepage = 'http://cran.r-project.org/web/packages/ncdf4' +description = """This package provides a high-level R interface to data files written using Unidata's netCDF library + (version 4 or earlier), which are binary data files that are portable across platforms and include metadata + information in addition to the data sets.""" + +toolchain = {'name': 'ictce', 'version': '5.3.0'} + +source_urls = [ + 'http://cran.freestatistics.org/src/contrib', + 'http://cran.r-project.org/src/contrib/Archive/ncdf4', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +r = 'R' +rver = '2.15.3' + +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [ + (r, rver), + ('netCDF', '4.2.1.1', '-zlib-1.2.5'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..47cf63ba0e957a97ec39e4b0d54135ac09606778 --- /dev/null +++ b/easybuild/easyconfigs/n/ncdf4/ncdf4-1.13-intel-2014b-R-3.1.1.eb @@ -0,0 +1,27 @@ +easyblock = 'RPackage' + +name = 'ncdf4' +version = '1.13' + +homepage = 'http://cran.r-project.org/web/packages/%(name)s' +description = """ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [ + 'http://cran.r-project.org/src/contrib/', + 'http://cran.r-project.org/src/contrib/Archive/$(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] + +r = 'R' +rver = '3.1.1' +versionsuffix = '-%s-%s' % (r, rver) + +dependencies = [ + (r, rver), + ('netCDF', '4.3.2'), + ('cURL', '7.37.1'), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb index 3522f8a87b99bd3113a31f70abdce86546a0d556..634fda5b4d876573afd6dfb3890e690f923f1745 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-GCC-4.7.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' @@ -14,7 +16,26 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +patches = ['ncurses-%(version)s_configure_darwin.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/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-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-5.9-20130406-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb index f954a9b12a271effc56ef267704bb2377c1bfc15..4f21474dcf5c3864913bd453cf823ed7be3e8e0b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmpolf-1.1.6.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' @@ -14,7 +16,26 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +patches = ['ncurses-%(version)s_configure_darwin.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/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-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-5.9-20130406-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb index 6a10d2ec63c363e31a77a54902e499945eed7dcf..a71c6aab72a3fb8caac5c469b119b2773d35b886 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.1.12rc1.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' @@ -14,7 +16,26 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +patches = ['ncurses-%(version)s_configure_darwin.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/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-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-5.9-20130406-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb index 4913ef008f8ebac65148f362d32443fcf595b7e6..f2a6bbb76a64f147336529b6ffe1f392c5a11593 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgmvolf-1.2.7.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' @@ -9,12 +11,31 @@ function-key mapping, and has all the other SYSV-curses enhancements over BSD Cu toolchain = {'name': 'cgmvolf', 'version': '1.2.7'} toolchainopts = {'optarch': True, 'pic': True} -sources = [SOURCE_TGZ] # In future, this URL will not be sufficient to obtain this tarball, because # the directory contains only a couple of older ncurses 5.9 snapshots. source_urls = ['ftp://invisible-island.net/ncurses/current/'] +sources = [SOURCE_TGZ] + +patches = ['ncurses-%(version)s_configure_darwin.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/' +] # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-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-5.9-20130406-cgoolf-1.1.7.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb index 8b7d3a2416c6ff2c10fe61a11447786c85987d29..5ef3e822adb21f9c224561aa2163a10ee719df8e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-cgoolf-1.1.7.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' @@ -14,7 +16,26 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +patches = ['ncurses-%(version)s_configure_darwin.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/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-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-5.9-20130406-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb index 1632ef23de6428be684ed244393e5390c6598973..96cc600747164cd4fca476a0954e658e52fc79bf 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' @@ -14,7 +16,26 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +patches = ['ncurses-%(version)s_configure_darwin.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/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-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-5.9-20130406-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb index 43375f2a293e09e47e1f46aac131252f7ffcc4ec..a1409a10e65d3f1c7bcd5d1ae0d6f59415770380 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406-gmvolf-1.7.12rc1.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9-20130406' @@ -14,7 +16,26 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TGZ] +patches = ['ncurses-%(version)s_configure_darwin.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/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-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-5.9-20130406_configure_darwin.patch b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406_configure_darwin.patch new file mode 100644 index 0000000000000000000000000000000000000000..067ec128f9927e469df5df128fdf4e1ee93444c0 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-20130406_configure_darwin.patch @@ -0,0 +1,11 @@ +--- ncurses-5.9-20130406/configure.orig 2013-04-07 00:09:21.000000000 +0200 ++++ ncurses-5.9-20130406/configure 2015-06-03 12:20:33.765043843 +0200 +@@ -5587,7 +5587,7 @@ + chmod +x mk_shared_lib.sh + ;; + darwin*) #(vi +- cf_try_cflags="no-cpp-precomp" ++ #cf_try_cflags="no-cpp-precomp" + CC_SHARED_OPTS="-dynamic" + MK_SHARED_LIB='${CC} ${CFLAGS} -dynamiclib -install_name ${libdir}/`basename $@` -compatibility_version ${ABI_VERSION} -current_version ${ABI_VERSION} -o $@' + test "$cf_cv_shlib_version" = auto && cf_cv_shlib_version=abi diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..6b7bb1c3472d6faa7a233f230a19c91c05b04dd3 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.1.29.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +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': '5.1.29'} +toolchainopts = {'optarch': True, 'shared': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..01680ab5b7d7480e3f51ccc11cc8751a58a70653 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.25.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +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': '5.2.25'} +toolchainopts = {'optarch': True, 'shared': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..6f00fdbd514cfcb8d9a437c6a016daff6de25974 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-CrayGNU-5.2.40.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +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': '5.2.40'} +toolchainopts = {'optarch': True, 'shared': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-GCC-4.7.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb index ad58285a8513af8aa7faca7eaaf8f469e2546599..37a2fff35a8b069cbc61d625bebc22aebefb37d2 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-GCC-4.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb index f972b6a4ffc003ebba3bababe376213801a7a1c8..96e1f454725a74c213ddbfa4b42b16958050853a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.7.3.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-GCC-4.8.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb index 5f56a5562114b5dfa1c257b65e92645b508b2607..5dd295c39e5434be465784d56190ab8a5df450ca 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.1.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-GCC-4.8.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb index 3068c78b44596e55e60ecb5be5483fd68b29f21b..3071876ad25b05ad6e61d3e2cab624d1afc84766 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -6,13 +8,29 @@ description = """The Ncurses (new curses) library is a free software emulation o 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.""" -# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html -patches = ['ncurses-5.9_configure_darwin.patch'] - toolchain = {'name': 'GCC', 'version': '4.8.2'} toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-GCC-4.8.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb index 52e0aac9ea3c614e3b263a864e2ed3826ad23033..c5e4c7e93d2561686ae904effb7417780d164d0b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.3.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-GCC-4.8.4.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb index 946a1c53383958239960c9bb5cd2b587d04feeeb..a769a56170102b10c9a568d33c1aef99ee6fc728 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.8.4.eb @@ -14,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-GCC-4.9.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb index 78b7618284c00eea1b85b0f2cfbe07486554ba27..512532996644497e265f5777fb4c6a1662437b69 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-GCC-4.9.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-foss-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb index b4ea71f97f0685c284357c6709729be956b08ec8..7278bb4ccf3979c0fe1c6796273eb42f6d728500 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2014b.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-foss-2015.05.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..37d7e0480953a411415f85fd60d72913cf8b5bc6 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015.05.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +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': '2015.05'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-foss-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb index 2f9501c9ae8a4cdab8fef461a1288387b751d442..cff4af273d5accf82686c9ab1e1909be6614758c 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-foss-2015a.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-gmpolf-1.4.8.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb index 15745294d9f475b510c91ff6fee807b7427c33d0..b529181479679c9688afe923db69e6eb1da965dd 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmpolf-1.4.8.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-gmvolf-1.7.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb index 062cbaeab624e4a1beceaaebcf9e41ebeb8994ab..aaa5b2bd78231932fa7427cb44eb37ee1ae49ee3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -14,7 +16,26 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-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-5.9-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb index a372492a64aafbef666f0010ff48d63122214623..f8ee92d0944a25c7ccd20ffdeb5b6455eaf672e0 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gmvolf-1.7.12rc1.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,7 +14,26 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['ftp://invisible-island.net/ncurses/current/'] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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/' +] + # Parallel build contains a race on etip.h, needed for c++/demo.cc. parallel = 1 +libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses5-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-5.9-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb index 38b356d5e1a763c4d098b5f53c18174b4aaa155e..9936cdbc6cdb6baa6b81ce5240396139575e01d8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.1.0-no-OFED.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb index 947e8e3afaf18759ff1a65ee0644e43086a5a411..b5428d27b07354508f725b3e6392f2a825824bb1 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goalf-1.5.12-no-OFED.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb index 4084c938c1c2a7782ffad1379754c2afd617a78a..21128a21c58cfc993c0cf129ed680a85f373221e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.4.12-no-OFED.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-gompi-1.5.16.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb index 9f6619baca56f6dd3813e005f73c170690c3208a..e272a823d6614bb8925b410002e8a92100a21885 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-gompi-1.5.16.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-goolf-1.4.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb index 33bb21037fd7ac4a65074b61bf3ce9ce27fe6e58..fa8d19afbbd1e5e93a2e837630a4038815f3cedc 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.4.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-goolf-1.5.14.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb index e67f480463340aeb85025cfe155c7007d32a4cad..cdf8cdb5ce9e70c915b5161862b9d950fa2ebe29 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.5.14.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-goolf-1.7.20.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..9a1708ba34ae2398814813b6de4c9c4e581e4fb3 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolf-1.7.20.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +homepage = 'http://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, +and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and +function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-goolfc-1.3.12.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb index 5a698183f4f79d5d5b3f3f7b4f42c0ffb3999300..36b5053e62a60abae1f717693dc908ea34b2a781 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-1.3.12.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-goolfc-2.6.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb index 4e33e95089d0a624fd05522fadf7811e2abeb808..292cec33e2bc3921dc6b5b481fb41cf2d544290b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-goolfc-2.6.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://ftpmirror.gnu.org/%(name)s'] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb index c0284ad94f484ff092d1be2ca13001b0672cb2f1..0b4bbba9adc30ef5d48081dffd653c3839a0f10b 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-3.2.2.u3.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-ictce-4.0.10.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb index 95388cfc5b6d2e549dfe51de58b354a4abfab48e..b5099d8795a6848fdd057092b96b3d36bc8e02c8 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.10.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-ictce-4.0.6.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb index 731485e77bb044ec79ba33d3a1fc5d357ba0406d..94e44f7817caddf76091fff227e9685266e954f3 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.0.6.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-ictce-4.1.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb index 8cb79c351b8087fe72e0ad91d2734e6effb94df3..b1c1a88d7577aa59bfaabeb478debe832afe4055 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-4.1.13.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-ictce-5.2.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb index ee127c7a3c35601056fd67f032ae7d9b2050208d..fed58a89dd1f2373cf76550ce214f954c5c1781e 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.2.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-ictce-5.3.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb index 020778b318ecb01f7c95c411c83762ec6a49c88c..bf996a362f89c915867564a47acc1d457d2a38d1 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.3.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-ictce-5.5.0.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb index a81155369d140411cd90b282723fa67c5a7b9cda..671b5796ac95d1834954ef17b311a0c30f00e242 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-5.5.0.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-ictce-6.2.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb index 84c486d4d929b95f9216aa4feb913fb6c0b2f709..61118f900516a33e99efa0b231d9b1730251b746 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.2.5.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-ictce-6.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb index ab5e8538f310a9b7db8fbfc439d47f8dbb93805b..278cc8d64a005f42fe4393c5ed8fa81fda2c0569 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-6.3.5.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -14,4 +16,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-ictce-7.1.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb index 2a7094da2181c35d84d55cbe5b65727abb8b8b48..38c7d0798803c85c251a0de30028904f91aa3e72 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.1.2.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-ictce-7.3.5.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..a12e4726630cca29876db01c1352d71ecc1052fa --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-ictce-7.3.5.eb @@ -0,0 +1,15 @@ +name = 'ncurses' +version = '5.9' + +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': 'ictce', 'version': '7.3.5'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..d67fc45cbf74de2b745b55b8a787038105ef7e8b --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014.06.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '5.9' + +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': '2014.06'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-intel-2014b.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb index 4aface2738e4be2af300db0b78beb5078d9da889..9fa751952c5838fd56e21106ba31e1b0fdf3e9ea 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2014b.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-intel-2015a.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb index 867d190ac8821b748d3d97dbba140bc2846b9615..24097805bc3a9413673fea1452241d1dba4b5ac7 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-intel-2015a.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,11 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.patch'] + configopts = [ - # default build, no custom configure options - '', + # default build + '--with-shared --enable-overwrite', # the UTF-8 enabled version (ncursesw) - '--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/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", "ncurses5-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-5.9-iomkl-4.6.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb index 9963e053c2ff37d9944dbbbd70e2452c8996e988..115d1bd981375350fa3b16238bffd34d11d45bde 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iomkl-4.6.13.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb index decfe9bc04b5d0a8b9dd9938a6ded2fea1eabc2d..e4351873f4eeb066925a1439d18deba08b7abc25 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-3.7.3.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9-iqacml-4.4.13.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb index f4b42632c95c69520cb058504ffa7e2c0b6ac29a..529b47259fc05498939d6f0744b21441088b9c26 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9-iqacml-4.4.13.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb index 6ab79de61f05db056443ca5117e231bf95dc29dc..dd70b0800a4df8ac05a21610aa6ae59cf96d69e6 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb @@ -1,3 +1,5 @@ +easyblock = 'ConfigureMake' + name = 'ncurses' version = '5.9' @@ -12,4 +14,23 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] +patches = ['ncurses-%(version)s_configure_darwin.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", "ncurses5-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-5.9_configure_darwin.patch b/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch index cbc78d120b898add4dc0050f506cc38492bb903d..293f47532a0c63bb189db74ba802f248ed848f3a 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9_configure_darwin.patch @@ -1,3 +1,5 @@ +# in relation to -no-cpp-precomp bug: https://lists.gnu.org/archive/html/bug-ncurses/2012-12/msg00001.html +# tried/proposed by Fotis, meant for MacOSX compatible ncurses builds... --- ncurses-5.9.orig/configure 2014-10-25 21:11:31.000000000 +0200 +++ ncurses-5.9/configure 2014-10-25 21:11:10.000000000 +0200 @@ -5584,7 +5584,7 @@ diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-goolf-1.4.10.eb index b46d95de455ed7cf103dcc5b897dc5da94856310..e0cfb1558e3ee268b3cfee1869c975f91e0305d3 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-goolf-1.4.10.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb index 57f1d3e4bb87ad0c08e3f8493c1f7f8263c0f10e..d47cb17c759e7cd7920c9d7158c04cfd5198a69e 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13-mt.eb @@ -13,7 +13,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True, 'openmp': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('netCDF', '4.2.1.1', versionsuffix), diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb index 7a7c4b81bc1d579b5b25067a6a42e8654ab789e4..400224b911f0f03f51b8476caa8b5c378e77d8e6 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-4.1.13.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-5.3.0.eb index 3b4f3e5332f61645e898b28a4e59051ab7ad0646..16ea5317c44ad2e4ce3acbefe0d99483abd17034 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-ictce-5.3.0.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-iqacml-3.7.3.eb index de008bf23555d4d20f93fd960eb202fd5a1321a0..d8cdaf41c40323ce847ca3ddbe5c1bc41c70c602 100644 --- a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++-4.2-iqacml-3.7.3.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'pic': True} sources = ['netcdf-cxx-%(version)s.tar.gz'] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.2.1-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.2.1-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..5fcb22ae6f56dabbb79b5bb89da19e82cea41bdf --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.2.1-foss-2014b.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.2.1' + +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': '2014b'} +toolchainopts = {'pic': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] + +dependencies = [('netCDF', '4.3.2')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.so'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goalf-1.1.0-no-OFED.eb index 091c9e9f897d879fca8b8a83653375fdbb1981c2..adc9cf91dce8705937f049531d0ae5891ac5ebd5 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', version)] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.4.10.eb index f4a44d81d372d3caab433671e5b83dcb65c56c8f..2caeeaf083e69a79e8a902d073bf3ec063200c31 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.4.10.eb @@ -5,11 +5,15 @@ homepage = 'http://www.unidata.ucar.edu/software/netcdf/' description = """NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" + toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb index a8cbfe5ddb1455f8d33c0106591d09829954ad4d..bd158f66c56af7e8f4cd8334a66a873497547b5b 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-goolf-1.5.14.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-3.2.2.u3.eb index fac88a30ba22ecbe6072ae301a0bc4a33114d93b..d4ddc1b2b51651134f94313c4d1fc0974cf375e6 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-3.2.2.u3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', version)] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb index 6b36f2c00bc417ca6deb2dd17b7a36f2d7a3dfa2..b50fb138ef03d9d48c8042a1ca76aefcdf0af319 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13-mt.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1', versionsuffix)] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13.eb index ef015a9175c618e7c70da65b94ebaa7cd1155038..40fd553f1f782847bb2b4300505360f5647c5b0a 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-4.1.13.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-5.3.0.eb index 4686402139143a8e419bd541bb60323a924b5216..09084630c19ea94ec3392e6903ac439a930d007e 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-5.3.0.eb @@ -6,12 +6,14 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..87478cf832f5e9c7202aa7f0c6116d5b29d03995 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-ictce-6.1.5.eb @@ -0,0 +1,18 @@ +name = 'netCDF-Fortran' +version = '4.2' + +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': 'ictce', 'version': '6.1.5'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [('netCDF', '4.2.1.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-iqacml-3.7.3.eb index b0bef7e67a1df40bcfef0efdd93c3cea7826effb..f7f72fcd3221fdd38f3d1b1e16f915dfee6d7de1 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.2-iqacml-3.7.3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.2.1.1')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..c51e1a79417f0f36af65a0ce5d1416721988d5ca --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2014b.eb @@ -0,0 +1,20 @@ +name = 'netCDF-Fortran' +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': 'foss', 'version': '2014b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [('netCDF', '4.3.2')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9b2aa29afe29efa0b1678fb196ff54cb3ee9e16a --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-foss-2015a.eb @@ -0,0 +1,20 @@ +name = 'netCDF-Fortran' +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': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [('netCDF', '4.3.2')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2014b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2014b.eb index 59ed0da09a80bc6eb812f550428a97327e6aa593..7823a5fa7da5d39fe723d2a57ba9865dd58ac9fd 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2014b.eb @@ -6,12 +6,14 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" - toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.3.2')] diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2015a.eb index ed31b043f1f29beaa08e1e5c0be905dd1c1de180..39adb73d6e43fdf3ce98084f3905cb6a098ee684 100644 --- a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.4.0-intel-2015a.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('netCDF', '4.3.2')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goalf-1.1.0-no-OFED.eb index e83acc3cca390c27b1f7b1af16aefc6b2e03d675..aaee694b4f58ae06541ec2a031439c1e8c738c7b 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.7')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb index 8bf5c28625a7b91f9e6676e8808c2081d7bfcdf4..6aa937d650d348e77a1b382adc58ef1ef7169b1b 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-goolf-1.4.10.eb @@ -9,7 +9,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.7')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-3.2.2.u3.eb index c00c2955522225cc4333739b4f807f311ca5351f..3d4e4b80346fe4a17108fecd10912e830b8d871a 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-3.2.2.u3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.7')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb index 4a0335f76409425c82f4fd171076d7bf03af3bac..1cf87a93d6b03b8ef32c01fe8f698438edbe4114 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-4.1.13.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '4.1.13'} toolchainopts = {'pic':True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('HDF5', '1.8.9'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb index eef9aa4fe1fbabad97bcae1d770c685093639ac4..2e121dba814b25d0730e17363cacb14e1c75bb2e 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.1.3-ictce-5.3.0.eb @@ -6,16 +6,18 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic':True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ - ('HDF5', '1.8.9'), - ('Doxygen', '1.8.1.1') - ] + ('HDF5', '1.8.9'), + ('Doxygen', '1.8.1.1'), +] moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goalf-1.1.0-no-OFED.eb index 827d6154dadc5c4db557e45cc3c6ce8273e60100..8a0164a41a6bb2016123103f7c22de95bce49532 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goalf-1.1.0-no-OFED.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('HDF5', '1.8.9'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goolf-1.4.10.eb index 3f8634ce6672e1d61619e2ad4c001c4b307f49e5..9278dcabb794b6cbf07553e64fa8febd1b251c1d 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-goolf-1.4.10.eb @@ -9,7 +9,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('HDF5', '1.8.9'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-3.2.2.u3.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-3.2.2.u3.eb index 738b574b640d44c88a7487eb2c559a70501336ac..70579f3686ec9decd7a8e2d716e6aceb433a41cb 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-3.2.2.u3.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-3.2.2.u3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '3.2.2.u3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ ('HDF5', '1.8.9'), diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.3.0.eb index b51011ebf8fd44e6c16d9136b9a1cc61bbeeef81..bf3bcad88f2eea802decbf9374295c7d59902011 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2-ictce-5.3.0.eb @@ -6,16 +6,18 @@ description = """NetCDF (network Common Data Form) is a set of software librarie and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [ - ('HDF5', '1.8.9'), - ('Doxygen', '1.8.1.1') - ] + ('HDF5', '1.8.9'), + ('Doxygen', '1.8.1.1'), +] moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb index 4f975041bc7545bfd52457ba719ab15f692121c8..8ae8d0db4f380f1dbfea9665a56bb2241fdd1c7a 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.4.10.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goolf', 'version': '1.4.10'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10-patch1')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb index a8fa0bc40a20c8c6cc7a1f2429f2a3119a417d59..452797370468a8d706be4e1a1e7b04df67788b83 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-goolf-1.5.14.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'goolf', 'version': '1.5.14'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10-patch1')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb index 1d208f1301b2d4915c6e4f480180b6d95df7810c..a518b2a451eaadd896c49f43988710278a7d6dcc 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13-mt.eb @@ -11,7 +11,10 @@ toolchain = {'name':'ictce','version':'4.1.13'} toolchainopts = {'pic': True, 'openmp': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs-mt')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb index a43794119f16467be15736098adb5779bc3052a3..9caf198302785c53e936ddd4eb64d6fa6afc46ca 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-4.1.13.eb @@ -10,7 +10,10 @@ toolchain = {'name':'ictce','version':'4.1.13'} toolchainopts = {'pic':True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb new file mode 100755 index 0000000000000000000000000000000000000000..081ab64f4b1abdbb590a0262cded9e6e016235c6 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0-zlib-1.2.5.eb @@ -0,0 +1,24 @@ +name = 'netCDF' +version = '4.2.1.1' +versionsuffix = '-zlib-1.2.5' + +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +dependencies = [ + ('HDF5', '1.8.10', '-gpfs%(versionsuffix)s'), + ('Doxygen', '1.8.2'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb index b2e2392049f2b9eb925c8946e7e574327dcf51c0..59a30799c776e9d9f53a634b0cd55f13b1c6d9c0 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.3.0.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.5.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.5.0.eb index 5e5d78307e82e1dc24b359fe54207bda48e0f909..a238c0cf33d0bc4c628e97ac4131702e959fb4b9 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-5.5.0.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..262ebc70b918d1801205fae5d973ed950294ed97 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-ictce-6.1.5.eb @@ -0,0 +1,19 @@ +name = 'netCDF' +version = '4.2.1.1' + +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': 'ictce', 'version': '6.1.5'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] + +dependencies = [('HDF5', '1.8.10', '-gpfs')] + +builddependencies = [('Doxygen', '1.8.3.1')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-intel-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-intel-2014b.eb index fa034d149822eb5571e4f90abd218b57540e679a..69ddb9f9ca998864fbff669e24c70152abf714f0 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-intel-2014b.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10', '-gpfs')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb index dd168910be3759ffd3e336830fe90766fecfbe6f..741f74cd63020f76f7c14a483f0fc3a3a1b773c7 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.2.1.1-iqacml-3.7.3.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'iqacml', 'version': '3.7.3'} toolchainopts = {'pic': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] dependencies = [('HDF5', '1.8.10-patch1')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb index 78d6d431c3e7005756656263aaf7b7eeb26d08c8..a3bce6fa83fc4fad45d72a032aa6e99a5bba358a 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.0-ictce-5.5.0.eb @@ -10,7 +10,10 @@ toolchain = {'name': 'ictce', 'version': '5.5.0'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] patches = [('netCDF-4.3.0_nc-config.in.cmake', 'netcdf-4.3.0')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..f0b637b12c033d26d77ddc2ce58d0f484c7a0089 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2014b.eb @@ -0,0 +1,38 @@ +name = 'netCDF' +version = '4.3.2' + +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': '2014b'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +patches = [ + 'netCDF-4.3.2-with-HDF-1.8.13.patch', + 'netCDF-4.3.2-parallel-HDF.patch', +] + +dependencies = [('HDF5', '1.8.13')] + +builddependencies = [ + ('CMake', '3.0.0'), + ('Doxygen', '1.8.7'), + ('cURL', '7.37.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=ON", + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=OFF", +] + +moduleclass = 'data' + diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d7b013c4185862449d8a96e37bda747cca799d2c --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-foss-2015a.eb @@ -0,0 +1,37 @@ +name = 'netCDF' +version = '4.3.2' + +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': '2015a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] + +patches = [ + 'netCDF-4.3.2-with-HDF-1.8.13.patch', + 'netCDF-4.3.2-parallel-HDF.patch', +] + +dependencies = [('HDF5', '1.8.13')] + +builddependencies = [ + ('CMake', '3.0.0'), + ('Doxygen', '1.8.7'), + ('cURL', '7.37.1'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=ON", + "-DCURL_LIBRARY=$EBROOTCURL/lib/libcurl.so -DCURL_INCLUDE_DIR=$EBROOTCURL/include -DBUILD_SHARED_LIBS=OFF", +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb index 5ab91b52fe086690d652f385c7e066e631199b6a..e848a71eec8578203e512fbc0567bc996c53a47c 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2014b.eb @@ -10,9 +10,15 @@ toolchain = {'name': 'intel', 'version': '2014b'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] -patches = ['netCDF-4.3.2-with-HDF-1.8.13.patch'] +patches = [ + 'netCDF-4.3.2-with-HDF-1.8.13.patch', + 'netCDF-4.3.2-parallel-HDF.patch', +] dependencies = [('HDF5', '1.8.13')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb index bb04604455283e68b4441597d9f019c8a77b7dd4..623ceccdb3dd0dabbbae570c719850035eedc5ee 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-intel-2015a.eb @@ -10,9 +10,15 @@ toolchain = {'name': 'intel', 'version': '2015a'} toolchainopts = {'pic': True, 'usempi': True} sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://www.unidata.ucar.edu/downloads/netcdf/ftp/'] +source_urls = [ + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/', + 'ftp://ftp.unidata.ucar.edu/pub/netcdf/old', +] -patches = ['netCDF-4.3.2-with-HDF-1.8.13.patch'] +patches = [ + 'netCDF-4.3.2-with-HDF-1.8.13.patch', + 'netCDF-4.3.2-parallel-HDF.patch', +] dependencies = [('HDF5', '1.8.13')] diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-parallel-HDF.patch b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-parallel-HDF.patch new file mode 100644 index 0000000000000000000000000000000000000000..d097592f1514f7e7fa84d23c3301e7d072d85f02 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.3.2-parallel-HDF.patch @@ -0,0 +1,21 @@ +#If a system installed sequential HDF5 exist and we use an external +#parallel HDF5 intsllation then the system installed h5cc will be used +#instead of the external h5pcc. Inspiration from netCDF 4.3.3.1 +#B. Hajgato March 1st 2015 +--- netcdf-4.3.2/CMakeLists.txt.org 2014-04-23 23:35:20.000000000 +0200 ++++ netcdf-4.3.2/CMakeLists.txt 2015-03-01 21:07:55.000000000 +0100 +@@ -637,8 +637,13 @@ + ENDIF(NOT MSVC) + + # Assert HDF5 version. ++ IF(HDF5_IS_PARALLEL) ++ SET(HDF5_CC h5pcc) ++ ELSE() ++ SET(HDF5_CC h5cc) ++ ENDIF() + SET(HDF5_VERSION_REQUIRED 1.8.6) +- execute_process(COMMAND sh -c "h5cc -showconfig | grep -i \"HDF5 version\" | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*$/\\1/'" ++ execute_process(COMMAND sh -c "${HDF5_CC} -showconfig | grep -i \"HDF5 version\" | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*$/\\1/'" + OUTPUT_VARIABLE HDF5_VERSION + ERROR_QUIET + ) diff --git a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.10-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.10-ictce-5.5.0-Python-2.7.6.eb index 172dead842adbe8c9e9db8a0f046c54b43ec95b1..8894ccbab97592745ee7fe1242c7d5b273e9e115 100644 --- a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.10-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.10-ictce-5.5.0-Python-2.7.6.eb @@ -8,7 +8,7 @@ description = """Pythonic manipulation of IPv4, IPv6, CIDR, EUI and MAC network toolchain = {'name': 'ictce', 'version': '5.5.0'} -source_urls = ['https://pypi.python.org/packages/source/n/netaddr/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/n/netaddr/netaddr-0.7.14-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.14-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..a12196a3b842855fb2c9423de1e83cbf33d78248 --- /dev/null +++ b/easybuild/easyconfigs/n/netaddr/netaddr-0.7.14-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'netaddr' +version = '0.7.14' + +homepage = 'https://pypi.python.org/pypi/netaddr' +description = """Pythonic manipulation of IPv4, IPv6, CIDR, EUI and MAC network addresses""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), +] + +options = {'modulename': 'netaddr'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..26cfac901b2e0a074459208268830a1f673a7d44 --- /dev/null +++ b/easybuild/easyconfigs/n/netifaces/netifaces-0.10.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'netifaces' +version = '0.10.4' + +homepage = 'https://pypi.python.org/pypi/netifaces' +description = """netifaces provides a (hopefully portable-ish) way for Python +programmers to get access to a list of the network interfaces on the local +machine, and to obtain the addresses of those network interfaces.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), +] + +options = {'modulename': 'netifaces'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..f6ae1e74b7a2539793d7a25daabd7c84d7620e75 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-1.9.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '1.9.1' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [ + (python, pythonver), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..9346ee7b4c1fe70e9d785cb97ce0c09b9f3d1c61 --- /dev/null +++ b/easybuild/easyconfigs/n/ngspice/ngspice-26-intel-2014b.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'ngspice' +version = '26' + +homepage = 'http://ngspice.sourceforge.net' +description = """Ngspice is a mixed-level/mixed-signal circuit simulator. Its code + is based on three open source software packages: Spice3f5, Cider1b1 + and Xspice. +""" + +toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [SOURCEFORGE_SOURCE] + +builddependencies = [ + ('Bison', '3.0.2'), + ('flex', '2.5.39'), +] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ngmakeidx', 'ngmultidec', 'ngnutmeg', 'ngproc2mod', 'ngsconvert', 'ngspice']], + 'dirs': [], +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..52f1df7369287e84717e58036bef9ddf34b18445 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.10-GNU-4.9.2-2.25.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.10' + +checksums = ['682c38305b2596967881f3d77bc3fc9c'] + +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': 'GNU', 'version': '4.9.2-2.25'} + +source_urls = ['ftp://oss.sgi.com/www/projects/libnuma/download/'] +sources = [SOURCE_TAR_GZ] + +builddependencies = [('Autotools', '20150215')] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.so', 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch b/easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch new file mode 100644 index 0000000000000000000000000000000000000000..0689e81b9fd2fe9675529721a284d10c1b5639cc --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.8.1-mkl.patch @@ -0,0 +1,215 @@ +fix issues in numpy distutils pkg w.r.t. detecting BLAS/LAPACK libraries +by Kenneth Hoste (HPC-UGent) +diff -ur numpy-1.8.1.orig/numpy/distutils/fcompiler/__init__.py numpy-1.8.1-2/numpy/distutils/fcompiler/__init__.py +--- numpy-1.8.1.orig/numpy/distutils/fcompiler/__init__.py 2014-03-25 20:43:24.000000000 +0100 ++++ numpy-1.8.1-2/numpy/distutils/fcompiler/__init__.py 2014-07-08 15:22:31.471064031 +0200 +@@ -628,7 +628,10 @@ + return options + + def library_option(self, lib): +- return "-l" + lib ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib + def library_dir_option(self, dir): + return "-L" + dir + +diff -ur numpy-1.8.1.orig/numpy/distutils/system_info.py numpy-1.8.1-2/numpy/distutils/system_info.py +--- numpy-1.8.1.orig/numpy/distutils/system_info.py 2014-03-25 20:43:24.000000000 +0100 ++++ numpy-1.8.1-2/numpy/distutils/system_info.py 2014-07-08 15:32:34.480063940 +0200 +@@ -600,7 +600,7 @@ + if is_string(default): + return [default] + return default +- return [b for b in [a.strip() for a in libs.split(',')] if b] ++ return [b for b in [a.strip().replace(':',',') for a in libs.split(',')] if b] + + def get_libraries(self, key='libraries'): + return self.get_libs(key, '') +@@ -642,6 +642,23 @@ + lib_dirs) + return info + ++ def check_libs_all(self,lib_dir,libs,opt_libs =[]): ++ """If static or shared libraries are available then return ++ their info dictionary. ++ ++ Checks for all libraries as shared libraries first, then ++ static (or vice versa if self.search_static_first is True). ++ """ ++ exts = self.library_extensions() ++ info = None ++ for ext in exts: ++ info = self._check_libs_all(lib_dir,libs,opt_libs,[ext]) ++ if info is not None: ++ break ++ if not info: ++ log.info(' libraries %s not found in %s', ','.join(libs), lib_dir) ++ return info ++ + def check_libs2(self, lib_dirs, libs, opt_libs=[]): + """If static or shared libraries are available then return + their info dictionary. +@@ -655,6 +672,18 @@ + lib_dirs) + return info + ++ def check_libs2_all(self, lib_dirs, libs, opt_libs =[]): ++ """If static or shared libraries are available then return ++ their info dictionary. ++ ++ Checks each library for shared or static. ++ """ ++ exts = self.library_extensions() ++ info = self._check_libs_all(lib_dirs,libs,opt_libs,exts) ++ if not info: ++ log.info(' libraries %s not found in %s', ','.join(libs), os.pathsep.join(lib_dirs)) ++ return info ++ + def _lib_list(self, lib_dir, libs, exts): + assert is_string(lib_dir) + liblist = [] +@@ -665,6 +694,9 @@ + lib_prefixes = ['lib'] + # for each library name, see if we can find a file for it. + for l in libs: ++ if l[0]=='-': ++ liblist.append(l) ++ continue + for ext in exts: + for prefix in lib_prefixes: + p = self.combine_paths(lib_dir, prefix + l + ext) +@@ -680,6 +712,19 @@ + break + return liblist + ++ def _lib_list_all(self, lib_dirs, libs, exts): ++ assert (type(lib_dirs)==list) ++ if lib_dirs: ++ assert is_string(lib_dirs[0]) ++ liblist=[] ++ for lib_dir in lib_dirs: ++ ls=self._lib_list(lib_dir,libs,exts) ++ for l in ls: ++ log.info("(_lib_list_all) Found %s in %s"%(l,lib_dir)) ++ if l not in liblist: ++ liblist.append(l) ++ return liblist ++ + def _check_libs(self, lib_dirs, libs, opt_libs, exts): + """Find mandatory and optional libs in expected paths. + +@@ -721,6 +766,22 @@ + else: + return None + ++ def _check_libs_all(self, lib_dirs, libs, opt_libs, exts): ++ found_libs_unordered = self._lib_list_all(lib_dirs, libs, exts) ++ # ensure same order as in lib_dirs ++ found_libs = [] ++ for lib_dir in libs: ++ if lib_dir in found_libs_unordered: ++ found_libs.append(lib_dir) ++ if len(found_libs) == len(libs): ++ info = {'libraries' : found_libs, 'library_dirs' : lib_dirs} ++ opt_found_libs = self._lib_list_all(lib_dirs, opt_libs, exts) ++ if len(opt_found_libs) == len(opt_libs): ++ info['libraries'].extend(opt_found_libs) ++ return info ++ else: ++ return ++ + def combine_paths(self, *args): + """Return a list of existing paths composed by all combinations + of items from the arguments. +@@ -953,9 +1014,11 @@ + lib_dirs = self.get_lib_dirs() + incl_dirs = self.get_include_dirs() + mkl_libs = self.get_libs('mkl_libs', self._lib_mkl) +- info = self.check_libs2(lib_dirs, mkl_libs) +- if info is None: ++ mkl = None ++ mkl = self.check_libs2_all(lib_dirs,mkl_libs) ++ if mkl is None: + return ++ info = mkl + dict_append(info, + define_macros=[('SCIPY_MKL_H', None)], + include_dirs=incl_dirs) +@@ -1017,16 +1080,13 @@ + atlas = None + lapack = None + atlas_1 = None +- for d in lib_dirs: +- atlas = self.check_libs2(d, atlas_libs, []) +- lapack_atlas = self.check_libs2(d, ['lapack_atlas'], []) +- if atlas is not None: +- lib_dirs2 = [d] + self.combine_paths(d, ['atlas*', 'ATLAS*']) +- lapack = self.check_libs2(lib_dirs2, lapack_libs, []) +- if lapack is not None: +- break +- if atlas: +- atlas_1 = atlas ++ atlas = self.check_libs2_all(lib_dirs, atlas_libs) ++ lapack_atlas = self.check_libs2_all(lib_dirs, ['lapack_atlas']) ++ if atlas is not None: ++ lib_dirs2 = lib_dirs + self.combine_paths(lib_dirs,['atlas*','ATLAS*']) ++ lapack = self.check_libs2_all(lib_dirs2, lapack_libs) ++ if atlas: ++ atlas_1 = atlas + log.info(self.__class__) + if atlas is None: + atlas = atlas_1 +@@ -1105,7 +1165,8 @@ + info = {} + atlas_libs = self.get_libs('atlas_libs', + self._lib_names + self._lib_atlas) +- atlas = self.check_libs2(lib_dirs, atlas_libs, []) ++ atlas = None ++ atlas = self.check_libs2_all(lib_dirs, atlas_libs) + if atlas is None: + return + include_dirs = self.get_include_dirs() +@@ -1153,8 +1214,10 @@ + lib_dirs = self.get_lib_dirs() + + lapack_libs = self.get_libs('lapack_libs', self._lib_names) +- info = self.check_libs(lib_dirs, lapack_libs, []) +- if info is None: ++ lapack = self.check_libs_all(lib_dirs, lapack_libs, []) ++ if lapack is not None: ++ info = lapack ++ else: + return + info['language'] = 'f77' + self.set_info(**info) +@@ -1548,8 +1611,10 @@ + lib_dirs = self.get_lib_dirs() + + blas_libs = self.get_libs('blas_libs', self._lib_names) +- info = self.check_libs(lib_dirs, blas_libs, []) +- if info is None: ++ blas = self.check_libs_all(lib_dirs, blas_libs, []) ++ if blas is not None: ++ info = blas ++ else: + return + info['language'] = 'f77' # XXX: is it generally true? + self.set_info(**info) +diff -ur numpy-1.8.1.orig/numpy/distutils/unixccompiler.py numpy-1.8.1-2/numpy/distutils/unixccompiler.py +--- numpy-1.8.1.orig/numpy/distutils/unixccompiler.py 2014-03-25 20:43:23.000000000 +0100 ++++ numpy-1.8.1-2/numpy/distutils/unixccompiler.py 2014-07-08 15:34:01.924063926 +0200 +@@ -111,3 +111,12 @@ + + replace_method(UnixCCompiler, 'create_static_lib', + UnixCCompiler_create_static_lib) ++ ++def UnixCCompiler_library_option(self, lib): ++ if lib[0]=='-': ++ return lib ++ else: ++ return "-l" + lib ++ ++replace_method(UnixCCompiler, 'library_option', ++ UnixCCompiler_library_option) diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.8.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..db3bc90ff514a87b12934f4ac91061cc44c09ff0 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.8.2-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.8.2' + +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-1.8.1-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.1.29-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.1.29-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..49b27458ee8f4f02c9bb19fde91697dc9b5e5456 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.1.29-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +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': 'CrayGNU', 'version': '5.1.29'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..fa04b4229933eef7eea6d6d85729bab4be9198ef --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.25-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +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': 'CrayGNU', 'version': '5.2.25'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..7d81f886bcbaf504db2b2a66bfd01e2948cb5696 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-CrayGNU-5.2.40-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +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': 'CrayGNU', 'version': '5.2.40'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['numpy-1.8.0-mkl.patch'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..bc4a69d14c69a93171d9b7d71f143ff4cbf813c3 --- /dev/null +++ b/easybuild/easyconfigs/n/numpy/numpy-1.9.2-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,26 @@ +name = 'numpy' +version = '1.9.2' + +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'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6a2ab2df295538ba8e9251e633c4844994418c4e --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-foss-2015a.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 = "OPARI2" +version = "1.1.2" + +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': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/opari2/'] + +checksums = [ + '9a262c7ca05ff0ab5f7775ae96f3539e', # opari2-1.1.2.tar.gz +] + +sanity_check_paths = { + 'files': ["bin/opari2", "include/opari2/pomp2_lib.h"], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..34e2fdbcea5512d2a15da831f62ae07863f27b20 --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-1.1.2-goolf-1.5.14.eb @@ -0,0 +1,29 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Authors:: Jordi Blasco +# License:: New BSD +# +## + +easyblock = 'ConfigureMake' + +name = "OPARI2" +version = "1.1.2" + +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-4.4.1-intel-2015a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d96cc487d50b0e3de4adc13cb941e826ad8eef0a --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-4.4.1-intel-2015a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '4.4.1' + +homepage = 'http://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] + +configopts = 'CC="$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/OTF2/OTF2-1.2.1-goolf-1.5.14.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..60c9ce8691c6e8f36bbdec05df5fac58981f76a5 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.2.1-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 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 = 'EB_Score_minus_P' + +name = "OTF2" +version = "1.2.1" + +homepage = 'http://www.score-p.org' +description = """The Open Trace Format 2 is a highly scalable, memory efficient event + trace data format plus support library. It will become the new standard trace format + for Scalasca, Vampir, and Tau and is open for other tools.""" + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +# http://www.vi-hps.org/upload/packages/otf2/otf2-1.2.1.tar.gz +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] + +sanity_check_paths = { + # note by Bernd Mohr: on some systems libraries end up in lib/ + 'files': ["bin/otf2-config", "include/otf2/otf2.h", ("lib64/libotf2.a", "lib/libotf2.a")], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4f583c01b16b6ce7120e5003306b9460ad846819 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-1.5.1-foss-2015a.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 = 'EB_Score_minus_P' + +name = "OTF2" +version = "1.5.1" + +homepage = 'http://www.score-p.org' +description = """The Open Trace Format 2 is a highly scalable, memory efficient event + trace data format plus support library. It will become the new standard trace format + for Scalasca, Vampir, and Tau and is open for other tools.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.vi-hps.org/upload/packages/otf2/'] + +checksums = [ + '16a9df46e0da78e374f5d12c8cdc1109', # otf2-1.5.1.tar.gz +] + +sanity_check_paths = { + # note by Bernd Mohr: on some systems libraries end up in lib/ + 'files': ["bin/otf2-config", "include/otf2/otf2.h", ("lib64/libotf2.a", "lib/libotf2.a")], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..eeea60d967c261b2eb2aac0aef4eb9b1bc200f5d --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-foss-2015a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Octave' +version = '3.8.2' + +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': '2015a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [ + ('PCRE', '8.36'), + ('ncurses', '5.9'), + ('libreadline', '6.3'), +] + +configopts = '--with-blas="$LIBBLAS"' + +sanity_check_paths = { + 'files': ['bin/octave'], + 'dirs': [] +} + +sanity_check_commands = [('octave', '--eval "1+2"')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..2b1159f0069a9e94a41687a4f0d5f762739e42db --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'Octave' +version = '3.8.2' + +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': '2015a'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['Octave-%(version)s_intel.patch'] + +dependencies = [ + ('PCRE', '8.36'), + ('ncurses', '5.9'), + ('libreadline', '6.3'), +] + +configopts = '--with-blas="$LIBBLAS"' + +sanity_check_paths = { + 'files': ['bin/octave'], + 'dirs': [] +} + +sanity_check_commands = [('octave', '--eval "1+2"')] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch b/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch new file mode 100644 index 0000000000000000000000000000000000000000..ec623d4749f185c2dfe32ed27b3cfd9f36965108 --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-3.8.2_intel.patch @@ -0,0 +1,51 @@ +fix build issue with Intel compilers that manifests itself as: +../../libgnu/stdio.h(948): error: declaration is incompatible with previous "getchar" (declared at line 542 of "/usr/include/stdio.h") + _GL_CXXALIAS_SYS (getchar, int, (void)); + ^ +see http://octave.1599824.n4.nabble.com/Build-issues-with-libgnu-tt4666148.html#a4666416 +patch available via https://savannah.gnu.org/bugs/index.php?43171 +--- octave-3.8.2/libgnu/fcntl.in.h ++++ octave-3.8.2/libgnu//fcntl.in.h +@@ -34,7 +34,7 @@ + extern "C" { ... } block, which leads to errors in C++ mode with the + overridden from gnulib. These errors are known to be gone + with g++ version >= 4.3. */ +-#if !(defined __GLIBC__ || defined __UCLIBC__) || (defined __cplusplus && defined GNULIB_NAMESPACE && !(__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3))) ++#if !(defined __GLIBC__ || defined __UCLIBC__) || (defined __cplusplus && defined GNULIB_NAMESPACE && (defined __ICC || !(__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3)))) + # include + #endif + #@INCLUDE_NEXT@ @NEXT_FCNTL_H@ +@@ -53,7 +53,7 @@ + extern "C" { ... } block, which leads to errors in C++ mode with the + overridden from gnulib. These errors are known to be gone + with g++ version >= 4.3. */ +-#if !(defined __GLIBC__ || defined __UCLIBC__) || (defined __cplusplus && defined GNULIB_NAMESPACE && !(__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3))) ++#if !(defined __GLIBC__ || defined __UCLIBC__) || (defined __cplusplus && defined GNULIB_NAMESPACE && (defined __ICC || !(__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 3)))) + # include + #endif + /* The include_next requires a split double-inclusion guard. */ + +--- octave-3.8.2/liboctave/cruft/misc/quit.h.orig 2015-04-22 21:47:08.614133593 +0200 ++++ octave-3.8.2/liboctave/cruft/misc/quit.h 2015-04-22 21:47:24.584562436 +0200 +@@ -23,16 +23,16 @@ + #if !defined (octave_quit_h) + #define octave_quit_h 1 + +-#ifdef __cplusplus +-#include +-extern "C" { +-#endif +- + #include + + #include + #include + ++#ifdef __cplusplus ++#include ++extern "C" { ++#endif ++ + #if defined (__WIN32__) && ! defined (_POSIX_VERSION) + + #define WIN32_LEAN_AND_MEAN diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..fe4211f53cee07ecb3e5b9109d38fb5b9c405c4e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.13-gompi-1.5.16-LAPACK-3.5.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.13' + +lapackver = '3.5.0' +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': 'gompi', 'version': '1.5.16'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + 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 = [ + (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + (large_src, '.'), + (timing_src, '.'), +] + +skipsteps = ['configure'] + +threading = 'USE_THREAD=1' +buildopts = 'BINARY=64 ' + threading + ' CC="$CC" FC="$F77"' +installopts = threading + " PREFIX=%(installdir)s" + +# extensive testing can be enabled by uncommenting the line below +#runtest = 'PATH=.:$PATH lapack-timing' + +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-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..23704a985eddb9b5275e0d10adf6b98ef2576c43 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.2.14-GNU-4.9.2-2.25-LAPACK-3.5.0.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'OpenBLAS' +version = '0.2.14' + +lapackver = '3.5.0' +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': 'GNU', 'version': '4.9.2-2.25'} + +lapack_src = 'lapack-%s.tgz' % lapackver +large_src = 'large.tgz' +timing_src = 'timing.tgz' +sources = [ + 'v%(version)s.tar.gz', + lapack_src, + 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 = [ + (lapack_src, '.'), # copy LAPACK tarball to unpacked OpenBLAS dir + (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/OpenCV/OpenCV-2.4.9-intel-2014.06.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..9bed0737f0cf6488b462f7443cc39df1038378dd --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-2.4.9-intel-2014.06.eb @@ -0,0 +1,76 @@ +easyblock = 'CMakeMake' + +name = 'OpenCV' +version = '2.4.9' + +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': '2014.06'} +toolchainopts = {'opt': True, 'optarch': True} + +sources = [SOURCELOWER_ZIP] +source_urls = [('http://sourceforge.net/projects/opencvlibrary/files/opencv-unix/%(version)s', 'download')] + +patches = ['OpenCV-%(version)s_with_IPP.patch'] + +osdependencies = ['gtk2-devel'] + +builddependencies = [ + ('CMake', '3.0.0'), +] + +python = 'Python' +pythonver = '2.7.8' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +java = 'Java' +javaver = '1.7.0_79' + +dependencies = [ + (python, pythonver), + ('zlib', '1.2.8'), + ('ffmpeg', '2.4'), + ('libjpeg-turbo', '1.3.1'), + ('libpng', '1.6.12'), + ('LibTIFF', '4.0.3'), + ('JasPer', '1.900.1'), + (java, javaver ,'', True), + ('ant', '1.9.3', '-%s-%s' % (java,javaver), True), + ('GLib', '2.40.0') +] + +preconfigopts = 'export IPPROOT=$EBROOTICC/ipp && ' + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts += '-DBUILD_PYTHON_SUPPORT=ON ' +configopts += '-DPYTHON_PACKAGES_PATH=$EBROOTPYTHON/lib/python%s/site-packages ' % pythonshortver +configopts += '-DBUILD_NEW_PYTHON_SUPPORT=ON ' +configopts += '-DZLIB_LIBRARY=$EBROOTZLIB/lib/libz.so ' +configopts += '-DZLIB_INCLUDE_DIR=$EBROOTZLIB/include ' +configopts += '-DTIFF_LIBRARY=$EBROOTLIBTIFF/lib/libtiff.so ' +configopts += '-DTIFF_INCLUDE_DIR=$EBROOTLIBTIFF/include ' +configopts += '-DPNG_LIBRARY=$EBROOTLIBPNG/lib/libpng.so ' +configopts += '-DPNG_INCLUDE_DIR=$EBROOTLIBPNG/include ' +configopts += '-DJPEG_LIBRARY=$EBROOTLIBJPEGMINTURBO/lib/libjpeg.so ' +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.so'] + + [ 'bin/opencv_%s' % x for x in ['haartraining', 'createsamples', 'performance', 'traincascade'] ], + 'dirs': ['include'] +} + +modextrapaths = { + 'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver, + 'CLASSPATH': 'share/OpenCV/java', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..9e1b2ca02bff6a99fc90b665e116eea2de44babd --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-foss-2015.05.eb @@ -0,0 +1,32 @@ +name = 'OpenFOAM' +version = '2.3.1' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2015.05'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + 'OpenFOAM-2.3.0_libreadline.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +dependencies = [ + ('libreadline', '6.3'), + ('SCOTCH', '6.0.4'), + ('ncurses', '5.9'), +] + +builddependencies = [('flex', '2.5.39')] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb index e568f8411eb1f656a81e3868d9bd8b1aeade2765..e2dcab157e948b20e9e328f43a4805ed7821250f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3-no-OFED.eb @@ -17,11 +17,10 @@ patches = ['pax_disable.patch'] configopts = '--with-threads=posix --enable-shared --enable-mpi-threads --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "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 ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "open-pal", "open-rte"]], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb index fe72e01efd4a0a9c5a3f4cb63224971c3da2232f..af837e08152447032188101eaaa88fc5f04944c1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-GCC-4.6.3.eb @@ -17,11 +17,10 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "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 ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "open-pal", "open-rte"]], + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..70d3c85032a28e19b0e16e7ef6cf63f13e131d4a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.4.5-ictce-5.5.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = "1.4.5" + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'ictce', 'version': '5.5.0'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +builddependencies = [ + ('Automake', '1.14'), + ('Autoconf', '2.69'), +] + +dependencies = [('hwloc', '1.7.2')] + +configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' +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-openib +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "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], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], +} + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb index 3f5d4cafd7932522ba9bf619518ebb02422b19e6..d88a606fa0874e2b4b4eddd005397d49a5617cf0 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.3-iccifort-2011.13.367.eb @@ -20,14 +20,11 @@ dependencies = [('hwloc', '1.6')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mca_common_sm", "mpi_cxx", "mpi_f77", "mpi_f90", "mpi", "ompitrace", "open-pal", + "otfaux", "otf", "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 ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", "otf", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb index 68114cf721a0f3006cfdc073c4a0c48ddc3e3ddb..b42d9a8b03342c501a030c846654b30116370dec 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-ClangGCC-1.1.3.eb @@ -21,12 +21,11 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb index 109447fa55dfbac944c050be136588b18a837429..fc479108fe13c08eb88b87078db0458a24537bc7 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.6.4.eb @@ -21,12 +21,11 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb index 983eb22945063bf4bc7bb4a77f041348e340fd08..8b588833b0c12bbf66e7797020c3a94ca1a0e326 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2-no-OFED.eb @@ -19,15 +19,14 @@ configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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 ["mpi_cxx", "mpi_f77" ,"mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], - 'dirs': ["include/openmpi/ompi/mpi/cxx"], + 'dirs': ["include/openmpi/ompi/mpi/cxx"], } moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb index 7d3922cea0136cb2867301cafe5283861876c889..168f6f9d236888fabac64ade04e006292e2fb169 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.4-GCC-4.7.2.eb @@ -21,12 +21,11 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb index 21bd882ac7c7d5cd897257b259cd66a684b78f1a..933369e32b802a241d5f062949027dd85601f6cc 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.2.eb @@ -24,12 +24,13 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", "open-rte", "vt", "vt-hyb", "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", - "mpif-mpi-io", "mpi", "mpi_portable_platform"]], + "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb index 90dc3e34495caafd9ecb1eb1212fe9d483784332..ccbc9394ec9eed2af9e1eccbe052d90063a61f14 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.7.3-no-OFED.eb @@ -12,18 +12,19 @@ toolchain = {'name': 'GCC', 'version': '4.7.3'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb index 5e9b5fcda835e62b138981267948153f87cccf49..ce23f55355012b7649e9e014603456c3b077bab5 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1-no-OFED.eb @@ -12,18 +12,19 @@ toolchain = {'name': 'GCC', 'version': '4.8.1'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path configopts += '--disable-dlopen ' # statically link component, don't do dynamic loading +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb index 394c231617a2cff59c9de1e4ccb7c84e213d8165..c6b40582c811ab933be965e5e3d4a70972a3c210 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.1.eb @@ -11,7 +11,9 @@ toolchain = {'name': 'GCC', 'version': '4.8.1'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path @@ -20,12 +22,11 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb index 6cac76d97d59e0e7575f8b51fb4e11f8cd057013..2afbc4733e247f52c6237f6660133c85b8f746f6 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2-no-OFED.eb @@ -12,7 +12,9 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --without-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path @@ -21,12 +23,11 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' dependencies = [('hwloc', '1.8.1')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb index 908f092bfae6509365da49a239152a4b3017abe1..8af372736a44fabbbb08930300abd29c4e875038 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.2.eb @@ -11,7 +11,9 @@ toolchain = {'name': 'GCC', 'version': '4.8.2'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path @@ -23,12 +25,11 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb index c9d45613dfcaa2cc5f82e6c8135f163547b72c27..2ae7377c3711c9dc395ade0bda8a717d614b459a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-GCC-4.8.3.eb @@ -11,7 +11,9 @@ toolchain = {'name': 'GCC', 'version': '4.8.3'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-1.6.5-vt_cupti_events.patch'] +patches = [ + 'OpenMPI-1.6.5-vt_cupti_events.patch', +] configopts = '--with-threads=posix --enable-shared --enable-mpi-thread-multiple --with-openib ' configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path @@ -23,12 +25,11 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev','libibverbs-devel')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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 ["mpi_cxx", "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb index 85b6644c9f22372ab8669187e7c9309ffa6728e2..4fc8978e4dd5bda028cdc3019bcd9366074d5edf 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.2.144.eb @@ -20,14 +20,11 @@ dependencies = [('hwloc', '1.8.1')] # needed for --with-openib osdependencies = [('libibverbs-dev', 'libibverbs-devel')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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 ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb index 4d2c94f271e8b1dc99698983c024d4e67251d9f8..0bb4349893a40dbd2b9e1ac16432eeb08305d867 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211-no-OFED.eb @@ -18,18 +18,14 @@ configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support dependencies = [('hwloc', '1.9')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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 ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], } moduleclass = 'mpi' - diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb index 79c31e1c3d020b4877cef79fbff6c3e7366c29f1..e9f2f244ec124a54d581a97c0e27e3266c7903bb 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.6.5-iccifort-2013_sp1.4.211.eb @@ -20,14 +20,11 @@ dependencies = [('hwloc', '1.9')] # needed for --with-openib osdependencies = [('libibverbs-dev','libibverbs-devel')] +libs = ["mpi_cxx", "mpi_f77", "mpi_f90", "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 ["mca_common_sm", "mpi_cxx", - "mpi_f77", "mpi_f90", - "mpi", "ompitrace", "open-pal", - "otfaux", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + ["include/%s.h" % x for x in ["mpi-ext", "mpif-common", "mpif-config", "mpif", "mpif-mpi-io", "mpi", "mpi_portable_platform"]], 'dirs': ["include/openmpi/ompi/mpi/cxx"], diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb index 1f4d38649b5ca572a646ba41325cbaad671b894c..6687a0ffa048b153e13d236b53057589a5e6ff9b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-GCC-4.8.2.eb @@ -23,12 +23,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb index 094489afc48e54abae3315a707f56c4481b3c3b7..10774dff41ae6028fb5708e770c44b6a5efdb2b3 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3-gcccuda-2.6.10.eb @@ -11,7 +11,15 @@ toolchain = {'name': 'gcccuda', 'version': '2.6.10'} sources = [SOURCELOWER_TAR_GZ] source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] -patches = ['OpenMPI-%(version)s-vt_cupti_events.patch'] +patches = [ + 'OpenMPI-%(version)s_common-cuda-lib.patch', + 'OpenMPI-%(version)s-vt_cupti_events.patch', +] + +builddependencies = [ + ('Automake', '1.14'), + ('Autoconf', '2.69') +] dependencies = [('hwloc', '1.8')] @@ -23,12 +31,10 @@ configopts += '--with-cuda=$CUDA_HOME ' # CUDA-aware build; N.B. --d # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3_common-cuda-lib.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3_common-cuda-lib.patch new file mode 100644 index 0000000000000000000000000000000000000000..4ba9ebab68df8a17794440a7e9657c4a2645d391 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.7.3_common-cuda-lib.patch @@ -0,0 +1,16 @@ +see http://permalink.gmane.org/gmane.comp.clustering.open-mpi.user/20404, +patch obtained via https://svn.open-mpi.org/trac/ompi/changeset/29762 +Index: /branches/v1.7/ompi/mca/pml/ob1/Makefile.am +=================================================================== +--- /branches/v1.7/ompi/mca/pml/ob1/Makefile.am (revision 29624) ++++ /branches/v1.7/ompi/mca/pml/ob1/Makefile.am (revision 29762) +@@ -68,4 +68,9 @@ + mca_pml_ob1_la_LDFLAGS = -module -avoid-version + ++if OPAL_cuda_support ++mca_pml_ob1_la_LIBADD = \ ++ $(top_ompi_builddir)/ompi/mca/common/cuda/libmca_common_cuda.la ++endif ++ + noinst_LTLIBRARIES = $(component_noinst) + libmca_pml_ob1_la_SOURCES = $(ob1_sources) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb index d9eca98720f24b4e306d24afaa12898be2360994..eeb7c2fe82787a088235bc35b36d73572986987b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.1-GCC-4.8.3.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb index fb7afbbd4177f8a113e1305d5a3b49b7b55a2ea8..a47fa4f0f1baf045c981ae93242504db83f386d1 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-GCC-4.9.2.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb index e1057430c2d4bc2d76a603cfb1a0177d6506467d..c6c6f0c9abedef3c520b51107fecf6f6e967bff9 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211-no-OFED.eb @@ -20,12 +20,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic dependencies = [('hwloc', '1.9')] +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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb index f73d19d32c411802545c5a64ac6066066ba5be7a..f5e9417cad30712278bc9b5e87c3d59d6da270cb 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.3-iccifort-2013_sp1.4.211.eb @@ -11,7 +11,6 @@ toolchain = {'name': 'iccifort', 'version': '2013_sp1.4.211'} 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 @@ -22,12 +21,10 @@ dependencies = [('hwloc', '1.9')] # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb index 3841ad29d2839ebf49c64c3f6de3824817058f48..2eb439ac3492244154f0a12b22fba050ff2f76f2 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.8.4.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb index e90682df3be715e07cd59d07f3a5cf02cb49b2ca..e009a632591c41042eb786fb2ec7e91a4870d763 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-GCC-4.9.2.eb @@ -21,12 +21,10 @@ configopts += '--disable-dlopen ' # statically link component, don't do dynamic # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb index a3c918320f1477209183bbab43419751d09c2324..780c3c78ba6dfab1b6a0032e5c5567383be30fc6 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.1.133-GCC-4.9.2.eb @@ -22,12 +22,10 @@ dependencies = [('hwloc', '1.10.0')] # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb index d7df86c8d6abbc91c50a7f612a16a123bd34e98f..ca0afea9dc034c006d7c3a8637f513f221a4b69a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.4-iccifort-2015.2.164-GCC-4.9.2.eb @@ -23,12 +23,10 @@ dependencies = [('hwloc', '1.10.0')] # 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 ["mpi_cxx", "mpi_mpifh", - "mpi", "ompitrace", "open-pal", - "open-rte", "vt", "vt-hyb", - "vt-mpi", "vt-mpi-unify"]] + + ["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"], } diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..095d22d991eba77e2a9063f2f903e35331f42f1b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-1.8.5-GNU-4.9.2-2.25.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '1.8.5' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GNU', 'version': '4.9.2-2.25'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] + +dependencies = [('hwloc', '1.10.1')] + +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/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6dae1dce8531dbe3c06c2fbc0797ec320d00c25e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-foss-2015a.eb @@ -0,0 +1,27 @@ +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': '2015a'} + +source_urls = [GOOGLECODE_SOURCE] +sources = ['libpgm-%(version)s.tar.gz'] + +configopts = '--with-pic' + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.so', 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' 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 new file mode 100644 index 0000000000000000000000000000000000000000..bb2adb94d7c0a397596e7d15a76752dd5c118861 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-intel-2015a.eb @@ -0,0 +1,27 @@ +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': '2015a'} + +source_urls = [GOOGLECODE_SOURCE] +sources = ['libpgm-%(version)s.tar.gz'] + +configopts = '--with-pic' + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.so', 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a127a7e7bb4ef441f8008815615495f0d2fc66ef --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m-intel-2015a.eb @@ -0,0 +1,24 @@ +name = 'OpenSSL' +version = '1.0.1m' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = [ + 'OpenSSL-%(version)s_icc-fixes.patch', + 'OpenSSL-%(version)s_fix-parallel.patch', +] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch new file mode 100644 index 0000000000000000000000000000000000000000..e30b04902bb9bf04bfe1075f5b7240ba5a4fe7ad --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_fix-parallel.patch @@ -0,0 +1,343 @@ +Fixes build with make -jx, where x is greater than 1 +based on patch for 1.0.1e by Armin K. +diff -ru openssl-1.0.1m.orig/crypto/Makefile openssl-1.0.1m/crypto/Makefile +--- openssl-1.0.1m.orig/crypto/Makefile 2015-03-19 14:38:24.000000000 +0100 ++++ openssl-1.0.1m/crypto/Makefile 2015-03-31 12:14:56.071786835 +0200 +@@ -85,11 +85,11 @@ + @if [ -z "$(THIS)" ]; then $(MAKE) -f $(TOP)/Makefile reflect THIS=$@; fi + + subdirs: +- @target=all; $(RECURSIVE_MAKE) ++ +@target=all; $(RECURSIVE_MAKE) + + files: + $(PERL) $(TOP)/util/files.pl Makefile >> $(TOP)/MINFO +- @target=files; $(RECURSIVE_MAKE) ++ +@target=files; $(RECURSIVE_MAKE) + + links: + @$(PERL) $(TOP)/util/mklink.pl ../include/openssl $(EXHEADER) +@@ -100,7 +100,7 @@ + # lib: $(LIB): are splitted to avoid end-less loop + lib: $(LIB) + @touch lib +-$(LIB): $(LIBOBJ) ++$(LIB): $(LIBOBJ) | subdirs + $(AR) $(LIB) $(LIBOBJ) + [ -z "$(FIPSLIBDIR)" ] || $(AR) $(LIB) $(FIPSLIBDIR)fipscanister.o + $(RANLIB) $(LIB) || echo Never mind. +@@ -111,7 +111,7 @@ + fi + + libs: +- @target=lib; $(RECURSIVE_MAKE) ++ +@target=lib; $(RECURSIVE_MAKE) + + install: + @[ -n "$(INSTALLTOP)" ] # should be set by top Makefile... +@@ -120,7 +120,7 @@ + (cp $$i $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i; \ + chmod 644 $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i ); \ + done; +- @target=install; $(RECURSIVE_MAKE) ++ +@target=install; $(RECURSIVE_MAKE) + + lint: + @target=lint; $(RECURSIVE_MAKE) +diff -ru openssl-1.0.1m.orig/engines/Makefile openssl-1.0.1m/engines/Makefile +--- openssl-1.0.1m.orig/engines/Makefile 2015-03-19 14:38:35.000000000 +0100 ++++ openssl-1.0.1m/engines/Makefile 2015-03-31 12:14:56.071786835 +0200 +@@ -72,7 +72,7 @@ + + all: lib subdirs + +-lib: $(LIBOBJ) ++lib: $(LIBOBJ) | subdirs + @if [ -n "$(SHARED_LIBS)" ]; then \ + set -e; \ + for l in $(LIBNAMES); do \ +@@ -89,7 +89,7 @@ + + subdirs: + echo $(EDIRS) +- @target=all; $(RECURSIVE_MAKE) ++ +@target=all; $(RECURSIVE_MAKE) + + files: + $(PERL) $(TOP)/util/files.pl Makefile >> $(TOP)/MINFO +@@ -128,7 +128,7 @@ + mv -f $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR)/engines/$$pfx$$l$$sfx.new $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR)/engines/$$pfx$$l$$sfx ); \ + done; \ + fi +- @target=install; $(RECURSIVE_MAKE) ++ +@target=install; $(RECURSIVE_MAKE) + + tags: + ctags $(SRC) +diff -ru openssl-1.0.1m.orig/Makefile.org openssl-1.0.1m/Makefile.org +--- openssl-1.0.1m.orig/Makefile.org 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/Makefile.org 2015-03-31 12:14:56.071786835 +0200 +@@ -273,17 +273,17 @@ + build_libs: build_crypto build_ssl build_engines + + build_crypto: +- @dir=crypto; target=all; $(BUILD_ONE_CMD) +-build_ssl: +- @dir=ssl; target=all; $(BUILD_ONE_CMD) +-build_engines: +- @dir=engines; target=all; $(BUILD_ONE_CMD) +-build_apps: +- @dir=apps; target=all; $(BUILD_ONE_CMD) +-build_tests: +- @dir=test; target=all; $(BUILD_ONE_CMD) +-build_tools: +- @dir=tools; target=all; $(BUILD_ONE_CMD) ++ +@dir=crypto; target=all; $(BUILD_ONE_CMD) ++build_ssl: build_crypto ++ +@dir=ssl; target=all; $(BUILD_ONE_CMD) ++build_engines: build_crypto ++ +@dir=engines; target=all; $(BUILD_ONE_CMD) ++build_apps: build_libs ++ +@dir=apps; target=all; $(BUILD_ONE_CMD) ++build_tests: build_libs ++ +@dir=test; target=all; $(BUILD_ONE_CMD) ++build_tools: build_libs ++ +@dir=tools; target=all; $(BUILD_ONE_CMD) + + all_testapps: build_libs build_testapps + build_testapps: +@@ -538,9 +538,9 @@ + dist_pem_h: + (cd crypto/pem; $(MAKE) -e $(BUILDENV) pem.h; $(MAKE) clean) + +-install: all install_docs install_sw ++install: install_docs install_sw + +-install_sw: ++install_dirs: + @$(PERL) $(TOP)/util/mkdir-p.pl $(INSTALL_PREFIX)$(INSTALLTOP)/bin \ + $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR) \ + $(INSTALL_PREFIX)$(INSTALLTOP)/$(LIBDIR)/engines \ +@@ -549,12 +549,19 @@ + $(INSTALL_PREFIX)$(OPENSSLDIR)/misc \ + $(INSTALL_PREFIX)$(OPENSSLDIR)/certs \ + $(INSTALL_PREFIX)$(OPENSSLDIR)/private ++ @$(PERL) $(TOP)/util/mkdir-p.pl \ ++ $(INSTALL_PREFIX)$(MANDIR)/man1 \ ++ $(INSTALL_PREFIX)$(MANDIR)/man3 \ ++ $(INSTALL_PREFIX)$(MANDIR)/man5 \ ++ $(INSTALL_PREFIX)$(MANDIR)/man7 ++ ++install_sw: install_dirs + @set -e; headerlist="$(EXHEADER)"; for i in $$headerlist;\ + do \ + (cp $$i $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i; \ + chmod 644 $(INSTALL_PREFIX)$(INSTALLTOP)/include/openssl/$$i ); \ + done; +- @set -e; target=install; $(RECURSIVE_BUILD_CMD) ++ +@set -e; target=install; $(RECURSIVE_BUILD_CMD) + @set -e; liblist="$(LIBS)"; for i in $$liblist ;\ + do \ + if [ -f "$$i" ]; then \ +@@ -634,12 +641,7 @@ + done; \ + done + +-install_docs: +- @$(PERL) $(TOP)/util/mkdir-p.pl \ +- $(INSTALL_PREFIX)$(MANDIR)/man1 \ +- $(INSTALL_PREFIX)$(MANDIR)/man3 \ +- $(INSTALL_PREFIX)$(MANDIR)/man5 \ +- $(INSTALL_PREFIX)$(MANDIR)/man7 ++install_docs: install_dirs + @pod2man="`cd ./util; ./pod2mantest $(PERL)`"; \ + here="`pwd`"; \ + filecase=; \ +diff -ru openssl-1.0.1m.orig/Makefile.shared openssl-1.0.1m/Makefile.shared +--- openssl-1.0.1m.orig/Makefile.shared 2015-01-20 13:33:36.000000000 +0100 ++++ openssl-1.0.1m/Makefile.shared 2015-03-31 12:14:56.071786835 +0200 +@@ -105,6 +105,7 @@ + SHAREDFLAGS="$${SHAREDFLAGS:-$(CFLAGS) $(SHARED_LDFLAGS)}"; \ + LIBPATH=`for x in $$LIBDEPS; do echo $$x; done | sed -e 's/^ *-L//;t' -e d | uniq`; \ + LIBPATH=`echo $$LIBPATH | sed -e 's/ /:/g'`; \ ++ [ -e $$SHLIB$$SHLIB_SOVER$$SHLIB_SUFFIX ] && exit 0; \ + LD_LIBRARY_PATH=$$LIBPATH:$$LD_LIBRARY_PATH \ + $${SHAREDCMD} $${SHAREDFLAGS} \ + -o $$SHLIB$$SHLIB_SOVER$$SHLIB_SUFFIX \ +@@ -122,6 +123,7 @@ + done; \ + fi; \ + if [ -n "$$SHLIB_SOVER" ]; then \ ++ [ -e "$$SHLIB$$SHLIB_SUFFIX" ] || \ + ( $(SET_X); rm -f $$SHLIB$$SHLIB_SUFFIX; \ + ln -s $$prev $$SHLIB$$SHLIB_SUFFIX ); \ + fi; \ +diff -ru openssl-1.0.1m.orig/test/Makefile openssl-1.0.1m/test/Makefile +--- openssl-1.0.1m.orig/test/Makefile 2015-03-19 14:38:37.000000000 +0100 ++++ openssl-1.0.1m/test/Makefile 2015-03-31 12:16:53.684158416 +0200 +@@ -130,7 +130,7 @@ + tags: + ctags $(SRC) + +-tests: exe apps $(TESTS) ++tests: exe $(TESTS) + + apps: + @(cd ..; $(MAKE) DIRS=apps all) +@@ -388,118 +388,118 @@ + link_app.$${shlib_target} + + $(RSATEST)$(EXE_EXT): $(RSATEST).o $(DLIBCRYPTO) +- @target=$(RSATEST); $(BUILD_CMD) ++ +@target=$(RSATEST); $(BUILD_CMD) + + $(BNTEST)$(EXE_EXT): $(BNTEST).o $(DLIBCRYPTO) +- @target=$(BNTEST); $(BUILD_CMD) ++ +@target=$(BNTEST); $(BUILD_CMD) + + $(ECTEST)$(EXE_EXT): $(ECTEST).o $(DLIBCRYPTO) +- @target=$(ECTEST); $(BUILD_CMD) ++ +@target=$(ECTEST); $(BUILD_CMD) + + $(EXPTEST)$(EXE_EXT): $(EXPTEST).o $(DLIBCRYPTO) +- @target=$(EXPTEST); $(BUILD_CMD) ++ +@target=$(EXPTEST); $(BUILD_CMD) + + $(IDEATEST)$(EXE_EXT): $(IDEATEST).o $(DLIBCRYPTO) +- @target=$(IDEATEST); $(BUILD_CMD) ++ +@target=$(IDEATEST); $(BUILD_CMD) + + $(MD2TEST)$(EXE_EXT): $(MD2TEST).o $(DLIBCRYPTO) +- @target=$(MD2TEST); $(BUILD_CMD) ++ +@target=$(MD2TEST); $(BUILD_CMD) + + $(SHATEST)$(EXE_EXT): $(SHATEST).o $(DLIBCRYPTO) +- @target=$(SHATEST); $(BUILD_CMD) ++ +@target=$(SHATEST); $(BUILD_CMD) + + $(SHA1TEST)$(EXE_EXT): $(SHA1TEST).o $(DLIBCRYPTO) +- @target=$(SHA1TEST); $(BUILD_CMD) ++ +@target=$(SHA1TEST); $(BUILD_CMD) + + $(SHA256TEST)$(EXE_EXT): $(SHA256TEST).o $(DLIBCRYPTO) +- @target=$(SHA256TEST); $(BUILD_CMD) ++ +@target=$(SHA256TEST); $(BUILD_CMD) + + $(SHA512TEST)$(EXE_EXT): $(SHA512TEST).o $(DLIBCRYPTO) +- @target=$(SHA512TEST); $(BUILD_CMD) ++ +@target=$(SHA512TEST); $(BUILD_CMD) + + $(RMDTEST)$(EXE_EXT): $(RMDTEST).o $(DLIBCRYPTO) +- @target=$(RMDTEST); $(BUILD_CMD) ++ +@target=$(RMDTEST); $(BUILD_CMD) + + $(MDC2TEST)$(EXE_EXT): $(MDC2TEST).o $(DLIBCRYPTO) +- @target=$(MDC2TEST); $(BUILD_CMD) ++ +@target=$(MDC2TEST); $(BUILD_CMD) + + $(MD4TEST)$(EXE_EXT): $(MD4TEST).o $(DLIBCRYPTO) +- @target=$(MD4TEST); $(BUILD_CMD) ++ +@target=$(MD4TEST); $(BUILD_CMD) + + $(MD5TEST)$(EXE_EXT): $(MD5TEST).o $(DLIBCRYPTO) +- @target=$(MD5TEST); $(BUILD_CMD) ++ +@target=$(MD5TEST); $(BUILD_CMD) + + $(HMACTEST)$(EXE_EXT): $(HMACTEST).o $(DLIBCRYPTO) +- @target=$(HMACTEST); $(BUILD_CMD) ++ +@target=$(HMACTEST); $(BUILD_CMD) + + $(WPTEST)$(EXE_EXT): $(WPTEST).o $(DLIBCRYPTO) +- @target=$(WPTEST); $(BUILD_CMD) ++ +@target=$(WPTEST); $(BUILD_CMD) + + $(RC2TEST)$(EXE_EXT): $(RC2TEST).o $(DLIBCRYPTO) +- @target=$(RC2TEST); $(BUILD_CMD) ++ +@target=$(RC2TEST); $(BUILD_CMD) + + $(BFTEST)$(EXE_EXT): $(BFTEST).o $(DLIBCRYPTO) +- @target=$(BFTEST); $(BUILD_CMD) ++ +@target=$(BFTEST); $(BUILD_CMD) + + $(CASTTEST)$(EXE_EXT): $(CASTTEST).o $(DLIBCRYPTO) +- @target=$(CASTTEST); $(BUILD_CMD) ++ +@target=$(CASTTEST); $(BUILD_CMD) + + $(RC4TEST)$(EXE_EXT): $(RC4TEST).o $(DLIBCRYPTO) +- @target=$(RC4TEST); $(BUILD_CMD) ++ +@target=$(RC4TEST); $(BUILD_CMD) + + $(RC5TEST)$(EXE_EXT): $(RC5TEST).o $(DLIBCRYPTO) +- @target=$(RC5TEST); $(BUILD_CMD) ++ +@target=$(RC5TEST); $(BUILD_CMD) + + $(DESTEST)$(EXE_EXT): $(DESTEST).o $(DLIBCRYPTO) +- @target=$(DESTEST); $(BUILD_CMD) ++ +@target=$(DESTEST); $(BUILD_CMD) + + $(RANDTEST)$(EXE_EXT): $(RANDTEST).o $(DLIBCRYPTO) +- @target=$(RANDTEST); $(BUILD_CMD) ++ +@target=$(RANDTEST); $(BUILD_CMD) + + $(DHTEST)$(EXE_EXT): $(DHTEST).o $(DLIBCRYPTO) +- @target=$(DHTEST); $(BUILD_CMD) ++ +@target=$(DHTEST); $(BUILD_CMD) + + $(DSATEST)$(EXE_EXT): $(DSATEST).o $(DLIBCRYPTO) +- @target=$(DSATEST); $(BUILD_CMD) ++ +@target=$(DSATEST); $(BUILD_CMD) + + $(METHTEST)$(EXE_EXT): $(METHTEST).o $(DLIBCRYPTO) +- @target=$(METHTEST); $(BUILD_CMD) ++ +@target=$(METHTEST); $(BUILD_CMD) + + $(SSLTEST)$(EXE_EXT): $(SSLTEST).o $(DLIBSSL) $(DLIBCRYPTO) +- @target=$(SSLTEST); $(FIPS_BUILD_CMD) ++ +@target=$(SSLTEST); $(FIPS_BUILD_CMD) + + $(ENGINETEST)$(EXE_EXT): $(ENGINETEST).o $(DLIBCRYPTO) +- @target=$(ENGINETEST); $(BUILD_CMD) ++ +@target=$(ENGINETEST); $(BUILD_CMD) + + $(EVPTEST)$(EXE_EXT): $(EVPTEST).o $(DLIBCRYPTO) +- @target=$(EVPTEST); $(BUILD_CMD) ++ +@target=$(EVPTEST); $(BUILD_CMD) + + $(EVPEXTRATEST)$(EXE_EXT): $(EVPEXTRATEST).o $(DLIBCRYPTO) +- @target=$(EVPEXTRATEST); $(BUILD_CMD) ++ +@target=$(EVPEXTRATEST); $(BUILD_CMD) + + $(ECDSATEST)$(EXE_EXT): $(ECDSATEST).o $(DLIBCRYPTO) +- @target=$(ECDSATEST); $(BUILD_CMD) ++ +@target=$(ECDSATEST); $(BUILD_CMD) + + $(ECDHTEST)$(EXE_EXT): $(ECDHTEST).o $(DLIBCRYPTO) +- @target=$(ECDHTEST); $(BUILD_CMD) ++ +@target=$(ECDHTEST); $(BUILD_CMD) + + $(IGETEST)$(EXE_EXT): $(IGETEST).o $(DLIBCRYPTO) +- @target=$(IGETEST); $(BUILD_CMD) ++ +@target=$(IGETEST); $(BUILD_CMD) + + $(JPAKETEST)$(EXE_EXT): $(JPAKETEST).o $(DLIBCRYPTO) +- @target=$(JPAKETEST); $(BUILD_CMD) ++ +@target=$(JPAKETEST); $(BUILD_CMD) + + $(ASN1TEST)$(EXE_EXT): $(ASN1TEST).o $(DLIBCRYPTO) +- @target=$(ASN1TEST); $(BUILD_CMD) ++ +@target=$(ASN1TEST); $(BUILD_CMD) + + $(SRPTEST)$(EXE_EXT): $(SRPTEST).o $(DLIBCRYPTO) +- @target=$(SRPTEST); $(BUILD_CMD) ++ +@target=$(SRPTEST); $(BUILD_CMD) + + $(HEARTBEATTEST)$(EXE_EXT): $(HEARTBEATTEST).o $(DLIBCRYPTO) +- @target=$(HEARTBEATTEST); $(BUILD_CMD_STATIC) ++ +@target=$(HEARTBEATTEST); $(BUILD_CMD_STATIC) + + $(CONSTTIMETEST)$(EXE_EXT): $(CONSTTIMETEST).o +- @target=$(CONSTTIMETEST) $(BUILD_CMD) ++ +@target=$(CONSTTIMETEST) $(BUILD_CMD) + + #$(AESTEST).o: $(AESTEST).c + # $(CC) -c $(CFLAGS) -DINTERMEDIATE_VALUE_KAT -DTRACE_KAT_MCT $(AESTEST).c diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch new file mode 100644 index 0000000000000000000000000000000000000000..16ab3306c72caf99ae179ed6ce2eb62465018c62 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1m_icc-fixes.patch @@ -0,0 +1,116 @@ +based on http://openssl.6102.n7.nabble.com/Compiling-OpenSSL-with-icc-td42304.html (http://cvs.openssl.org/chngview?cn=23036) +diff -ru openssl-1.0.1m.orig/Configure openssl-1.0.1m/Configure +--- openssl-1.0.1m.orig/Configure 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/Configure 2015-03-31 12:50:44.965133568 +0200 +@@ -351,7 +351,7 @@ + # If you compiler does not, do complement config command line with one! + "linux-armv4", "gcc:-O3 -Wall::-D_REENTRANT::-ldl:BN_LLONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL BF_PTR:${armv4_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + #### IA-32 targets... +-"linux-ia32-icc", "icc:-DL_ENDIAN -O2 -no_cpprt::-D_REENTRANT::-ldl:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-KPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", ++"linux-ia32-icc", "icc:-DL_ENDIAN -O2::-D_REENTRANT::-ldl -no_cpprt:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-KPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-elf", "gcc:-DL_ENDIAN -O3 -fomit-frame-pointer -Wall::-D_REENTRANT::-ldl:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-aout", "gcc:-DL_ENDIAN -O3 -fomit-frame-pointer -march=i486 -Wall::(unknown):::BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_asm}:a.out", + #### +@@ -359,8 +359,9 @@ + "linux-ppc64", "gcc:-m64 -DB_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_RISC1 DES_UNROLL:${ppc64_asm}:linux64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + "linux-ia64", "gcc:-DL_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_UNROLL DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-ia64-ecc","ecc:-DL_ENDIAN -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", +-"linux-ia64-icc","icc:-DL_ENDIAN -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", ++"linux-ia64-icc","icc:-DL_ENDIAN -O2 -Wall::-D_REENTRANT::-ldl -no_cpprt:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-x86_64", "gcc:-m64 -DL_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT DES_UNROLL:${x86_64_asm}:elf:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", ++"linux-x86_64-icc", "icc:-DL_ENDIAN -DTERMIO -O2::-D_REENTRANT::-ldl -no_cpprt:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT DES_UNROLL:${x86_64_asm}:elf:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + "linux64-s390x", "gcc:-m64 -DB_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL:${s390x_asm}:64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + #### So called "highgprs" target for z/Architecture CPUs + # "Highgprs" is kernel feature first implemented in Linux 2.6.32, see +@@ -1416,6 +1417,7 @@ + } + if ($iccver>=8) + { ++ $cflags=~s/\-KPIC/-fPIC/; + # Eliminate unnecessary dependency from libirc.a. This is + # essential for shared library support, as otherwise + # apps/openssl can end up in endless loop upon startup... +@@ -1423,13 +1425,18 @@ + } + if ($iccver>=9) + { +- $cflags.=" -i-static"; +- $cflags=~s/\-no_cpprt/-no-cpprt/; ++ $lflags.=" -i-static"; ++ $lflags=~s/\-no_cpprt/-no-cpprt/; + } + if ($iccver>=10) + { +- $cflags=~s/\-i\-static/-static-intel/; ++ $lflags=~s/\-i\-static/-static-intel/; + } ++ if ($iccver>=11) ++ { ++ $cflags.=" -no-intel-extensions"; # disable Cilk ++ $lflags=~s/\-no\-cpprt/-no-cxxlib/; ++ } + } + + # Unlike other OSes (like Solaris, Linux, Tru64, IRIX) BSD run-time +diff -ru openssl-1.0.1m.orig/crypto/aes/aes_x86core.c openssl-1.0.1m/crypto/aes/aes_x86core.c +--- openssl-1.0.1m.orig/crypto/aes/aes_x86core.c 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/aes/aes_x86core.c 2015-03-31 12:28:27.768182812 +0200 +@@ -89,8 +89,10 @@ + #endif + + #undef ROTATE +-#if defined(_MSC_VER) || defined(__ICC) ++#if defined(_MSC_VER) + # define ROTATE(a,n) _lrotl(a,n) ++#elif defined(__ICC) ++# define ROTATE(a,n) _rotl(a,n) + #elif defined(__GNUC__) && __GNUC__>=2 + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE(a,n) ({ register unsigned int ret; \ +diff -ru openssl-1.0.1m.orig/crypto/des/des_locl.h openssl-1.0.1m/crypto/des/des_locl.h +--- openssl-1.0.1m.orig/crypto/des/des_locl.h 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/des/des_locl.h 2015-03-31 12:52:29.287245531 +0200 +@@ -162,8 +162,10 @@ + } \ + } + +-# if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) || defined(__ICC) ++# if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) + # define ROTATE(a,n) (_lrotr(a,n)) ++#elif defined(__ICC) ++#define ROTATE(a,n) (_rotr(a,n)) + # elif defined(__GNUC__) && __GNUC__>=2 && !defined(__STRICT_ANSI__) && !defined(OPENSSL_NO_ASM) && !defined(OPENSSL_NO_INLINE_ASM) && !defined(PEDANTIC) + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE(a,n) ({ register unsigned int ret; \ +diff -ru openssl-1.0.1m.orig/crypto/md32_common.h openssl-1.0.1m/crypto/md32_common.h +--- openssl-1.0.1m.orig/crypto/md32_common.h 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/md32_common.h 2015-03-31 12:53:03.737932332 +0200 +@@ -142,8 +142,10 @@ + */ + #undef ROTATE + #ifndef PEDANTIC +-# if defined(_MSC_VER) || defined(__ICC) ++# if defined(_MSC_VER) + # define ROTATE(a,n) _lrotl(a,n) ++# elif defined(__ICC) ++# define ROTATE(a,n) _rotl(a,n) + # elif defined(__MWERKS__) + # if defined(__POWERPC__) + # define ROTATE(a,n) __rlwinm(a,n,0,31) +diff -ru openssl-1.0.1m.orig/crypto/rc5/rc5_locl.h openssl-1.0.1m/crypto/rc5/rc5_locl.h +--- openssl-1.0.1m.orig/crypto/rc5/rc5_locl.h 2015-03-19 14:37:10.000000000 +0100 ++++ openssl-1.0.1m/crypto/rc5/rc5_locl.h 2015-03-31 12:51:52.976509433 +0200 +@@ -146,9 +146,12 @@ + *((c)++)=(unsigned char)(((l)>> 8L)&0xff), \ + *((c)++)=(unsigned char)(((l) )&0xff)) + +-#if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) || defined(__ICC) ++#if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) + # define ROTATE_l32(a,n) _lrotl(a,n) + # define ROTATE_r32(a,n) _lrotr(a,n) ++#elif defined(__ICC) ++#define ROTATE_l32(a,n) _rotl(a,n) ++#define ROTATE_r32(a,n) _rotr(a,n) + #elif defined(__GNUC__) && __GNUC__>=2 && !defined(__STRICT_ANSI__) && !defined(OPENSSL_NO_ASM) && !defined(OPENSSL_NO_INLINE_ASM) && !defined(PEDANTIC) + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE_l32(a,n) ({ register unsigned int ret; \ diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6800732437215cd1ea418f5f5ad0b87c94b3f865 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-foss-2015a.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.1p' + +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': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = ['OpenSSL-%(version)s_icc-fixes.patch'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..733ddd9ac4e3328e8a6d9fe7229406ccadb08ad2 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-goolf-1.7.20.eb @@ -0,0 +1,19 @@ +name = 'OpenSSL' +version = '1.0.1p' + +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': 'goolf', 'version': '1.7.20'} +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-1.0.1p-intel-2015a.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..9e06d07cee82de9d2b8e5cffdd472f7488a2f4e8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p-intel-2015a.eb @@ -0,0 +1,21 @@ +name = 'OpenSSL' +version = '1.0.1p' + +homepage = 'http://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://www.openssl.org/source/'] + +patches = ['OpenSSL-%(version)s_icc-fixes.patch'] + +dependencies = [('zlib', '1.2.8')] + +runtest = 'test' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p_icc-fixes.patch b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p_icc-fixes.patch new file mode 100644 index 0000000000000000000000000000000000000000..4609252d6d2b23d2c3e8e54a0f245a4c049e5768 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.0.1p_icc-fixes.patch @@ -0,0 +1,100 @@ +diff -ru openssl-1.0.1p.orig/Configure openssl-1.0.1p/Configure +--- openssl-1.0.1p.orig/Configure 2015-07-09 14:21:24.000000000 +0200 ++++ openssl-1.0.1p/Configure 2015-07-11 14:02:52.000000000 +0200 +@@ -351,7 +351,7 @@ + # If you compiler does not, do complement config command line with one! + "linux-armv4", "gcc:-O3 -Wall::-D_REENTRANT::-ldl:BN_LLONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL BF_PTR:${armv4_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + #### IA-32 targets... +-"linux-ia32-icc", "icc:-DL_ENDIAN -O2 -no_cpprt::-D_REENTRANT::-ldl:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-KPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", ++"linux-ia32-icc", "icc:-DL_ENDIAN -O2::-D_REENTRANT::-ldl -no_cpprt:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-KPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-elf", "gcc:-DL_ENDIAN -O3 -fomit-frame-pointer -Wall::-D_REENTRANT::-ldl:BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_elf_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-aout", "gcc:-DL_ENDIAN -O3 -fomit-frame-pointer -march=i486 -Wall::(unknown):::BN_LLONG ${x86_gcc_des} ${x86_gcc_opts}:${x86_asm}:a.out", + #### +@@ -359,8 +359,9 @@ + "linux-ppc64", "gcc:-m64 -DB_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_RISC1 DES_UNROLL:${ppc64_asm}:linux64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + "linux-ia64", "gcc:-DL_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_UNROLL DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-ia64-ecc","ecc:-DL_ENDIAN -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", +-"linux-ia64-icc","icc:-DL_ENDIAN -O2 -Wall -no_cpprt::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", ++"linux-ia64-icc","icc:-DL_ENDIAN -O2 -Wall::-D_REENTRANT::-ldl -no_cpprt:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_RISC1 DES_INT:${ia64_asm}:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR)", + "linux-x86_64", "gcc:-m64 -DL_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT DES_UNROLL:${x86_64_asm}:elf:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", ++"linux-x86_64-icc", "icc:-DL_ENDIAN -DTERMIO -O2::-D_REENTRANT::-ldl -no_cpprt:SIXTY_FOUR_BIT_LONG RC4_CHUNK DES_INT DES_UNROLL:${x86_64_asm}:elf:dlfcn:linux-shared:-fPIC::.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + "linux64-s390x", "gcc:-m64 -DB_ENDIAN -O3 -Wall::-D_REENTRANT::-ldl:SIXTY_FOUR_BIT_LONG RC4_CHAR RC4_CHUNK DES_INT DES_UNROLL:${s390x_asm}:64:dlfcn:linux-shared:-fPIC:-m64:.so.\$(SHLIB_MAJOR).\$(SHLIB_MINOR):::64", + #### So called "highgprs" target for z/Architecture CPUs + # "Highgprs" is kernel feature first implemented in Linux 2.6.32, see +@@ -1416,6 +1417,7 @@ + } + if ($iccver>=8) + { ++ $cflags=~s/\-KPIC/-fPIC/; + # Eliminate unnecessary dependency from libirc.a. This is + # essential for shared library support, as otherwise + # apps/openssl can end up in endless loop upon startup... +@@ -1423,13 +1425,18 @@ + } + if ($iccver>=9) + { +- $cflags.=" -i-static"; +- $cflags=~s/\-no_cpprt/-no-cpprt/; ++ $lflags.=" -i-static"; ++ $lflags=~s/\-no_cpprt/-no-cpprt/; + } + if ($iccver>=10) + { +- $cflags=~s/\-i\-static/-static-intel/; ++ $lflags=~s/\-i\-static/-static-intel/; + } ++ if ($iccver>=11) ++ { ++ $cflags.=" -no-intel-extensions"; # disable Cilk ++ $lflags=~s/\-no\-cpprt/-no-cxxlib/; ++ } + } + + # Unlike other OSes (like Solaris, Linux, Tru64, IRIX) BSD run-time +diff -ru openssl-1.0.1p.orig/crypto/aes/aes_x86core.c openssl-1.0.1p/crypto/aes/aes_x86core.c +--- openssl-1.0.1p.orig/crypto/aes/aes_x86core.c 2015-07-09 14:21:24.000000000 +0200 ++++ openssl-1.0.1p/crypto/aes/aes_x86core.c 2015-07-11 14:02:52.000000000 +0200 +@@ -89,8 +89,10 @@ + #endif + + #undef ROTATE +-#if defined(_MSC_VER) || defined(__ICC) ++#if defined(_MSC_VER) + # define ROTATE(a,n) _lrotl(a,n) ++#elif defined(__ICC) ++# define ROTATE(a,n) _rotl(a,n) + #elif defined(__GNUC__) && __GNUC__>=2 + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE(a,n) ({ register unsigned int ret; \ +diff -ru openssl-1.0.1p.orig/crypto/des/des_locl.h openssl-1.0.1p/crypto/des/des_locl.h +--- openssl-1.0.1p.orig/crypto/des/des_locl.h 2015-07-09 14:21:24.000000000 +0200 ++++ openssl-1.0.1p/crypto/des/des_locl.h 2015-07-11 14:02:52.000000000 +0200 +@@ -162,8 +162,10 @@ + } \ + } + +-# if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) || defined(__ICC) ++# if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) + # define ROTATE(a,n) (_lrotr(a,n)) ++#elif defined(__ICC) ++#define ROTATE(a,n) (_rotr(a,n)) + # elif defined(__GNUC__) && __GNUC__>=2 && !defined(__STRICT_ANSI__) && !defined(OPENSSL_NO_ASM) && !defined(OPENSSL_NO_INLINE_ASM) && !defined(PEDANTIC) + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE(a,n) ({ register unsigned int ret; \ +diff -ru openssl-1.0.1p.orig/crypto/rc5/rc5_locl.h openssl-1.0.1p/crypto/rc5/rc5_locl.h +--- openssl-1.0.1p.orig/crypto/rc5/rc5_locl.h 2015-07-09 14:21:24.000000000 +0200 ++++ openssl-1.0.1p/crypto/rc5/rc5_locl.h 2015-07-11 14:02:52.000000000 +0200 +@@ -146,9 +146,12 @@ + *((c)++)=(unsigned char)(((l)>> 8L)&0xff), \ + *((c)++)=(unsigned char)(((l) )&0xff)) + +-#if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) || defined(__ICC) ++#if (defined(OPENSSL_SYS_WIN32) && defined(_MSC_VER)) + # define ROTATE_l32(a,n) _lrotl(a,n) + # define ROTATE_r32(a,n) _lrotr(a,n) ++#elif defined(__ICC) ++#define ROTATE_l32(a,n) _rotl(a,n) ++#define ROTATE_r32(a,n) _rotr(a,n) + #elif defined(__GNUC__) && __GNUC__>=2 && !defined(__STRICT_ANSI__) && !defined(OPENSSL_NO_ASM) && !defined(OPENSSL_NO_INLINE_ASM) && !defined(PEDANTIC) + # if defined(__i386) || defined(__i386__) || defined(__x86_64) || defined(__x86_64__) + # define ROTATE_l32(a,n) ({ register unsigned int ret; \ diff --git a/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..a404ae249a69ff7ba31a7938932183dd587671a8 --- /dev/null +++ b/easybuild/easyconfigs/o/ordereddict/ordereddict-1.1-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,24 @@ +easyblock = "PythonPackage" + +name = 'ordereddict' +version = '1.1' + +homepage = 'https://pypi.python.org/pypi/ordereddict' +description = """Drop-in substitute for Py2.7's new collections.OrderedDict. +The recipe has big-oh performance that matches regular dictionaries (amortized +O(1) insertion/deletion/lookup and O(n) iteration/repr/copy/equality_testing).""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://pypi.python.org/packages/source/o/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.3' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..d485c2eb5712568c2707c76737dbc0facb1fd307 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.2.0-goolf-1.5.14.eb @@ -0,0 +1,46 @@ +## +# 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_07-02.html +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '5.2.0' + +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': 'goolf', 'version': '1.5.14'} + +# 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/PAPI/PAPI-5.4.0-foss-2015a.eb b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..cbf18980bca4811f0997088527ee305a5621c3db --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-5.4.0-foss-2015a.eb @@ -0,0 +1,45 @@ +## +# 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 = '5.4.0' + +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'} + +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/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb index e95902eec830e5311c8f31fc5cc59e80c3a0f24f..4a9ef5925f14b7d11c1ca601fddf4ecf13978508 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goalf-1.1.0-no-OFED.eb @@ -4,15 +4,15 @@ name = 'PCRE' version = '8.12' 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.""" +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': 'goalf', 'version': '1.1.0-no-OFED'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb index 0f58883e8e531fb7cd723cde2485caf9a0f2e867..5916d698fc1f9082c2cca5747400d90876155684 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-goolf-1.4.10.eb @@ -4,15 +4,15 @@ name = 'PCRE' version = '8.12' 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.""" +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': 'goolf', 'version': '1.4.10'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb index ae806687ed93f8f1c9a0bea81b4cda0229ebd9a0..e5f29eb85e583a56a26614919094ca460d342bf8 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-4.0.6.eb @@ -4,15 +4,15 @@ name = 'PCRE' version = '8.12' 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.""" +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': 'ictce', 'version': '4.0.6'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb index 0a2a52870426bb96f8de06b8b3f2901c7c58d222..871d373c07e239c49385a39dba53307b5c9a054b 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.3.0.eb @@ -4,16 +4,15 @@ name = 'PCRE' version = '8.12' 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.""" - +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': 'ictce', 'version': '5.3.0'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb index 82e14a704ffdfc1c9618b6f7667328d829bc7717..365ae1e42a966e5feb64cf2d21924e35ca6043e1 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.12-ictce-5.5.0.eb @@ -4,17 +4,15 @@ name = 'PCRE' version = '8.12' 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. -""" +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': 'ictce', 'version': '5.5.0'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = ['http://prdownloads.sourceforge.net/pcre'] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb index fd30422f0b8be97036316c25b84dec07a39d5188..a4df16eaada18086aca6026c399b45256e24c3a2 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.35-intel-2014b.eb @@ -4,17 +4,15 @@ name = 'PCRE' version = '8.35' 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. -""" +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': '2014b'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..7881c04da420044f2a9277d589e959b39d66b53b --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-foss-2015a.eb @@ -0,0 +1,18 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.36' + +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': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +configopts = "--with-pic --disable-cpp" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb index 64ff0ffd54fd326687b25366e944738e980161f7..f2529df084483600e9dc344a55d96031cd95b5c5 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.36-intel-2015a.eb @@ -4,17 +4,15 @@ name = 'PCRE' version = '8.36' 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. -""" +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': '2015a'} toolchainopts = {'optarch': True, 'pic': True} -configopts = "--with-pic --disable-cpp" - source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] +configopts = "--with-pic --disable-cpp" + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb index a6ab7c41555ced86b01c011319965f6a703b0fc6..eef9a27cd74d3ec567c4ae0d2d72a3d9a96e147f 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.19-gompi-1.4.12-no-OFED.eb @@ -1,12 +1,14 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## -easyblock = 'ConfigureMake' name = "PDT" version = "3.19" @@ -20,31 +22,11 @@ description = """Program Database Toolkit (PDT) is a framework for analyzing sou toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} -# http://tau.uoregon.edu/pdt_releases/pdtoolkit-3.19.tar.gz sources = ['pdtoolkit-%(version)s.tar.gz'] source_urls = ['http://tau.uoregon.edu/pdt_releases/'] -prefix_opt = '-prefix=' - -# notes by Bernd Mohr -# Compiler suite should always be specified -- MUCH quicker and SAVER than autodetect -# -KAI|-KCC|-GNU|-CC|-c++|-cxx|-xlC|-pgCC|-icpc|-ecpc -configopts = '-GNU' - -keeppreviousinstall = True - -# notes by Bernd Mohr -# Use hardcoded x86_64 or "import platform; machine = platform.machine()" here? -sanity_check_paths = { - 'files': ["x86_64/bin/cparse", "x86_64/include/pdb.h", "x86_64/lib/libpdb.a"], - 'dirs': [], -} - -skipsteps = ['build'] - -modextrapaths = { - 'PATH': "x86_64/bin", - 'LD_LIBRARY_PATH': "x86_64/lib", -} +checksums = [ + '5c5e1e6607086aa13bf4b1b9befc5864', # pdtoolkit-3.19.tar.gz +] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb index 7faa216ef2db1a4fc8d1759cbca2eeae3c82620a..f50e7519a2ac13354066b88d16058fc84ae3e9e2 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.19-ictce-5.3.0.eb @@ -1,12 +1,14 @@ +## # This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild -# Copyright:: Copyright 2013 Juelich Supercomputing Centre, Germany +# +# Copyright:: Copyright 2013-2015 Juelich Supercomputing Centre, Germany # Authors:: Bernd Mohr -# License:: New BSD +# Markus Geimer +# License:: 3-clause BSD # -# This work is based from experiences from the UNITE project +# This work is based on experiences from the UNITE project # http://apps.fz-juelich.de/unite/ ## -easyblock = 'ConfigureMake' name = "PDT" version = "3.19" @@ -20,31 +22,11 @@ description = """Program Database Toolkit (PDT) is a framework for analyzing sou toolchain = {'name': 'ictce', 'version': '5.3.0'} -# http://tau.uoregon.edu/pdt_releases/pdtoolkit-3.19.tar.gz sources = ['pdtoolkit-%(version)s.tar.gz'] source_urls = ['http://tau.uoregon.edu/pdt_releases/'] -prefix_opt = '-prefix=' - -# notes by Bernd Mohr -# Compiler suite should always be specified -- MUCH quicker and SAVER than autodetect -# -KAI|-KCC|-GNU|-CC|-c++|-cxx|-xlC|-pgCC|-icpc|-ecpc -configopts = '-GNU' - -keeppreviousinstall = True - -# notes by Bernd Mohr -# Use hardcoded x86_64 or "import platform; machine = platform.machine()" here? -sanity_check_paths = { - 'files': ["x86_64/bin/cparse", "x86_64/include/pdb.h", "x86_64/lib/libpdb.a"], - 'dirs': [], -} - -skipsteps = ['build'] - -modextrapaths = { - 'PATH': "x86_64/bin", - 'LD_LIBRARY_PATH': "x86_64/lib", -} +checksums = [ + '5c5e1e6607086aa13bf4b1b9befc5864', # pdtoolkit-3.19.tar.gz +] moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4acb86b02182eb26cf833201e8ae3242291af8a0 --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-foss-2015a.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 = "3.20" + +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': 'foss', 'version': '2015a'} + +sources = ['pdtoolkit-%(version)s.tar.gz'] +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] + +checksums = [ + 'c3edabe202926abe04552e33cd39672d', # pdtoolkit-3.20.tar.gz +] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb b/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..bb1e979e805cd021d8d5d004d8f85da8e6045c3f --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.20-goolf-1.5.14.eb @@ -0,0 +1,48 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Authors:: Jordi Blasco +# License:: New BSD +# +## + +easyblock = 'ConfigureMake' + +name = "PDT" +version = "3.20" + +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'} + +# http://tau.uoregon.edu/pdt_releases/pdtoolkit-3.19.tar.gz +sources = ['pdtoolkit-%(version)s.tar.gz'] +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] + +prefix_opt = '-prefix=' + +# notes by Bernd Mohr +# Compiler suite should always be specified -- MUCH quicker and SAVER than autodetect +# -KAI|-KCC|-GNU|-CC|-c++|-cxx|-xlC|-pgCC|-icpc|-ecpc +configopts = '-GNU' + +keeppreviousinstall = True + +# notes by Bernd Mohr +# Use hardcoded x86_64 or "import platform; machine = platform.machine()" here? +sanity_check_paths = { + 'files': ["x86_64/bin/cparse", "x86_64/include/pdb.h", "x86_64/lib/libpdb.a"], + 'dirs': [], +} + +skipsteps = ['build'] + +modextrapaths = { + 'PATH': "x86_64/bin", + 'LD_LIBRARY_PATH': "x86_64/lib", +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.5.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.5.3-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..4842cf5227d14881f0ab60b5e9a0c397bd50444b --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.5.3-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,32 @@ +name = 'PETSc' +version = '3.5.3' +versionsuffix = '-Python-2.7.9' + +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': '2015a'} +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', '1.57.0', versionsuffix), + ('FIAT', '1.5.0', versionsuffix), + ('METIS', '5.1.0'), + (parmetis, parmetis_ver), + ('ScientificPython', '2.9.4', versionsuffix), + ('SCOTCH', '6.0.4'), + ('SuiteSparse', '4.4.3', '-%s-%s' % (parmetis, parmetis_ver)), + ('Hypre', '2.10.0b'), +] + +builddependencies = [('CMake', '3.2.1')] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb new file mode 100644 index 0000000000000000000000000000000000000000..50bb76fbb335ca5b24752327a4eac513666913cc --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.07-x86_64.eb @@ -0,0 +1,30 @@ +easyblock = 'PackedBinary' + +name = 'PLINK' +version = '1.07-x86_64' + +homepage = 'http://pngu.mgh.harvard.edu/~purcell/plink/' +description = 'plink-1.07-src: Whole-genome association analysis toolset' + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['%(namelower)s-%(version)s.zip'] +source_urls = ['http://pngu.mgh.harvard.edu/~purcell/plink/dist/'] + +checksums = ['fd0bafeda42151b20534e4f97b0d97df'] + +files_to_copy = [ + 'plink', + 'gPLINK.jar', + 'test.map', + 'test.ped', + 'COPYING.txt', + 'README.txt', +] + +sanity_check_paths = { + 'files': ['plink', 'gPLINK.jar', 'test.map', 'test.ped', 'COPYING.txt', 'README.txt'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..b6955fcdccd6e403ab07f71b7d5e4bcc71650a50 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4-ictce-7.1.2.eb @@ -0,0 +1,33 @@ +# by Ward Poelmans + +easyblock = 'ConfigureMake' + +name = 'PLUMED' +version = '2.0.4' + +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': 'ictce', 'version': '7.1.2'} + +source_urls = ['https://github.com/plumed/plumed2/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = ['PLUMED-%(version)s_eb-env-vars.patch'] + +preconfigopts = " ./configure.sh linux.icc && source sourceme.sh # " +preinstallopts = " export PLUMED_PREFIX=%(installdir)s && " + +sanity_check_paths = { + 'files': ['bin/plumed', 'lib/libplumedKernel.so', 'lib/libplumed.so'], + 'dirs': ['lib/plumed'] +} + +modextrapaths = {'PLUMED_KERNEL': 'lib/libplumedKernel.so'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4_eb-env-vars.patch b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4_eb-env-vars.patch new file mode 100644 index 0000000000000000000000000000000000000000..c96081c3a8842949dfb15f4faffcacd2aa40ad27 --- /dev/null +++ b/easybuild/easyconfigs/p/PLUMED/PLUMED-2.0.4_eb-env-vars.patch @@ -0,0 +1,39 @@ +# patch to work around the hideous build system of plumed. We use the values +# EB sets in the build system. +diff -urN plumed-2.0.4.orig/configurations/linux.icc plumed-2.0.4/configurations/linux.icc +--- plumed-2.0.4.orig/configurations/linux.icc 2014-09-15 11:41:47.000000000 +0200 ++++ plumed-2.0.4/configurations/linux.icc 2014-12-01 14:54:42.000000000 +0100 +@@ -2,21 +2,21 @@ + #CHECK_BOUNDARIES=-D_GLIBCXX_DEBUG + +-LIBS=-ldl ++LIBS:=-ldl $(LIBS) +-DYNAMIC_LIBS=-lstdc++ -llapack -lblas ++DYNAMIC_LIBS:=-lstdc++ $(LIBS) $(LIBLAPACK) + DOUBLEPRECISION=-r8 + +-CPPFLAGS=-D__PLUMED_HAS_DLOPEN $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) +-CXXFLAGS=-O -fPIC -Wall -wd981,383,1418 +-CFLAGS=-O -fPIC -Wall ++CPPFLAGS:=-D__PLUMED_HAS_DLOPEN $(CHECK_BOUNDARIES) -I. $(PLUMED_INCLUDE) $(CPPFLAGS) ++CXXFLAGS:=-O -fPIC -Wall -wd981,383,1418 $(CXXFLAGS) ++CFLAGS:=-O -fPIC -Wall $(CFLAGS) + +-LDFLAGS=-rdynamic ++LDFLAGS:=-rdynamic $(LDFLAGS) + SOEXT=so +-LDSO=icc -shared $(CFLAGS) +-LD=icpc +-LDF90=ifort +-CXX=icpc +-CC=icc +-FC=ifort ++LDSO:=$(CC) -shared $(CFLAGS) ++LD:=$(CXX) ++LDF90:=$(F90) ++CXX:=$(CXX) ++CC:=$(CC) ++FC:=$(F77) + + GCCDEP=g++ + diff --git a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb index 061dd6e1103fb5a5224cf5e66dadbcc0082f4f38..849c3d613e2ee8adc8eb6b6fb5198aff52f31936 100644 --- a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-goolf-1.4.10.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/ ## -easyblock = "Toolchain" +easyblock = 'Bundle' name = 'PRACE' version = '20130605' diff --git a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb index 84d13bb360ba1326e92b8a7a117d78f21c129a03..63cc6c8164b31069dd2ff65826d2c34bc6f2fc60 100644 --- a/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/PRACE/PRACE-20130605-ictce-5.3.0.eb @@ -10,7 +10,7 @@ # http://hpcbios.readthedocs.org/en/latest/ ## -easyblock = "Toolchain" +easyblock = 'Bundle' name = 'PRACE' version = '20130605' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..2060e3874c7fc694274a63e808fd851725b2d1ec --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-goolf-1.4.10.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 = '4.8.0' + +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': 'goolf', 'version': '1.4.10'} +toolchainopts = {'opt': True, '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-4.8.0-ictce-5.3.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..427477bf963cc96c4830a83e4901011d9532ffc3 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-4.8.0-ictce-5.3.0.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 = '4.8.0' + +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': 'ictce', 'version': '5.3.0'} +toolchainopts = {'opt': True, '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/Pango/Pango-1.36.7-intel-2014b.eb b/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb index eba092fa74dbff3556a55abdf3f4d868248afbbb..1de69091f3cac89a54a47177dea05eb9ab7473d9 100644 --- a/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Pango/Pango-1.36.7-intel-2014b.eb @@ -22,6 +22,7 @@ dependencies = [ ('GLib', '2.40.0'), ('HarfBuzz', '0.9.35'), ('GObject-Introspection', '1.42.0'), + ('libXft', '2.3.2'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..b35839d741496302dede27af67f3654b2ae8e44e --- /dev/null +++ b/easybuild/easyconfigs/p/Parallel-ForkManager/Parallel-ForkManager-1.06-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli +# License:: MIT/GPL +# +## + +easyblock = 'PerlModule' + +name = 'Parallel-ForkManager' +version = '1.06' + +homepage = 'http://search.cpan.org/~szabgab/Parallel-ForkManager-1.06/lib/Parallel/ForkManager.pm' +description = """A simple parallel processing fork manager""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://search.cpan.org/CPAN/authors/id/S/SZ/SZABGAB/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver) +] + +options = {'modulename': 'Parallel::ForkManager'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/Paraview/Paraview-4.1.0-intel-2014b.eb b/easybuild/easyconfigs/p/Paraview/Paraview-4.1.0-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..2f704c2b24fe560c93bd75fa5c066e894dbea016 --- /dev/null +++ b/easybuild/easyconfigs/p/Paraview/Paraview-4.1.0-intel-2014b.eb @@ -0,0 +1,22 @@ +easyblock = 'CMakeMake' + +name = 'Paraview' +version = '4.1.0' + +homepage = "http://www.paraview.org" +description = "Paraview is a scientific parallel visualizer" + +toolchain = {'name': 'intel', 'version': '2014b'} +toolchainopts = {'usempi': False, 'pic': True} + +download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['http://www.paraview.org/paraview-downloads/%s' % download_suffix] +sources = ["ParaView-v%(version)s-source.tar.gz"] + +dependencies = [('Qt','4.8.6')] + +builddependencies = [('CMake', '3.0.0')] + +separate_build_dir = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb b/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..0a7acf4ed3d0cf069e0cea33394e1c39e2537bfc --- /dev/null +++ b/easybuild/easyconfigs/p/PeakSeq/PeakSeq-1.3-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 +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = "PeakSeq" +version = "1.3" + +homepage = 'http://info.gersteinlab.org/PeakSeq' +description = """ PeakSeq is a program for identifying and ranking peak regions in ChIP-Seq + experiments. It takes as input, mapped reads from a ChIP-Seq experiment, mapped reads from + a control experiment and outputs a file with peak regions ranked with increasing Q-values.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://archive.gersteinlab.org/proj/PeakSeq/Scoring_ChIPSeq/Code/C/'] +sources = ['%(name)s.zip'] + +# as the tarball doesn't contain the version we verify the checksum to be sure +# we don't download a newer version and consider it as 1.3 +checksums = [('md5', '32b4d71b2ec9455c7db69516b1bd4910')] + +buildopts = ' CC="$CXX"' + +files_to_copy = ["bin", "README" ] + +sanity_check_paths = { + 'files': ["bin/PeakSeq"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb index 197f8c762ae811cdaf5876b5fadec37258902c9a..c7d3a27ade6493118e1ff63c2e2c320ef1605b8d 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.0-intel-2014b.eb @@ -812,6 +812,59 @@ exts_list = [ 'source_tmpl': 'Lingua-EN-PluralToSingular-0.14.tar.gz', 'source_urls': ['http://cpan.metacpan.org/authors/id/B/BK/BKB/'], }), + ('Set::Scalar', '1.29', { + 'source_tmpl': 'Set-Scalar-1.29.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DAVIDO/'], + }), + ('Text::CSV', '1.32', { + 'source_tmpl': 'Text-CSV-1.32.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MA/MAKAMAKA/'], + }), + ('Number::Format', '1.73', { + 'source_tmpl': 'Number-Format-1.73.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/W/WR/WRW/'], + }), + ('Template::Plugin::Number::Format', '1.06', { + 'source_tmpl': 'Template-Plugin-Number-Format-1.06.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DA/DARREN/'], + }), + ('Set::IntSpan::Fast', '1.15', { + 'source_tmpl': 'Set-IntSpan-Fast-1.15.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/A/AN/ANDYA/'], + }), + ('Text::Table', '1.15', { + 'source_tmpl': 'Text-Table-1.130.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/'], + }), + ('SQL::Abstract', '1.81', { + 'source_tmpl': 'SQL-Abstract-1.81.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RI/RIBASUSHI/'], + }), + ('GD::Graph', '1.49', { + 'source_tmpl': 'GDGraph-1.49.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/R/RU/RUZ/'], + }), + ('IPC::Run', '0.94', { + 'source_tmpl': 'IPC-Run-0.94.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/T/TO/TODDR/'], + }), + ('LWP::Simple', '6.13', { + 'source_tmpl': 'libwww-perl-6.13.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/E/ET/ETHER/'], + }), + ('Test::Pod', '1.50', { + 'source_tmpl': 'Test-Pod-1.50.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/D/DW/DWHEELER/'], + }), + ('XML::Twig', '3.49', { + 'source_tmpl': 'XML-Twig-3.49.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIROD/'], + }), + ('Class::DBI::SQLite', '0.11', { + 'source_tmpl': 'Class-DBI-SQLite-0.11.tar.gz', + 'source_urls': ['http://search.cpan.org/CPAN/authors/id/M/MI/MIYAGAWA/'], + }), + ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.20.2-GCC-4.9.2-bare.eb b/easybuild/easyconfigs/p/Perl/Perl-5.20.2-GCC-4.9.2-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..a79c30c3b23261209f3c9142a184dc598ec7f79b --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.20.2-GCC-4.9.2-bare.eb @@ -0,0 +1,19 @@ +name = 'Perl' +version = '5.20.2' +versionsuffix = '-bare' + +homepage = 'http://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.cpan.org/src/5.0'] +sources = [SOURCELOWER_TAR_GZ] + +# bare, no extensions +exts_list = [] + +runtest = 'test' + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..524dd9ba3d66e30769478b0dd7d5c993f7e2cab5 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '2.8.1' + +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': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..04c7f0efa3cf824724db3ccf6669ee49e194a57c --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-2.8.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '2.8.1' + +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': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..65d0c45c59d1130cd39a00d9e14b219d489fe854 --- /dev/null +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5a7-goolf-1.4.10.eb @@ -0,0 +1,47 @@ +# 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 = 'CmdCp' + +name = 'Pindel' +version = '0.2.5a7' + +homepage = 'http://gmt.genome.wustl.edu/packages/pindel/' +description = """ Pindel can detect breakpoints of large deletions, medium sized + insertions, inversions, tandem duplications and other structural variants at single-based + resolution from next-gen sequence data. It uses a pattern growth approach to identify the + breakpoints of these variants from paired-end short reads. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/genome/pindel/archive/'] +sources = ['v%(version)s.tar.gz'] + +patches = ['pindel-perl-path.patch'] + +dependencies = [ + ('SAMtools', '0.1.19'), + ('zlib', '1.2.7') +] + +cmds_map = [('.*', "CPATH=$EBROOTSAMTOOLS/include/bam:$CPATH ./INSTALL $EBROOTSAMTOOLS")] + +files_to_copy = [ + (['pindel', 'sam2pindel', 'pindel2vcf', 'bam2pindel.pl', 'Adaptor.pm'], 'bin'), + "demo", + "gmt", + "gmt-web", + "test", + "README.md", + "RELEASE" +] + +sanity_check_paths = { + 'files': ['bin/pindel', 'bin/sam2pindel', 'bin/pindel2vcf', 'bin/bam2pindel.pl'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Pindel/pindel-perl-path.patch b/easybuild/easyconfigs/p/Pindel/pindel-perl-path.patch new file mode 100644 index 0000000000000000000000000000000000000000..db0214c68067c373f7df63d6fabacf7748bdc270 --- /dev/null +++ b/easybuild/easyconfigs/p/Pindel/pindel-perl-path.patch @@ -0,0 +1,9 @@ +diff -ru pindel-0.2.5a7.orig/bam2pindel.pl pindel-0.2.5a7/bam2pindel.pl +--- pindel-0.2.5a7.orig/bam2pindel.pl 2014-09-16 20:53:13.000000000 +0200 ++++ pindel-0.2.5a7/bam2pindel.pl 2015-06-03 21:12:57.775900885 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/env perl + + ######################################################################################################## + # # diff --git a/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb new file mode 100644 index 0000000000000000000000000000000000000000..2fa31617c3e4a25f5a0e3c218dfa2896dcb6d49f --- /dev/null +++ b/easybuild/easyconfigs/p/Platanus/Platanus-1.2.1-linux-x86_64.eb @@ -0,0 +1,21 @@ +easyblock = 'Binary' + +name = 'Platanus' +version = '1.2.1' +versionsuffix = '-linux-x86_64' + +homepage = 'http://platanus.bio.titech.ac.jp/' +description = """PLATform for Assembling NUcleotide Sequences""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://platanus.bio.titech.ac.jp/Platanus_release/20130901010201'] +sources = ['platanus'] +checksums = ['02cf92847ec704d010a54df293b9c60a'] + +sanity_check_paths = { + 'files': ['platanus'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..f0f5501b846be81899908f970ee1dec54dd300a7 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-9.3.5-intel-2014b.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '9.3.5' + +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': '2014b'} + +osdependencies = [('openssl-devel', 'libssl-dev')] + +java = 'Java' +javaver = '1.7.0_60' + +dependencies = [ + (java, javaver, '', True), + ('libreadline', '6.3'), + ('zlib', '1.2.8'), +# ('OpenSSL', '1.0.1i'), # OS dependency should be preferred for security reasons +] + +builddependencies = [ + ('Bison', '3.0.2'), + ('flex', '2.5.39'), + ('Perl', '5.20.0'), +] + +sanity_check_paths = { + 'files': ['bin/psql'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..44847179dbc8290d3e3a879ceb86f0180d86c22d --- /dev/null +++ b/easybuild/easyconfigs/p/PyAMG/PyAMG-2.2.1-intel-2014b-Python-2.7.8.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = 'PyAMG' +version = '2.2.1' + +homepage = 'http://pyamg.org' +description = """PyAMG is a library of Algebraic Multigrid (AMG) solvers with a convenient Python interface.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.8' +pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +options = {'modulename': 'pyamg'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/pyamg' % pythonshortversion], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..34baa22804d89152435f3c81c5f4da3c15549848 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,36 @@ +# 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' + +homepage = 'http://www.riverbankcomputing.co.uk/software/pyqt' +description = """PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = ['%(name)s-x11-gpl-%(version)s.tar.gz'] +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] + +python = 'Python' +pyver = '2.7.9' +pythonshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SIP', '4.16.8', versionsuffix), + ('Qt', '4.8.6'), +] + +configopts = "configure-ng.py --confirm-license" +configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver +configopts += " --no-sip-files" + +options = {'modulename': 'PyQt4'} + +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..789bf13b2c388d94d322bd13b25f9b5cd7ddb424 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt/PyQt-4.11.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,36 @@ +# 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' + +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': '2015a'} + +sources = ['%(name)s-x11-gpl-%(version)s.tar.gz'] +source_urls = ['http://sourceforge.net/projects/pyqt/files/PyQt4/PyQt-%(version)s'] + +python = 'Python' +pyver = '2.7.9' +pythonshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SIP', '4.16.8', versionsuffix), + ('Qt', '4.8.6'), +] + +configopts = "configure-ng.py --confirm-license" +configopts += " --destdir=%%(installdir)s/lib/python%s/site-packages " % pythonshortver +configopts += " --no-sip-files" + +options = {'modulename': 'PyQt4'} + +modextrapaths = {'PYTHONPATH': 'lib/python%s/site-packages' % pythonshortver} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..580a294eeedf7226ed8ab553c3af1191fcec8d16 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-3.11-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = "PyYAML" +version = "3.11" + +homepage = "https://pypi.python.org/pypi/PyYAML/" +description = """PyYAML is a YAML parser and emitter for the Python programming language.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = "2.7.9" +py_short_ver = ".".join(pythonversion.split(".")[0:2]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('libyaml', '0.1.6'), +] + +options = {'modulename': 'yaml'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/yaml' % py_short_ver], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb new file mode 100644 index 0000000000000000000000000000000000000000..e38ac2e14374369d22101b2eebb8a25636d4d3de --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.6.0-intel-2015a-Python-2.7.9-zmq3.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '14.6.0' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) +zmqversion = '3.2.5' + +versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) + +dependencies = [ + (python, pythonversion), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pyshortver], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-foss-2015a-Python-2.7.9-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-foss-2015a-Python-2.7.9-zmq3.eb new file mode 100644 index 0000000000000000000000000000000000000000..fca9d5270f1ccb81d9fa54919ff1f98b9de7063a --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-foss-2015a-Python-2.7.9-zmq3.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '14.7.0' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) +zmqversion = '3.2.5' + +versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) + +dependencies = [ + (python, pythonversion), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pyshortver], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.9-zmq3.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.9-zmq3.eb new file mode 100644 index 0000000000000000000000000000000000000000..0986a01c066bcb50dce5cc9cb5408a3bef5ccb57 --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-14.7.0-intel-2015a-Python-2.7.9-zmq3.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '14.7.0' + +homepage = 'http://www.zeromq.org/bindings:python' +description = """Python bindings for ZeroMQ""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) +zmqversion = '3.2.5' + +versionsuffix = '-%s-%s-%s' % (python, pythonversion, 'zmq%s' % zmqversion.split('.')[0]) + +dependencies = [ + (python, pythonversion), + ('ZeroMQ', zmqversion), +] + +options = {'modulename': 'zmq'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/zmq' % pyshortver], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..103bb389984d984835204c8c461891a1f7f74388 --- /dev/null +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Pygments' +version = '2.0.2' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': ['bin/pygmentize'], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s.egg' % (pyshortver, pyshortver)], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..06251d78729ed65fad7d46aec6481f664ed56e0a --- /dev/null +++ b/easybuild/easyconfigs/p/Pygments/Pygments-2.0.2-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Pygments' +version = '2.0.2' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': ['bin/pygmentize'], + 'dirs': ['lib/python%s/site-packages/%%(name)s-%%(version)s-py%s.egg' % (pyshortver, pyshortver)], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..2453963f1849687e2a80eda38d641202cf40e3f7 --- /dev/null +++ b/easybuild/easyconfigs/p/Pyke/Pyke-1.1.1-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'Pyke' +version = '1.1.1' + +homepage = 'http://sourceforge.net/projects/pyke/' +description = """Pyke introduces a form of Logic Programming (inspired by Prolog) +to the Python community by providing a knowledge-based inference engine +(expert system) written in 100% Python.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_ZIP] + +python = "Python" +pythonversion = '2.7.3' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('numpy','1.6.2', versionsuffix), + ('scipy', '0.11.0', versionsuffix), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb index a0f450f70fd5da0bba44ca3a55826d5390443d6a..43ff3feba7790c36001122a64fc7d70826fec35f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goalf-1.1.0-no-OFED-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb index 53b60641322ae403d2d35d672c4cc6a584d31b39..f825fd87bd2b9a40df2c89c63725d9351cc179ac 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-gompi-1.4.12-no-OFED-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb index ed1944c3f288728538d3c4d81fb226e0f309fa84..18d0d4a8df4ba5018da9e938ead4ad9836e072fb 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-goolf-1.4.10-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb index d9118da1063fb338ac6992dbfbe30fe3e4433440..23ddabe854a26e4f7d5889e51b683eb310c2161d 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.0.6-bare.eb @@ -11,7 +11,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] -patches = ['python_libffi_int128_icc.patch'] +patches = [ + 'python_libffi_int128_icc.patch', + 'Python-%(version)s_svnversion-cmd.patch', +] dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb index da9bd1c2a45d9767c7cb9fbb6f27a87554f0ab93..f747214b5c04de81ef7d934c297ae4e88c91fd55 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-4.1.13-bare.eb @@ -11,7 +11,10 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] -patches = ['python_libffi_int128_icc.patch'] +patches = [ + 'python_libffi_int128_icc.patch', + 'Python-%(version)s_svnversion-cmd.patch', +] dependencies = [ ('bzip2', '1.0.6'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb index ae0e9d0e0895a947a110a64b56929455ff32819b..0228eae5bec85243ecadf62db0050da407306ff8 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.2.0-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb index 6d976f526fe56e3370000393ca7ab00b09231d06..fc44c37e78ed1f71580f531eaf88776d834d9af1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6-ictce-5.3.0-bare.eb @@ -11,6 +11,8 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True} source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] +patches = ['Python-%(version)s_svnversion-cmd.patch'] + dependencies = [ ('bzip2', '1.0.6'), ('zlib', '1.2.7'), diff --git a/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch b/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch new file mode 100644 index 0000000000000000000000000000000000000000..ba79adb02e019dc4eb4548603fb52e16fd86d3a8 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.5.6_svnversion-cmd.patch @@ -0,0 +1,14 @@ +replace svnversion call with mimiced output for non-SVN tarballs for older versions of svnversion, i.e 'exported' +author: Kenneth Hoste (Ghent University) +--- Python-2.5.6/configure.orig 2015-04-29 10:40:05.254502098 +0200 ++++ Python-2.5.6/configure 2015-04-29 10:42:01.739388944 +0200 +@@ -4242,7 +4242,8 @@ + + if test $SVNVERSION = found + then +- SVNVERSION="svnversion \$(srcdir)" ++ #SVNVERSION="svnversion \$(srcdir)" ++ SVNVERSION="echo exported" + else + SVNVERSION="echo exported" + fi 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 new file mode 100644 index 0000000000000000000000000000000000000000..1d7d341095b002171b4b6c938aaca6c388b4b2ae --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-foss-2015a.eb @@ -0,0 +1,145 @@ +name = 'Python' +version = '2.7.10' + +homepage = 'http://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.2' +scipyversion = '0.15.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.10.2'), + ('Tk', '8.6.4', '-no-X11'), +# ('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 +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.6', { + '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', # % numpyversion, + ], + }), + ('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', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.22', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + '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', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.2', { + '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', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + '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', '0.7.14', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + }), + ('jsonpointer', '1.9', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], + }), + ('mistune', '0.7', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], + }), + ('tornado', '4.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], + }), +] + +moduleclass = 'lang' 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 new file mode 100644 index 0000000000000000000000000000000000000000..a808b9876cc689116ca968b40eb4fe4e9e72eddd --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.10-intel-2015a.eb @@ -0,0 +1,145 @@ +name = 'Python' +version = '2.7.10' + +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': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.2' +scipyversion = '0.15.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), + ('SQLite', '3.8.10.2'), + ('Tk', '8.6.4', '-no-X11'), +# ('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 +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# package versions updated May 28th 2015 +exts_list = [ + ('setuptools', '16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '7.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.6', { + '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', # % numpyversion, + ], + }), + ('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', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.22', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + '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', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.2', { + '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', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + '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', '0.7.14', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2015.4', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), + ('MarkupSafe', '0.23', { + 'source_urls': ['https://pypi.python.org/packages/source/M/MarkupSafe'], + }), + ('Jinja2', '2.8', { + 'source_urls': ['https://pypi.python.org/packages/source/J/Jinja2'], + }), + ('jsonpointer', '1.9', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonpointer'], + }), + ('jsonschema', '2.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/j/jsonschema'], + }), + ('functools32', '3.2.3-2', { + 'source_urls': ['https://pypi.python.org/packages/source/f/functools32'], + }), + ('mistune', '0.7', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mistune'], + }), + ('tornado', '4.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado'], + }), + ('Pygments', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/P/Pygments'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb index 56258048337e9bc6049e069c6f7258f927f1d979..b447f3f5c56fd2e47691d2c592643a6c91b818fd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmpolf-1.1.6.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,10 +48,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -64,10 +64,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb index eea5ccfa5e6eb83a09a905b21c60ef47ba6c9b5a..3b9b9b0071c316fa3fe06218d68bf14614ce8525 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.1.12rc1.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,10 +46,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -62,10 +62,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb index a6794c06c9aa48b86f980a6b04002829ac443b91..e9411a98a07021ce56ce98dd659466ea3fabd664 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgmvolf-1.2.7.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,10 +48,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -64,10 +64,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb index dc891b7530dadb90f37a1b9cd6384a8e207a49f2..9d81cee86be481950aecd7b7cd7177b15061ad19 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-cgoolf-1.1.7.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,10 +46,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -62,10 +62,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb index 51cfbe46067e12f8e6ef64de2d961f98d7c3bda0..b7dfb64df9b022f6ee658b86b4a939eb89230cd7 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmpolf-1.4.8.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,10 +48,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -64,10 +64,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb index 311b197edff6988f1a2189e3bafcddfbf22c6d55..5eb4c88938f924fa0a64e6ef4a9473c64461dc4a 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,10 +48,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -64,10 +64,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb index 80c8900b947895ad5a070c7c92b4aea6871c4ca3..878951cc6e476ff20a71f61cae0f90c4c87951dc 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-gmvolf-1.7.12rc1.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,10 +48,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -64,10 +64,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb index f847189fab56f6b43c8599df330d2327403b1016..957d719fbd04d9e4a5f8b3b4013515b0f7e2330e 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-goalf-1.1.0-no-OFED.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,10 +48,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -64,10 +64,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 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 b2a76a28d3d51f880e02e95ac3bab465cbc8cf2b..49da1ce96f947abec5e8960eb4c7843f940bb27e 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 @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,10 +48,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -64,10 +64,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 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 077f9d9e7ea9c571fd12861ea22e594185482331..ff029a2234b253e799e285d736c993318aab0490 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 @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,10 +48,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -64,10 +64,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb index 930a85f6838b3f1ed7568c5f126ce4188d144661..2ef8f9fc886b0c840beb8606ddd784e6dc44c807 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.0.6.eb @@ -29,13 +29,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,10 +48,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -64,10 +64,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb index f86e56278893fd4b5c154f5f52e85fe5e9ae401c..b5075a6a9a6b213bb75c831b9e13cc8944b748b9 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-ictce-4.1.13.eb @@ -29,13 +29,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,10 +48,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -64,10 +64,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 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 401dc6dd76f5c211c6facc51c8ed1d1751a6c78b..e1bc68f6d19e46a49866fb09dbcefbdf7cd67a93 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 @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,10 +46,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -62,10 +62,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 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 e19d9c8443c2b1fb97fb796a41b8287c62585820..1f6678ca7318f61796fe2f8a1f41f82f6c4c34b9 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 @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,10 +46,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -62,10 +62,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 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 91d0cee83bf8973b86d13880588107698fca83ea..bcc80770f8f66f12972c6de62e95d72a7e4f6db6 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 @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,10 +46,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -62,10 +62,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb index 31732a9f475988e02366053b3d8abc035de20b3f..262801c6c11f6379519725f54257f4cd766edc65 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iomkl-4.6.13.eb @@ -29,13 +29,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,10 +48,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -64,10 +64,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb index 3dd0016674cc219469869bb61d827fddc36735af..7713f868794252a35e8ed9367d982ca37a95195f 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.3-iqacml-3.7.3.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -52,10 +52,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -68,10 +68,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb index 47b8de7acf5f39655fa9a1edef151d5e3bc0d352..0acac864f5d5fbbd256bc084da5ef05aeac5eecd 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-goalf-1.5.12-no-OFED.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -46,10 +46,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -62,10 +62,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 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 a9868e2f664661ba815b48216e1bdf71a84b2817..b8e12d524c621f9a7c70eeb390ce3a616a008923 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 @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,10 +48,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -64,10 +64,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb index b3e31e4ea33697f2ba2e561c1e922714e47b7edb..9fda7777e647ec648efc6a1847c7c6b49aeec6ee 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-ictce-4.1.13.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -51,10 +51,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -67,10 +67,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 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 ec5e6c7a3afea19c88e9fb48a98ddebb2c77e606..6f7edf431ee89ec321ee2d9fe7e68be3451ffc67 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 @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,10 +49,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -65,10 +65,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 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 4625232be850544d5fab58ae34d34c7021e4966d..3c2a47e51e8e3f9beb52133219152d1cf1e89fad 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 @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,10 +49,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -65,10 +65,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb index 1496901c9926c47fd1559df55b1b07c5e170fd72..c8797b36e9be938d5a2c3dd5973165470445b453 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.5-iqacml-3.7.3.eb @@ -31,13 +31,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '0.6c11', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -53,10 +53,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -69,10 +69,10 @@ exts_list = [ }), ('dateutil', '2.1', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 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 ba61389fd535b22ba37560cc3bad465adbeced54..de11eaf35665adcb3e69194ac8576d31c5301c91 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 @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '1.4.2', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.0', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,10 +48,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -64,10 +64,10 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb index 575fabb0e68fb9ec8e89a0f6241d2c14d1243a8b..b8f2f71c1298a2e06a92f29c7f861226b4c8ffce 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.6-ictce-4.1.13.eb @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '1.4.2', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.0', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -51,10 +51,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -67,10 +67,10 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 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 8b621ebdeef869fd6f29befd0dfa00230505d503..be1053a62d683f0385756f0b3478ca21b2bbf9a6 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 @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '1.4.2', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.0', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -51,10 +51,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -67,10 +67,10 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 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 8ef1b28d6b44423d09e189b3adeb2333f9c2b2ae..caf05b2cc7ffaef59b1e10abb4068850df96ce40 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 @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,10 +48,10 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -64,10 +64,10 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 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 2dd2282def9f0124780dcb315ad6da668d240edb..5c19bcd953243787c7508def9cf5a974e6dca284 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 @@ -30,13 +30,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,19 +48,19 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + 'source_urls': ['https://pypi.python.org/packages/source/b/blist/'], }), ('six', '1.7.3', { - 'source_urls': ['http://pypi.python.org/packages/source/s/six/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], }), ('mpi4py', '1.3.1', { 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('paycheck', '1.0.2', { - 'source_urls': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -70,7 +70,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 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 478804a887a1a9060946a5d2e2fb85ccc5b9d659..f1ec579fbec9c3a7b1921495625b9a9fe82a8768 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 @@ -34,13 +34,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -52,16 +52,16 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + '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': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -74,7 +74,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 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 new file mode 100644 index 0000000000000000000000000000000000000000..b6208992739be2617df8f408dead087b982bb260 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.8-intel-2014.06.eb @@ -0,0 +1,101 @@ +name = 'Python' +version = '2.7.8' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2014.06'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.8.1' +scipyversion = '0.14.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# libffi build in python is still broken, see http://bugs.python.org/issue4130 +patches = ['python-2.7_libffi-include-xmmintrin.patch'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# Version updated 08/JULY/2014 +exts_list = [ + ('setuptools', '5.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '1.5.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.3', { + '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-%s-mkl.patch' % numpyversion, + ], + }), + ('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', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('lockfile', '0.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.20.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + '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', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.14.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), +] + +moduleclass = 'lang' 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 65ec137785e91910a2e4ddf7b6399997824d1e4e..1ae3ec0c5f68a8a57c9dece5f47ad8fbc7a256db 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 @@ -31,13 +31,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,16 +49,16 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + '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': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -71,7 +71,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], 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 ad901ece9fbaff287920b693ed1be4b1e9b626ab..60923e701c5052fa8a481553de1671add9450089 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 @@ -30,13 +30,13 @@ dependencies = [ # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,16 +48,16 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + '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': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -70,7 +70,7 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..5c84059a20ec16c4d4fde4364365fa1d4c2edd28 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29-bare.eb @@ -0,0 +1,39 @@ +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': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True, 'opt': 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'), +# ('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'), 'tk-devel'] + +# bare installation: no extensions included +exts_list = [] + +buildopts = 'LINKCC="$CC -dynamic"' + +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..2e085966c758de3a5210a92427e332cdcbe089d1 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.1.29.eb @@ -0,0 +1,115 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('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'), 'tk-devel'] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + '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', # % numpyversion, + ], + }), + ('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', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + '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', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + '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', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..1e9572eb837c8293f7b1806493415e91e16564e7 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25-bare.eb @@ -0,0 +1,39 @@ +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': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'opt': 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'), +# ('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'), 'tk-devel'] + +# bare installation: no extensions included +exts_list = [] + +buildopts = 'LINKCC="$CC -dynamic"' + +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..0c1b139dda1b53898424010860b9a0faa7ce969b --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.25.eb @@ -0,0 +1,115 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('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'), 'tk-devel'] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + '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', # % numpyversion, + ], + }), + ('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', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + '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', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + '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', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..3fafaaa920caee5a5d3baca1e7a7db3b6b600aed --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40-bare.eb @@ -0,0 +1,39 @@ +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': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'opt': 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'), +# ('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'), 'tk-devel'] + +# bare installation: no extensions included +exts_list = [] + +buildopts = 'LINKCC="$CC -dynamic"' + +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..186e5f94df6d0b1b73da88e9499b5d89613f3df1 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-CrayGNU-5.2.40.eb @@ -0,0 +1,115 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('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'), 'tk-devel'] + +buildopts = 'LINKCC="$CC -dynamic"' + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + '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', # % numpyversion, + ], + }), + ('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', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + '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', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + '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', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] + +sanity_check_commands = [ + ('python', '--version'), + ('python', '-c "import _ctypes"'), # make sure that foreign function interface (libffi) works + ('python', '-c "import _ssl"'), # make sure SSL support is enabled one way or another + ('python', '-c "import readline"'), # make sure readline module is installed (requires libreadline) + ('python', '-c "import Tkinter"'), # make sure Tkinter module is installed (requires Tk) +] + +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 3974b6e842cc2e8f426b4c3cc523eeddf32b2863..7f438347a5a4904fab5f7963107845601804365c 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 @@ -18,6 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), # ('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 new file mode 100644 index 0000000000000000000000000000000000000000..abb705a349eff8e55418d662e9496d829061fe0a --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-foss-2015.05.eb @@ -0,0 +1,116 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'https://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'foss', 'version': '2015.05'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['https://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'), +# ('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')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('https://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + }), + ('scipy', scipyversion, { + 'source_urls': [('https://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': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '0.10.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['https://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + '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', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2014.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + +moduleclass = 'lang' 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 669c54c38def38ad20ea465ba06ed10f72c93a7f..dc26dc666bfb39985b0054631347a2f9838c65f7 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 @@ -18,6 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), # ('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 0f382d98ba28f7dffb470d9d02ef7218203ca876..bb297e5eb8f68b2d2e970f14b84b1ec274cdb0f8 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 @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), # ('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 ] @@ -30,13 +31,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # package versions updated Jan 19th 2015 exts_list = [ ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.4', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -45,16 +46,16 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + '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': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], @@ -70,7 +71,7 @@ exts_list = [ }), ('dateutil', '2.4.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], @@ -107,6 +108,9 @@ exts_list = [ ('pytz', '2014.10', { 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), ] moduleclass = 'lang' 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 e206b78e2281315e6393f95bb337007c7a1b61dd..ad2c37f79adb5bd9c619d6a67fe1f88a565f3bbb 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 @@ -17,6 +17,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), # ('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 4ec2b0ce97f5b557d133c0f317f7e5f5a9edfd96..27281d943cfd6eb641909c9b57adfafa60f61f65 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 @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), # ('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 ] @@ -30,13 +31,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # package versions updated Jan 19th 2015 exts_list = [ ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.4', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -45,16 +46,16 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + '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': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], @@ -70,7 +71,7 @@ exts_list = [ }), ('dateutil', '2.4.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], @@ -107,6 +108,9 @@ exts_list = [ ('pytz', '2014.10', { 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), ] moduleclass = 'lang' 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 new file mode 100644 index 0000000000000000000000000000000000000000..c011298dc9c62f9feb9698ce0bfd77041e9b7a7f --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.9-goolf-1.7.20.eb @@ -0,0 +1,117 @@ +name = 'Python' +version = '2.7.9' + +homepage = 'https://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.1' +scipyversion = '0.14.1' + +source_urls = ['https://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'), + #('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')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '11.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.0.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.4', { + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], + }), + ('numpy', numpyversion, { + 'source_urls': [('https://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], + }), + ('scipy', scipyversion, { + 'source_urls': [('https://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': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], + }), + ('paycheck', '1.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/ '], + }), + ('pbr', '0.10.8', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.21.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.0', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + 'source_tmpl': 'liac-%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/l/liac-arff/'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'source_urls': ['https://ftp.dlitz.net/pub/dlitz/crypto/pycrypto/'], + }), + ('ecdsa', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + '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', '0.7.13', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), + ('mock', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mock'], + }), + ('pytz', '2014.10', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], + }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), +] + + +moduleclass = 'lang' 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 d2c02867a99986b1654a7b3135f9f887745381cb..d6a4eb1b3cb4883decd61523e54d63b252e278d8 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 @@ -18,6 +18,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), # ('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 db9c0d75b8a10507b69ce7d6cf4500715c0c6ee3..2c04d1e9a7f0df30f246722274fcc90c2ef4f67a 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 @@ -20,6 +20,7 @@ dependencies = [ ('libreadline', '6.3'), ('ncurses', '5.9'), ('SQLite', '3.8.8.1'), + ('Tk', '8.6.3', '-no-X11'), # ('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 ] @@ -30,13 +31,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # package versions updated Jan 19th 2015 exts_list = [ ('setuptools', '11.3.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '6.0.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.4', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -48,16 +49,16 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + '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': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('pbr', '0.10.8', { 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], @@ -73,7 +74,7 @@ exts_list = [ }), ('dateutil', '2.4.0', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], @@ -110,6 +111,9 @@ exts_list = [ ('pytz', '2014.10', { 'source_urls': ['https://pypi.python.org/packages/source/p/pytz'], }), + ('pandas', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb index ff366c2d52272be6b29bd06831bec04f254b13d3..ddf1d2d85390d0b5008ba7ad9c9c0430af53978d 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-goalf-1.1.0-no-OFED.eb @@ -27,14 +27,14 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('distribute', '0.6.26', { - 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], + 'source_urls': ['https://pypi.python.org/packages/source/d/distribute'], 'modulename': 'setuptools', }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('Cython', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 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 1a4686291942d7ddbab6c9b520457705620c9002..86066e4a5eb3c5b8aee0fd1ac75d70b0338099d7 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 @@ -27,14 +27,14 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('distribute', '0.6.26', { - 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], + 'source_urls': ['https://pypi.python.org/packages/source/d/distribute'], 'modulename': 'setuptools', }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('Cython', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb index bfaa166f08083142b29728446e585824144359dd..b01168b83e9499e9210ad557aaaf0aa49d6bbc61 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.2.3-ictce-4.0.6.eb @@ -29,14 +29,14 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('distribute', '0.6.26', { - 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], + 'source_urls': ['https://pypi.python.org/packages/source/d/distribute'], 'modulename': 'setuptools', }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -51,13 +51,13 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('Cython', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 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 92a41bf7e7e7fe9f1716e02bd0218954e8528653..de9617eacf2ef57da0be8ee59774497069f65761 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 @@ -27,14 +27,14 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('distribute', '0.6.26', { - 'source_urls': ['http://pypi.python.org/packages/source/d/distribute'], + 'source_urls': ['https://pypi.python.org/packages/source/d/distribute'], 'modulename': 'setuptools', }), ('pip', '1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.1.2', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,13 +49,13 @@ exts_list = [ 'source_urls': ['http://bitbucket.org/mpi4py/mpi4py/downloads/'], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('Cython', '0.19.1', { 'source_urls': ['http://www.cython.org/release/'], }), ('deap', '0.9.1', { - 'source_urls': ['https://deap.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb index c462546fe3d8cf19de2b3cf2d9dde0961ae91681..f23e383d176628ba6472fa95773734311b7feb2e 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-goolf-1.4.10.eb @@ -27,13 +27,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '1.1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools'], }), ('pip', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.0', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb index 51dd82cdf95cc72082d74e1c2aa4f2e0fb3feb65..28d140c742f4d100facb9394ce8d32bbe5f444bd 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-4.1.13.eb @@ -29,13 +29,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '1.1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools'], }), ('pip', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.0', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], diff --git a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb index f1f4f3af6bf991251867eb107aba10b6890f3a8c..a66a2c142af3ca2a7e7069c0d3b79f8116a6ac83 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.3.2-ictce-5.3.0.eb @@ -29,13 +29,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # order is important! exts_list = [ ('setuptools', '1.1.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools'], }), ('pip', '1.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.0', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], 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 b64218f00fd6327fb8cce99333c92af381ac6dbe..b7690d84fc789d268975ed57c180e3a805a710ff 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 @@ -31,13 +31,13 @@ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] # Version updated 08/JULY/2014 exts_list = [ ('setuptools', '5.4.1', { - 'source_urls': ['http://pypi.python.org/packages/source/s/setuptools/'], + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], }), ('pip', '1.5.6', { - 'source_urls': ['http://pypi.python.org/packages/source/p/pip/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], }), ('nose', '1.3.3', { - 'source_urls': ['http://pypi.python.org/packages/source/n/nose/'], + 'source_urls': ['https://pypi.python.org/packages/source/n/nose/'], }), ('numpy', numpyversion, { 'source_urls': [('http://sourceforge.net/projects/numpy/files/NumPy/%s' % numpyversion, 'download')], @@ -49,16 +49,19 @@ exts_list = [ 'source_urls': [('http://sourceforge.net/projects/scipy/files/scipy/%s' % scipyversion, 'download')], }), ('blist', '1.3.6', { - 'source_urls': ['http://pypi.python.org/packages/source/b/blist/'], + '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': ['http://pypi.python.org/packages/source/p/paycheck/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/paycheck/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], }), ('argparse', '1.2.1', { - 'source_urls': ['http://argparse.googlecode.com/files/'], + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], }), ('lockfile', '0.9.1', { 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], @@ -73,10 +76,13 @@ exts_list = [ }), ('dateutil', '2.2', { 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', - 'source_urls': ['http://pypi.python.org/packages/source/p/python-dateutil/'], + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], }), ('deap', '1.0.1', { 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.1_setup-open-README-utf8.patch', + ], }), ('decorator', '3.4.0', { 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], 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 new file mode 100644 index 0000000000000000000000000000000000000000..91935078a9cf5e99aa877a2ed58a34f89ad551bc --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.4.1-intel-2015a.eb @@ -0,0 +1,109 @@ +name = 'Python' +version = '3.4.1' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.8.1' +scipyversion = '0.14.0' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# libffi build in python is still broken, see http://bugs.python.org/issue4130 +patches = ['python-3.4_libffi-include-xmmintrin.patch'] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('OpenSSL', '1.0.1g'), # OS dependency should be preferred for security reasons +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +# order is important! +# Version updated 08/JULY/2014 +exts_list = [ + ('setuptools', '5.4.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '1.5.6', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.3', { + '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-%s-mkl.patch' % numpyversion, + ], + }), + ('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/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('argparse', '1.2.1', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('lockfile', '0.9.1', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + # tarball has changed upstream, so make sure we get the right version by verifying the checksum + 'checksums': ['ce61468d4c1263e3005737bbed2641f0'], + }), + ('Cython', '0.20.2', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.7.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.1', { + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.1_setup-open-README-utf8.patch', + ], + }), + ('decorator', '3.4.0', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.1', { + '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', '0.11', { + 'source_urls': ['https://pypi.python.org/packages/source/e/ecdsa/'], + }), + ('paramiko', '1.14.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyparsing/'], + }), +] + +moduleclass = 'lang' 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 new file mode 100644 index 0000000000000000000000000000000000000000..1aa8ae3172171511140ecfdad221c2b954ee7db1 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.4.3-intel-2015a.eb @@ -0,0 +1,113 @@ +name = 'Python' +version = '3.4.3' + +homepage = 'http://python.org/' +description = "Python is a programming language that lets you work more quickly and integrate your systems more effectively." + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +numpyversion = '1.9.2' +scipyversion = '0.15.1' + +source_urls = ['http://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] + +# python needs bzip2 to build the bz2 package +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.8'), + ('libreadline', '6.3'), + ('ncurses', '5.9'), +# ('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 +] + +osdependencies = [('openssl-devel', 'libssl-dev')] + +# order is important! +# package versions updated Jan 19th 2015 +exts_list = [ + ('setuptools', '15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + }), + ('pip', '6.1.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pip/'], + }), + ('nose', '1.3.6', { + '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', # % numpyversion, + ], + }), + ('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/'], + 'patches': [ + 'paycheck-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('argparse', '1.3.0', { + 'source_urls': ['https://pypi.python.org/packages/source/a/argparse/'], + }), + ('pbr', '0.11.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pbr/'], + }), + ('lockfile', '0.10.2', { + 'source_urls': ['https://pypi.python.org/packages/source/l/lockfile/'], + }), + ('Cython', '0.22', { + 'source_urls': ['http://www.cython.org/release/'], + }), + ('six', '1.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/six/'], + }), + ('dateutil', '2.4.2', { + 'source_tmpl': 'python-%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/python-dateutil/'], + }), + ('deap', '1.0.2', { + 'source_tmpl': '%(name)s-%(version)s.post2.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/d/deap/'], + 'patches': [ + 'deap-1.0.2_setup-open-README-utf8.patch', + ], + }), + ('decorator', '3.4.2', { + 'source_urls': ['https://pypi.python.org/packages/source/d/decorator/'], + }), + ('arff', '2.0.2', { + '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', '1.15.2', { + 'source_urls': ['https://pypi.python.org/packages/source/p/paramiko/'], + }), + ('pyparsing', '2.0.3', { + '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', '0.7.14', { + 'source_urls': ['https://pypi.python.org/packages/source/n/netaddr'], + }), +] diff --git a/easybuild/easyconfigs/p/Python/deap-1.0.1_setup-open-README-utf8.patch b/easybuild/easyconfigs/p/Python/deap-1.0.1_setup-open-README-utf8.patch new file mode 100644 index 0000000000000000000000000000000000000000..b7c896999f7e9f9aac6bd383cc831c140705a95f --- /dev/null +++ b/easybuild/easyconfigs/p/Python/deap-1.0.1_setup-open-README-utf8.patch @@ -0,0 +1,17 @@ +--- deap-1.0.1.orig/setup.py 2014-04-08 15:49:52.000000000 +0200 ++++ deap-1.0.1/setup.py 2015-05-21 22:25:37.345008000 +0200 +@@ -1,4 +1,5 @@ + #!/usr/bin/env python ++import codecs + import sys + from distutils.core import setup + try: +@@ -11,7 +12,7 @@ + setup(name='deap', + version=deap.__revision__, + description='Distributed Evolutionary Algorithms in Python', +- long_description=open('README.txt').read(), ++ long_description=codecs.open('README.txt', encoding='utf-8').read(), + author='deap Development Team', + author_email='deap-users@googlegroups.com', + url='http://deap.googlecode.com', diff --git a/easybuild/easyconfigs/p/Python/deap-1.0.2_setup-open-README-utf8.patch b/easybuild/easyconfigs/p/Python/deap-1.0.2_setup-open-README-utf8.patch new file mode 100644 index 0000000000000000000000000000000000000000..6dece6f5d82227b12b2e097eb186bbed8e93c95e --- /dev/null +++ b/easybuild/easyconfigs/p/Python/deap-1.0.2_setup-open-README-utf8.patch @@ -0,0 +1,17 @@ +--- deap-1.0.2.orig/setup.py 2015-05-12 04:06:49.000000000 +0200 ++++ deap-1.0.2/setup.py 2015-05-21 19:06:03.792820042 +0200 +@@ -1,4 +1,5 @@ + #!/usr/bin/env python ++import codecs + import sys + from distutils.core import setup + try: +@@ -10,7 +11,7 @@ + from pypandoc import convert + except ImportError: + print("warning: pypandoc module not found, could not convert Markdown to RST") +- read_md = lambda f: open(f, 'r').read() ++ read_md = lambda f: codecs.open(f, encoding='utf-8').read() + else: + read_md = lambda f: convert(f, 'rst') + diff --git a/easybuild/easyconfigs/p/Python/numpy-1.8.1-mkl.patch b/easybuild/easyconfigs/p/Python/numpy-1.8.1-mkl.patch index 363f95c19f2c6cc7bcf21c58c0bb84e9a2f17248..0689e81b9fd2fe9675529721a284d10c1b5639cc 100644 --- a/easybuild/easyconfigs/p/Python/numpy-1.8.1-mkl.patch +++ b/easybuild/easyconfigs/p/Python/numpy-1.8.1-mkl.patch @@ -1,3 +1,5 @@ +fix issues in numpy distutils pkg w.r.t. detecting BLAS/LAPACK libraries +by Kenneth Hoste (HPC-UGent) diff -ur numpy-1.8.1.orig/numpy/distutils/fcompiler/__init__.py numpy-1.8.1-2/numpy/distutils/fcompiler/__init__.py --- numpy-1.8.1.orig/numpy/distutils/fcompiler/__init__.py 2014-03-25 20:43:24.000000000 +0100 +++ numpy-1.8.1-2/numpy/distutils/fcompiler/__init__.py 2014-07-08 15:22:31.471064031 +0200 diff --git a/easybuild/easyconfigs/p/Python/paycheck-1.0.2_setup-open-README-utf8.patch b/easybuild/easyconfigs/p/Python/paycheck-1.0.2_setup-open-README-utf8.patch new file mode 100644 index 0000000000000000000000000000000000000000..193336def433c6c3acab7bb88054dedea320425e --- /dev/null +++ b/easybuild/easyconfigs/p/Python/paycheck-1.0.2_setup-open-README-utf8.patch @@ -0,0 +1,22 @@ +open README file with utf-8 encoding, to avoid error like: +UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 577: ordinal not in range(128) +author: Kenneth Hoste (HPC-UGent) +--- paycheck-1.0.2/setup.py.orig 2015-05-21 16:09:24.300074046 +0200 ++++ paycheck-1.0.2/setup.py 2015-05-21 16:11:43.503945542 +0200 +@@ -1,6 +1,7 @@ + from distutils.cmd import Command + from distutils.core import setup + ++import codecs + import sys + if sys.version_info >= (3, 0): + try: +@@ -24,7 +25,7 @@ + name = 'paycheck', + version ='1.0.2', + description ='A Python QuickCheck implementation', +- long_description = open("README.txt").read(), ++ long_description = codecs.open("README.txt", encoding='utf-8').read(), + author ='Mark Chadwick', + author_email ='mark.chadwick@gmail.com', + maintainer ='Gregory Crosswhite', diff --git a/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..fa5b729bcb665c94125a32b00bba0743f166fa49 --- /dev/null +++ b/easybuild/easyconfigs/p/pBWA/pBWA-0.5.9_1.21009-goolf-1.4.10.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2013-2014 Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## +easyblock = "MakeCp" + +name = 'pBWA' +version = '0.5.9_1.21009' + +homepage = 'http://pbwa.sourceforge.net/' +description = "pBWA is a parallel implementation of the popular software BWA." + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = ['%(name)s_%(version)s.zip'] +source_urls = [('http://sourceforge.net/projects/pbwa/files/latest', 'download')] + +dependencies = [('BWA', '0.7.4')] + +files_to_copy = [(['pBWA','qualfa2fq.pl','solid2fastq.pl' ], 'bin')] + +sanity_check_paths = { + 'files': ['bin/pBWA','bin/qualfa2fq.pl','bin/solid2fastq.pl'], + 'dirs': ['.'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.11.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/pandas/pandas-0.11.0-goolf-1.4.10-Python-2.7.3.eb index 350eeb2738cd584055aef1e569146a057c7f0fb1..7d470be431d49288e5d6ebc71f9883b9dc85cd8f 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.11.0-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.11.0-goolf-1.4.10-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "pandas" version = "0.11.0" -homepage = "http://pypi.python.org/pypi/pandas/" +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.""" diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-4.1.13-Python-2.7.3.eb index 683efb783b0793dc130fb7ecd2d2edc73ec1cddf..644c39f1d8ea0ee0f6de8927bd79e10a1c65fd10 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-4.1.13-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "pandas" version = "0.11.0" -homepage = "http://pypi.python.org/pypi/pandas/" +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.""" diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-5.3.0-Python-2.7.3.eb index 9d8a5aeb674cc1cffd6002e4703eaffb1b06fdfa..236486c7f62ed145f550dda62394266bf135f3e3 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.11.0-ictce-5.3.0-Python-2.7.3.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "pandas" version = "0.11.0" -homepage = "http://pypi.python.org/pypi/pandas/" +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.""" diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.12.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/p/pandas/pandas-0.12.0-ictce-5.5.0-Python-2.7.6.eb index b38ad74c90fbae0901313892c7a8c84ee64f2c46..934bb2474116b4d523638278218e96f4c131adff 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.12.0-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.12.0-ictce-5.5.0-Python-2.7.6.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "pandas" version = "0.12.0" -homepage = "http://pypi.python.org/pypi/pandas/" +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.""" diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.13.1-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/p/pandas/pandas-0.13.1-ictce-5.5.0-Python-2.7.6.eb index f0ae8b6a9fc8dcac728fdb33a8a236d9802e0d48..36528b21fe915b8be413344e5de6e4c61efd5abb 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-0.13.1-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-0.13.1-ictce-5.5.0-Python-2.7.6.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "pandas" version = "0.13.1" -homepage = "http://pypi.python.org/pypi/pandas/" +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.""" diff --git a/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..a94b0b1e5d69c3763503b27262d199cf584c1806 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-0.16.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,31 @@ +easyblock = "PythonPackage" + +name = "pandas" +version = "0.16.0" + +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': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = "2.7.9" + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +py_short_ver = ".".join(pythonversion.split(".")[0:2]) +pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) + +sanity_check_paths = { + 'files': [("%s-%%(version)s-py%s.egg" % (pylibdir, py_short_ver), + "%s-%%(version)s-py%s-linux-x86_64.egg" % (pylibdir, py_short_ver))], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/parallel/parallel-20150322-GCC-4.9.2.eb b/easybuild/easyconfigs/p/parallel/parallel-20150322-GCC-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..d8b12a2b080acec628f369cebd36483dc390cfe4 --- /dev/null +++ b/easybuild/easyconfigs/p/parallel/parallel-20150322-GCC-4.9.2.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'parallel' +version = '20150322' + +homepage = 'http://savannah.gnu.org/projects/parallel/' +description = """parallel: Build and execute shell commands in parallel""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['http://ftp.gnu.org/gnu/parallel'] + +dependencies = [ + ('Perl', '5.20.2', '-bare'), +] + +sanity_check_paths = { + 'files': ['bin/parallel'], + 'dirs': [] +} + +moduleclass = 'tools' 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/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index dd8127de7fc7b815a20c5efbbfa5e1a8f8e8b918..05e281d1d75ce5ce814470a3e857840dea6e9e57 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -3,15 +3,13 @@ easyblock = 'PythonPackage' name = 'paycheck' version = '1.0.2' -homepage = 'http://pypi.python.org/pypi/paycheck/' +homepage = 'https://pypi.python.org/pypi/paycheck/' description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, rather than testing its results for a given input.""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = [ - 'http://pypi.python.org/packages/source/p/paycheck/', - ] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb index c1a1ef52b457ab50b38eaf1f3d0d61ec6dc4f8cd..67f7bc47b5b16626ecd6903a11191ef2bd2cf97a 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-goolf-1.4.10-Python-2.7.3.eb @@ -3,14 +3,12 @@ easyblock = 'PythonPackage' name = 'paycheck' version = '1.0.2' -homepage = 'http://pypi.python.org/pypi/paycheck/' +homepage = 'https://pypi.python.org/pypi/paycheck/' description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, rather than testing its results for a given input.""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = [ - 'http://pypi.python.org/packages/source/p/paycheck/', - ] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb index 9d393ee3936c37a43d7346cda2c134805d1b687f..0f1fade586e32c6a8dc263b15c40b89285766017 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-4.1.13-Python-2.7.3.eb @@ -3,15 +3,13 @@ easyblock = 'PythonPackage' name = 'paycheck' version = '1.0.2' -homepage = 'http://pypi.python.org/pypi/paycheck/' +homepage = 'https://pypi.python.org/pypi/paycheck/' description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, rather than testing its results for a given input.""" toolchain = {'name': 'ictce', 'version': '4.1.13'} -source_urls = [ - 'http://pypi.python.org/packages/source/p/paycheck/', - ] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb index 295d530de8abae1d0e9b173e97fe7f39fa2afc5f..5170a4d2bd316400aba1314bdfb537f2c75bfaf1 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-ictce-5.3.0-Python-2.7.3.eb @@ -3,16 +3,13 @@ easyblock = 'PythonPackage' name = 'paycheck' version = '1.0.2' -homepage = 'http://pypi.python.org/pypi/paycheck/' +homepage = 'https://pypi.python.org/pypi/paycheck/' description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, rather than testing its results for a given input.""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = [ - 'http://pypi.python.org/packages/source/p/paycheck/', - ] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb index 66535a0069fd9acf4febfe163e7f09ed06931423..f140852405768fee38989e584f22905b8ae66e86 100644 --- a/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/paycheck/paycheck-1.0.2-iomkl-4.6.13-Python-2.7.3.eb @@ -3,15 +3,13 @@ easyblock = 'PythonPackage' name = 'paycheck' version = '1.0.2' -homepage = 'http://pypi.python.org/pypi/paycheck/' +homepage = 'https://pypi.python.org/pypi/paycheck/' description = """PayCheck is a half-baked implementation of ScalaCheck, which itself is an implementation of QuickCheck for Haskell. PayCheck is useful for defining a specification of what a function should do, rather than testing its results for a given input.""" toolchain = {'name': 'iomkl', 'version': '4.6.13'} -source_urls = [ - 'http://pypi.python.org/packages/source/p/paycheck/', - ] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = 'Python' diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..2b1f46d33d4f93d7fde1a264b24ceb29eb283e9e --- /dev/null +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'pbs_python' +version = '4.6.0' + +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': '2015a'} + +source_urls = ['http://ftp.sara.nl/pub/outgoing/'] +sources = [SOURCE_TAR_GZ] + +patches = ['pbs_python-%(version)s_CC.patch'] + +python = 'Python' +pythonver = '2.7.9' +pythonshortver = '.'.join(pythonver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +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%s/site-packages' % pythonshortver +modextrapaths = {"PYTHONPATH": pythonpath} + +sanity_check_paths = { + 'files': [], + 'dirs': ["%s/pbs" % pythonpath] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0_CC.patch b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0_CC.patch new file mode 100644 index 0000000000000000000000000000000000000000..00d8259263e834a2cc8ff02487903c9b7d8de2f9 --- /dev/null +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0_CC.patch @@ -0,0 +1,20 @@ +--- pbs_python-4.6.0/setup.py.in.orig 2015-04-01 13:51:18.158956461 +0200 ++++ pbs_python-4.6.0/setup.py.in 2015-04-01 13:52:02.249359723 +0200 +@@ -37,7 +37,7 @@ + if LooseVersion(VERSION) >= LooseVersion('5.0'): + + inc=os.environ.get('PBS_PYTHON_INCLUDEDIR','/usr/include/torque') +- os.environ['CC']='g++' ++ os.environ['CC']= os.environ.get('CXX', 'g++') + os.environ['CFLAGS']=' '.join(os.environ.get('CFLAGS','').split(' ')+['-I%s'%inc]) + + if not os.path.exists(os.path.join(inc,'log.h')): +@@ -55,7 +55,7 @@ + elif LooseVersion(VERSION) >= LooseVersion('4.2'): + + inc=os.environ.get('PBS_PYTHON_INCLUDEDIR','/usr/include/torque') +- os.environ['CC']='g++' ++ os.environ['CC']= os.environ.get('CXX', 'g++') + os.environ['CFLAGS']=' '.join(os.environ.get('CFLAGS','').split(' ')+['-I%s'%inc]) + + if not os.path.exists(os.path.join(inc,'log.h')): diff --git a/easybuild/easyconfigs/p/picard/picard-1.109.eb b/easybuild/easyconfigs/p/picard/picard-1.109.eb new file mode 100644 index 0000000000000000000000000000000000000000..b02c4dfde3bc59612325564d3d90cc1b3e535b8e --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-1.109.eb @@ -0,0 +1,14 @@ +name = 'picard' +version = '1.109' + +homepage = 'http://sourceforge.net/projects/picard' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-tools-%(version)s.zip'] + +dependencies = [('Java', '1.7.0_10')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.32.6-goolf-1.7.20.eb b/easybuild/easyconfigs/p/pixman/pixman-0.32.6-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..9a915bad5f07f1c75fafd779994dd2c1d9efaacf --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.32.6-goolf-1.7.20.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.32.6' + +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': 'goolf', 'version': '1.7.20'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.so'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.32.6-intel-2015a.eb b/easybuild/easyconfigs/p/pixman/pixman-0.32.6-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..480001289ad988385e94f2c6319de9908c524083 --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.32.6-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = "pixman" +version = '0.32.6' + +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': '2015a'} + +source_urls = ['http://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.so'], + 'dirs': [] +} + +moduleclass = 'vis' 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 new file mode 100644 index 0000000000000000000000000000000000000000..ddfabeac319be3fb4087d9d16b23eb25aa74df47 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.27.1-intel-2015a.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.27.1' + +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).""" + +# don't use PAX, it might break. +tar_config_opts = True + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://pkgconfig.freedesktop.org/releases/'] + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pyhull/pyhull-1.5.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pyhull/pyhull-1.5.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..c71d39213eabb29e697b2ca5ec77ebd5d6b02805 --- /dev/null +++ b/easybuild/easyconfigs/p/pyhull/pyhull-1.5.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,34 @@ +easyblock = "PythonPackage" + +name = "pyhull" +version = "1.5.4" +homepage = "http://pythonhosted.org/pyhull/" +description = """Pyhull is a Python wrapper to qhull (http://www.qhull.org/) for the computation of the convex hull, + Delaunay triangulation and Voronoi diagram. It is written as a Python C extension, with both high-level and low-level + interfaces to qhull. +""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +patches = ['pyhull-%(version)s_use-provided-Qhull.patch'] + +python = "Python" +pythonversion = "2.7.9" +py_short_ver = ".".join(pythonversion.split(".")[0:2]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('Qhull', '2012.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pv)s/site-packages/pyhull-%%(version)s-py%(pv)s-linux-x86_64.egg' % {'pv': py_short_ver}], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyhull/pyhull-1.5.4_use-provided-Qhull.patch b/easybuild/easyconfigs/p/pyhull/pyhull-1.5.4_use-provided-Qhull.patch new file mode 100644 index 0000000000000000000000000000000000000000..718405a70d8d1806ddcb8498808c7bdea0a75aff --- /dev/null +++ b/easybuild/easyconfigs/p/pyhull/pyhull-1.5.4_use-provided-Qhull.patch @@ -0,0 +1,26 @@ +let pyhull use provided Qhull rather than having it (re)build (parts of) Qhull itself +author: Kenneth Hoste (HPC-UGent) +--- pyhull-1.5.4/setup.py.orig 2015-04-07 21:30:35.000000000 +0200 ++++ pyhull-1.5.4/setup.py 2015-04-08 11:24:48.913427316 +0200 +@@ -7,14 +7,18 @@ + from setuptools import setup, Extension, find_packages + + src_dir = "src" +-include_dirs = glob.glob(os.path.join("src", "libqhull")) +-sources = glob.glob(os.path.join("src", "libqhull", "*.c")) ++include_dirs = [os.path.join(os.getenv('EBROOTQHULL'), 'include', 'libqhull')] ++library_dirs = [os.path.join(os.getenv('EBROOTQHULL'), 'lib')] ++sources = [] + if sys.platform.strip() == "darwin": + include_dirs += glob.glob(os.path.join("src", "fmemopen")) + sources += glob.glob(os.path.join("src", "fmemopen", "*.c")) + extension = Extension('pyhull._pyhull', + include_dirs=include_dirs, +- sources=[os.path.join(src_dir, '_pyhull.c')] + sources) ++ library_dirs=library_dirs, ++ libraries=['qhull'], ++ sources=[os.path.join(src_dir, '_pyhull.c')] + sources, ++ ) + + long_description = """ + Pyhull is a Python wrapper to Qhull (http://www.qhull.org/) for the diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb new file mode 100644 index 0000000000000000000000000000000000000000..5534c8acd72190eb46a779eb1c74300f8b0d2443 --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9-gmatteo-20150407.eb @@ -0,0 +1,39 @@ +easyblock = "PythonPackage" + +name = 'pymatgen' +version = '3.0.13' + +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': '2015a'} + +commit = 'd9b9a17' +extrasuff = 'gmatteo-20150407' + +source_urls = ['https://github.com/gmatteo/pymatgen/archive/%s.tar.gz#' % commit] +sources = ['%%(name)s-%%(version)s-%s.tar.gz' % extrasuff] +checksums = ['461ad0f8bb8109f547dc3b708240f85f'] + +python = 'Python' +pythonversion = '2.7.9' + +versionsuffix = '-%s-%s-%s' % (python, pythonversion, extrasuff) + +dependencies = [ + (python, pythonversion), + ('spglib', '1.7.3'), +] + +py_short_ver = '.'.join(pythonversion.split('.')[0:2]) +pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) + +sanity_check_paths = { + 'files': ['bin/pmg', 'bin/ipmg', + ("%s-%%(version)s-py%s.egg" % (pylibdir, py_short_ver), + "%s-%%(version)s-py%s-linux-x86_64.egg" % (pylibdir, py_short_ver))], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..31bebaefdd2aa1f2db5ee1525ba16595109080d6 --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-3.0.13-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,35 @@ +easyblock = "PythonPackage" + +name = 'pymatgen' +version = '3.0.13' + +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': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('spglib', '1.7.3'), +] + +py_short_ver = '.'.join(pythonversion.split('.')[0:2]) +pylibdir = "lib/python%s/site-packages/%s" % (py_short_ver, name) + +sanity_check_paths = { + 'files': ['bin/pmg', 'bin/ipmg', + ("%s-%%(version)s-py%s.egg" % (pylibdir, py_short_ver), + "%s-%%(version)s-py%s-linux-x86_64.egg" % (pylibdir, py_short_ver))], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..27ca7fc128c87d64d772124c23f496c83b48b0d2 --- /dev/null +++ b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'pysqlite' +version = '2.6.3' + +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': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SQLite', '3.8.8.1'), # also dependency for Python itself +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s%%(version_major)s' % pyshortver], +} + +options = {'modulename': '%(name)s%(version_major)s'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..cbbee774d89dd7763e7d1b6f2967d2ff33356c28 --- /dev/null +++ b/easybuild/easyconfigs/p/pysqlite/pysqlite-2.6.3-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'pysqlite' +version = '2.6.3' + +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': 'intel', 'version': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pyver = '2.7.9' +pyshortver = '.'.join(pyver.split('.')[:2]) +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('SQLite', '3.8.8.1'), # also dependency for Python itself +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/%%(name)s%%(version_major)s' % pyshortver], +} + +options = {'modulename': '%(name)s%(version_major)s'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 2643e2c09c934b3913b5ff863bba2605323d471c..ee4f9a4c40f156693e3a5fe2cedb8398a7801ecf 100644 --- a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -10,18 +10,17 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True, 'usempi': True} source_urls = ["https://launchpad.net/python-meep/1.4/1.4/+download/"] sources = [SOURCELOWER_TAR] -patches = [ - 'MPI_destructor_1.3.patch' - ] +patches = ['MPI_destructor_1.3.patch'] python = 'Python' pythonver = '2.7.3' versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ('Meep', '1.2'), - ('SWIG', '2.0.4', '-%s-%s' % (python, pythonver)) - ] + (python, pythonver), + ('Meep', '1.2'), +] + +builddependencies = [('SWIG', '2.0.4', '-%s-%s' % (python, pythonver))] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb index 67aaeea480fcd9d91be129f3f7ba7486c3f3609a..562323eb536f9a577814dbb56f3ca67c42117619 100644 --- a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-goolf-1.4.10-Python-2.7.3.eb @@ -10,18 +10,17 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True, 'usempi': True} source_urls = ["https://launchpad.net/python-meep/1.4/1.4/+download/"] sources = [SOURCELOWER_TAR] -patches = [ - 'MPI_destructor_1.3.patch' - ] +patches = ['MPI_destructor_1.3.patch'] python = 'Python' pythonver = '2.7.3' versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ('Meep', '1.2'), - ('SWIG', '2.0.4', '-%s-%s' % (python, pythonver)) - ] + (python, pythonver), + ('Meep', '1.2'), +] + +builddependencies = [('SWIG', '2.0.4', '-%s-%s' % (python, pythonver))] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb index dccd4207fd04e8b69dff1912ea3250ad384786ee..afe2d60a9bdfb90c75399c3ccecda1137250d4d3 100644 --- a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-ictce-4.0.6-Python-2.7.3.eb @@ -10,18 +10,17 @@ toolchainopts = {'pic': True, 'opt': True, 'optarch': True, 'usempi': True} source_urls = ["https://launchpad.net/python-meep/1.4/1.4/+download/"] sources = [SOURCELOWER_TAR] -patches = [ - 'MPI_destructor_1.3.patch' - ] +patches = ['MPI_destructor_1.3.patch'] python = 'Python' pythonver = '2.7.3' versionsuffix = '-%s-%s' % (python, pythonver) dependencies = [ - (python, pythonver), - ('Meep', '1.2'), - ('SWIG', '2.0.4', '-%s-%s' % (python, pythonver)) - ] + (python, pythonver), + ('Meep', '1.2'), +] + +builddependencies = [('SWIG', '2.0.4', '-%s-%s' % (python, pythonver))] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..bfb66e3979bc5d2b6c851647e501c167b0b075f9 --- /dev/null +++ b/easybuild/easyconfigs/p/python-meep/python-meep-1.4.2-intel-2015a-Python-2.7.9-Meep-1.3.eb @@ -0,0 +1,28 @@ +name = 'python-meep' +version = '1.4.2' + +homepage = 'https://code.launchpad.net/python-meep' +description = """Python wrapper for the Meep FDTD solver.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True, 'usempi': True} + +source_urls = ["https://launchpad.net/python-meep/1.4/1.4/+download/"] +sources = [SOURCELOWER_TAR] + +patches = ['MPI_destructor_1.3.patch'] + +python = 'Python' +pythonver = '2.7.9' +meep = 'Meep' +meepver = '1.3' +versionsuffix = '-%s-%s-%s-%s' % (python, pythonver, meep, meepver) + +dependencies = [ + (python, pythonver), + (meep, meepver), +] + +builddependencies = [('SWIG', '2.0.12', '-%s-%s' % (python, pythonver))] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb index 9aa673f99d68812c56f9a914354631b02ef3726b..dd5a337d1f1e054a3faf4b11e511b2f3e95fc4c4 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-ictce-7.1.2.eb @@ -24,4 +24,8 @@ sanity_check_paths = { 'dirs': [], } +modextrapaths = { + 'CPATH': ['qhull/include'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb index 35f7fe3a7216c8e173c56b6f8b5d3a91efea132b..188d2a929cf42ff1542fdc71ba7cda856d2d4797 100644 --- a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2014b.eb @@ -24,4 +24,8 @@ sanity_check_paths = { 'dirs': [], } +modextrapaths = { + 'CPATH': ['qhull/include'], +} + moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d32af2c6540224508acf563247fcfea61264f422 --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2012.1-intel-2015a.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2012.1' + +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': '2015a'} + +sources = ['%(namelower)s-%(version)s-src.tgz'] +source_urls = ['http://www.qhull.org/download/'] + +patches = ['Qhull-2012.1-intel-fix.patch'] + +builddependencies = [('CMake', '3.2.1', '', ('GCC', '4.9.2'))] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull.so'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb index feb10d4a75d6bb0dda9c1a6efdb1c0ca87c60835..b6405c19b67e256ca1ed16ae9201f9bb2ba07531 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goalf-1.1.0-no-OFED.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb index e8472dac116c8b9a467210f1980b37d0f16f03c5..54ce3a579116ca6d7177630df94edcc586269834 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-gompi-1.4.12-no-OFED.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'gompi', 'version': '1.4.12-no-OFED'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb index c489c5aa682dc189801d00ca78badd7605f47344..7ff79c377b5198a587e9dc201c0e58d95c22a62a 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.4.10.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goolf', 'version': '1.4.10'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..f353838078f048fb559a78b277cef22c148d331c --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-goolf-1.5.14.eb @@ -0,0 +1,17 @@ +name = 'Qt' +version = '4.8.4' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'goolf', 'version': '1.5.14'} + +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'] + +dependencies = [('GLib', '2.34.3')] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb index 4a7a10534b010eb44940b5c9b222ccc771571d71..327564fbd37590ead581dacbcb8d8ae43e6b4c91 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.0.6.eb @@ -1,15 +1,15 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '4.0.6'} toolchainopts = {'lowopt': True} # use -O1 source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb index a411477c0b4a84ffa9789a5b47ee2c5ea1822563..1bfd983e7ea37100374862fce292afac457e637c 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-4.1.13.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb index 3c0ae0a9af0e5c4e53a5345aa2721d80a94d6b7c..3644b946c0012a29bf16e5db620a715058efb1bd 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.4-ictce-5.3.0.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.4' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '5.3.0'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb index 7569a7cd7bfeabf0f8b1b45e509cd00ac2b78270..6abe0d811d8c00c835f93de23f247811415d9769 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-gmpolf-1.4.8.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.5' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'gmpolf', 'version': '1.4.8'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb index d39e90c9e46e3001311fb5366759aca6da0491b0..7bcfcdfee8aa4c73f770b512c2d457e0df2a0369 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-goolf-1.5.14.eb @@ -1,12 +1,15 @@ name = 'Qt' version = '4.8.5' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goolf', 'version': '1.5.14'} -source_urls = ['http://download.qt-project.org/official_releases/qt/4.8/4.8.5/'] +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'] dependencies = [('GLib', '2.34.3')] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb index 312d6b1990967b49de842fb1ab05f316e7b8cd8f..bfd0e1cd2f9a992b5073639f0fd9bf63b809d3ea 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.5-ictce-4.1.13.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.5' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'ictce', 'version': '4.1.13'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..0bfab5d015d1905fb336ac9a6d5af9dba426fb6a --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-foss-2015a.eb @@ -0,0 +1,17 @@ +name = 'Qt' +version = '4.8.6' + +homepage = 'http://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'foss', 'version': '2015a'} + +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'] + +dependencies = [('GLib', '2.42.1')] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-goolf-1.5.14.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-goolf-1.5.14.eb index 6435694c00b4b278b079abc8dfe17f99b1088b54..a829af981d63808ed2586e5de22dc5a824b9ee63 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-goolf-1.5.14.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.6' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'goolf', 'version': '1.5.14'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb index 1c0c56d935b9a88c00e6de0793f06c3de8ade6d9..61b425c25a0f0433ee83b57b89f57e8a0f21dd17 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2014b.eb @@ -1,14 +1,14 @@ name = 'Qt' version = '4.8.6' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'intel', 'version': '2014b'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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'] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb index aa253ef5eb61b7029bee2827281a37e20c4ec584..1ab132124a8bd7aea8a1cb8ad1d8504745434a20 100644 --- a/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6-intel-2015a.eb @@ -1,18 +1,21 @@ name = 'Qt' version = '4.8.6' -homepage = 'http://qt-project.org/' +homepage = 'http://qt.io/' description = "Qt is a comprehensive cross-platform C++ application framework." toolchain = {'name': 'intel', 'version': '2015a'} source_urls = [ - 'http://origin.releases.qt-project.org/qt4/source/', - 'http://master.qt-project.org/archive/qt/%(version_major_minor)s/%(version)s/' + '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-4.8.6_icc-qUnused.patch'] +patches = [ + 'Qt-%(version)s_icc-qUnused.patch', + 'Qt-%(version)s_phonon-export.patch', +] dependencies = [('GLib', '2.40.0')] diff --git a/easybuild/easyconfigs/q/Qt/Qt-4.8.6_phonon-export.patch b/easybuild/easyconfigs/q/Qt/Qt-4.8.6_phonon-export.patch new file mode 100644 index 0000000000000000000000000000000000000000..4170411ac114fdf21b10742f9aa496b493a89172 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt/Qt-4.8.6_phonon-export.patch @@ -0,0 +1,15 @@ +fixed for error "undefined reference to `vtable for Phonon::ObjectDescriptionModel<(Phonon::ObjectDescriptionType)0>'" +that occurs (only) on some systems (e.g. RHEL6/Sandy Bridge) +based on https://forum.qt.io/topic/35044/build-failure-4-8-5-on-mac-with-phonon/9 +author: Kenneth Hoste (HPC-UGent) +--- qt-everywhere-opensource-src-4.8.6/src/3rdparty/phonon/phonon/objectdescriptionmodel.h.orig 2015-06-22 23:18:54.723573581 +0300 ++++ qt-everywhere-opensource-src-4.8.6/src/3rdparty/phonon/phonon/objectdescriptionmodel.h 2015-06-22 23:19:16.902399019 +0300 +@@ -141,7 +141,7 @@ + + /* Required to ensure template class vtables are exported on both symbian + and existing builds. */ +-#if (defined(Q_OS_SYMBIAN) && defined(Q_CC_RVCT)) || defined(Q_CC_CLANG) ++#if (defined(Q_OS_SYMBIAN) && defined(Q_CC_RVCT)) || defined(Q_CC_CLANG) || defined(Q_CC_INTEL) + // RVCT compiler (2.2.686) requires the export declaration to be on the class to export vtables + // MWC compiler works both ways + // GCCE compiler is unknown (it can't compile QtCore yet) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb index 9409f95fc206cd19a6e196e4177f62b5e4d9200b..d000d6ec7f80957c94aa1346e31e5480b3f1790d 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb index 4a03ccc94bd4e3b3aaff407cb3c90d8d7e7e0949..a34afc570a3cbd1764e03b523fae1b6489b3b583 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goalf-1.1.0-no-OFED.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb index d97dae5c5d8dd5c07024fde7d92ab102129c0b7d..5ef2e6d1b1259e0ff9d2cfaef8185595504f11b2 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb index d7fb61f42cb35e3be57acdace48cca8609ec54ab..1e036026dae443c9e666fc69773b46cde049838a 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-goolf-1.4.10.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = ['yambo-3.2.5_fix-objects-files.patch'] diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb index 04f547b28a8e665ed375dcd49da27afa4509a9c4..464f26364720517fb45c03ef4514efdb3d95a354 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb index 479e526fb358b8c079887fe5c8316cf5665d683b..cd0fac60cb1d3a870bf4f02d2a78eb9108afdcfd 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-4.0.6.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb index 1b9a405ed89847f871fa0c890342dc25af73533c..9533b73dfd3f2bae3abb7e33f8d6eb663cbd2a9e 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb index 5740815aa1c84140baf6e0da8cfaf4a064d38aff..b3212736f0f818b3149ac2340a4fd42cfab244e4 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.3.0.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb index bf87cf39af9adacab29cce8aa61d4f3cd13ccf63..ae347ad0bd17c206cd887e1aa73880c5f050de2e 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0-hybrid.eb @@ -30,9 +30,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = [ diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb index a341ebad381bd60aae7be259ee6334a7407eda82..2a054ef2d33c93919abe85746ea69a0c1753280f 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-5.0.2-ictce-5.5.0.eb @@ -29,9 +29,8 @@ missing_sources = [ 'xspectra-5.0.2.tar.gz', # nowhere to be found ] source_urls = [ + 'http://files.qe-forge.org/index.php?file=', # all sources, except espresso*.tar.gz 'http://www.qe-forge.org/gf/download/frsrelease/116/403/', # espresso-5.0.2.tar.gz - 'http://www.qe-forge.org/gf/download/frsrelease/64/97/', # wannier90-1.2.tar.gz - 'http://files.qe-forge.org/index.php?file=', # others ] patches = [ diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..cfe8ae2e84fd695aeeb2b7cda35b7376d983108a --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-goolf-1.7.20-R-3.2.0.eb @@ -0,0 +1,140 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.1' +rver = '3.2.0' +versionsuffix = '-R-%s' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [('R', rver)] + +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://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# 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', '0.14.0', bioconductor_options), + ('Biobase', '2.28.0', bioconductor_options), + ('S4Vectors', '0.6.3', bioconductor_options), + ('IRanges', '2.2.5', bioconductor_options), + ('GenomeInfoDb', '1.4.1', bioconductor_options), + ('AnnotationDbi', '1.30.1', bioconductor_options), + ('XVector', '0.8.0', bioconductor_options), + ('zlibbioc', '1.14.0', bioconductor_options), + ('Biostrings', '2.36.2', bioconductor_options), + ('GenomicRanges', '1.20.5', bioconductor_options), + ('Rsamtools', '1.20.4', bioconductor_options), + ('lambda.r', '1.1.7', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.1', ext_options), + ('BiocParallel', '1.2.9', bioconductor_options), + ('GenomicAlignments', '1.4.1', bioconductor_options), + ('ShortRead', '1.26.0', bioconductor_options), + ('graph', '1.46.0', bioconductor_options), + ('affyio', '1.36.0', bioconductor_options), + ('BiocInstaller', '1.18.4', bioconductor_options), + ('preprocessCore', '1.30.0', bioconductor_options), + ('affy', '1.46.1', bioconductor_options), + ('GO.db', '3.1.2', bioconductor_options), + ('limma', '3.24.14', bioconductor_options), + ('RBGL', '1.44.0', bioconductor_options), + ('org.Hs.eg.db', '3.1.2', bioconductor_options), + ('AnnotationForge', '1.10.1', bioconductor_options), + ('KEGG.db', '3.1.2', bioconductor_options), + ('annaffy', '1.40.0', bioconductor_options), + ('gcrma', '2.40.0', bioconductor_options), + ('oligoClasses', '1.30.0', bioconductor_options), + ('edgeR', '3.10.2', bioconductor_options), + ('PFAM.db', '3.1.2', bioconductor_options), + ('perm', '1.0-0.0', ext_options), + ('baySeq', '2.2.0', bioconductor_options), + ('qvalue', '2.0.0', bioconductor_options), + ('impute', '1.42.0', bioconductor_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.22.0', bioconductor_options), + ('hgu133plus2.db', '3.1.3', bioconductor_options), + ('illuminaio', '0.10.0', bioconductor_options), + ('rtracklayer', '1.28.6', bioconductor_options), + ('biomaRt', '2.24.0', bioconductor_options), + ('GenomicFeatures', '1.20.1', bioconductor_options), + ('bumphunter', '1.8.0', bioconductor_options), + ('multtest', '2.24.0', bioconductor_options), + ('siggenes', '1.42.0', bioconductor_options), + ('DynDoc', '1.46.0', bioconductor_options), + ('genoset', '1.22.0', bioconductor_options), + ('NOISeq', '2.12.0', bioconductor_options), + ('Rgraphviz', '2.12.0', bioconductor_options), + ('RNASeqPower', '1.8.0', bioconductor_options), + ('annotate', '1.46.1', bioconductor_options), + ('GSEABase', '1.30.2', bioconductor_options), + ('genefilter', '1.50.0', bioconductor_options), + ('Category', '2.34.2', bioconductor_options), + ('GOstats', '2.34.0', bioconductor_options), + ('BSgenome', '1.36.3', bioconductor_options), + ('VariantAnnotation', '1.14.6', bioconductor_options), + ('biovizBase', '1.16.0', bioconductor_options), + ('OrganismDbi', '1.10.0', bioconductor_options), + ('ggbio', '1.16.1', bioconductor_options), + ('geneplotter', '1.46.0', bioconductor_options), + ('DESeq2', '1.8.1', bioconductor_options), + ('ReportingTools', '2.8.0', bioconductor_options), + ('affycoretools', '1.40.5', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.1.2', bioconductor_options), + ('Homo.sapiens', '1.1.2', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), + ('AgiMicroRna', '2.18.0', bioconductor_options), + ('GenomeGraphs', '1.28.0', bioconductor_options), + ('geneLenDataBase', '1.4.0', bioconductor_options), + ('goseq', '1.20.0', bioconductor_options), + ('KEGGREST', '1.8.0', bioconductor_options), + ('KEGGgraph', '1.26.0', bioconductor_options), + ('KEGGprofile', '1.10.0', bioconductor_options), + ('GEOquery', '2.34.0', bioconductor_options), + ('minfi', '1.14.0', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), + ('methylumi', '2.14.0', bioconductor_options), + ('lumi', '2.20.2', bioconductor_options), + ('widgetTools', '1.46.0', bioconductor_options), + ('tkWidgets', '1.46.0', bioconductor_options), + ('Mfuzz', '2.28.0', bioconductor_options), + ('maSigPro', '1.40.0', bioconductor_options), + ('SPIA', '2.20.0', bioconductor_options), + ('Gviz', '1.12.1', bioconductor_options), + ('cummeRbund', '2.10.0', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..1f51e42d0121918da62eb6d5449ad7ed46b05fa7 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.1-intel-2015a-R-3.2.1.eb @@ -0,0 +1,140 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.1' +rver = '3.2.1' +versionsuffix = '-R-%s' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [('R', rver)] + +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://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.1/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# 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', '0.14.0', bioconductor_options), + ('Biobase', '2.28.0', bioconductor_options), + ('S4Vectors', '0.6.3', bioconductor_options), + ('IRanges', '2.2.5', bioconductor_options), + ('GenomeInfoDb', '1.4.1', bioconductor_options), + ('AnnotationDbi', '1.30.1', bioconductor_options), + ('XVector', '0.8.0', bioconductor_options), + ('zlibbioc', '1.14.0', bioconductor_options), + ('Biostrings', '2.36.2', bioconductor_options), + ('GenomicRanges', '1.20.5', bioconductor_options), + ('Rsamtools', '1.20.4', bioconductor_options), + ('lambda.r', '1.1.7', ext_options), + ('futile.options', '1.0.0', ext_options), + ('futile.logger', '1.4.1', ext_options), + ('BiocParallel', '1.2.9', bioconductor_options), + ('GenomicAlignments', '1.4.1', bioconductor_options), + ('ShortRead', '1.26.0', bioconductor_options), + ('graph', '1.46.0', bioconductor_options), + ('affyio', '1.36.0', bioconductor_options), + ('BiocInstaller', '1.18.4', bioconductor_options), + ('preprocessCore', '1.30.0', bioconductor_options), + ('affy', '1.46.1', bioconductor_options), + ('GO.db', '3.1.2', bioconductor_options), + ('limma', '3.24.14', bioconductor_options), + ('RBGL', '1.44.0', bioconductor_options), + ('org.Hs.eg.db', '3.1.2', bioconductor_options), + ('AnnotationForge', '1.10.1', bioconductor_options), + ('KEGG.db', '3.1.2', bioconductor_options), + ('annaffy', '1.40.0', bioconductor_options), + ('gcrma', '2.40.0', bioconductor_options), + ('oligoClasses', '1.30.0', bioconductor_options), + ('edgeR', '3.10.2', bioconductor_options), + ('PFAM.db', '3.1.2', bioconductor_options), + ('perm', '1.0-0.0', ext_options), + ('baySeq', '2.2.0', bioconductor_options), + ('qvalue', '2.0.0', bioconductor_options), + ('impute', '1.42.0', bioconductor_options), + ('samr', '2.0', ext_options), + ('DEGseq', '1.22.0', bioconductor_options), + ('hgu133plus2.db', '3.1.3', bioconductor_options), + ('illuminaio', '0.10.0', bioconductor_options), + ('rtracklayer', '1.28.6', bioconductor_options), + ('biomaRt', '2.24.0', bioconductor_options), + ('GenomicFeatures', '1.20.1', bioconductor_options), + ('bumphunter', '1.8.0', bioconductor_options), + ('multtest', '2.24.0', bioconductor_options), + ('siggenes', '1.42.0', bioconductor_options), + ('DynDoc', '1.46.0', bioconductor_options), + ('genoset', '1.22.0', bioconductor_options), + ('NOISeq', '2.12.0', bioconductor_options), + ('Rgraphviz', '2.12.0', bioconductor_options), + ('RNASeqPower', '1.8.0', bioconductor_options), + ('annotate', '1.46.1', bioconductor_options), + ('GSEABase', '1.30.2', bioconductor_options), + ('genefilter', '1.50.0', bioconductor_options), + ('Category', '2.34.2', bioconductor_options), + ('GOstats', '2.34.0', bioconductor_options), + ('BSgenome', '1.36.3', bioconductor_options), + ('VariantAnnotation', '1.14.6', bioconductor_options), + ('biovizBase', '1.16.0', bioconductor_options), + ('OrganismDbi', '1.10.0', bioconductor_options), + ('ggbio', '1.16.1', bioconductor_options), + ('geneplotter', '1.46.0', bioconductor_options), + ('DESeq2', '1.8.1', bioconductor_options), + ('ReportingTools', '2.8.0', bioconductor_options), + ('affycoretools', '1.40.5', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.1.2', bioconductor_options), + ('Homo.sapiens', '1.1.2', bioconductor_options), + ('BSgenome.Hsapiens.UCSC.hg19', '1.4.0', bioconductor_options), + ('AgiMicroRna', '2.18.0', bioconductor_options), + ('GenomeGraphs', '1.28.0', bioconductor_options), + ('geneLenDataBase', '1.4.0', bioconductor_options), + ('goseq', '1.20.0', bioconductor_options), + ('KEGGREST', '1.8.0', bioconductor_options), + ('KEGGgraph', '1.26.0', bioconductor_options), + ('KEGGprofile', '1.10.0', bioconductor_options), + ('GEOquery', '2.34.0', bioconductor_options), + ('minfi', '1.14.0', bioconductor_options), + ('FDb.InfiniumMethylation.hg19', '2.2.0', bioconductor_options), + ('methylumi', '2.14.0', bioconductor_options), + ('lumi', '2.20.2', bioconductor_options), + ('widgetTools', '1.46.0', bioconductor_options), + ('tkWidgets', '1.46.0', bioconductor_options), + ('Mfuzz', '2.28.0', bioconductor_options), + ('maSigPro', '1.40.0', bioconductor_options), + ('SPIA', '2.20.0', bioconductor_options), + ('Gviz', '1.12.1', bioconductor_options), + ('cummeRbund', '2.10.0', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocInstaller', 'GenomicFeatures'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..aa48ed3b8142fba4c91dd7a6b160279657cd6de6 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-devtools/R-bundle-devtools-20150520-intel-2015a-R-3.1.3.eb @@ -0,0 +1,49 @@ +easyblock = 'Bundle' + +name = 'R-bundle-devtools' +version = '20150520' +rver = '3.1.3' +versionsuffix = '-R-%s' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [ + ('R', rver), + ('R-bundle-extra', '20150323', '-R-%s' % rver), +] + +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)s_%(version)s.tar.gz' +} + +# !! order of packages is important !! +exts_list = [ + ('memoise', '0.2.1', ext_options), + ('whisker', '0.3-2', ext_options), + ('rstudioapi', '0.3.1', ext_options), + ('roxygen2', '4.1.1', ext_options), + ('git2r', '0.10.1', ext_options), + ('rversions', '1.0.0', ext_options), + ('devtools', '1.8.0', ext_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['devtools'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..1bde4e9f5d00a790d810f00df655a78076d4c28e --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-extra/R-bundle-extra-20150323-intel-2015a-R-3.1.3.eb @@ -0,0 +1,100 @@ +easyblock = 'Bundle' + +name = 'R-bundle-extra' +version = '20150323' +rver = '3.1.3' +versionsuffix = '-R-%s' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [ + ('R', rver), + ('cURL', '7.41.0'), + ('libxml2', '2.9.2'), +] + +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 packages have a different download url +bioconductor_options = { + 'source_urls': [ + 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', + ], + 'source_tmpl': name_tmpl, +} + +# !! order of packages is important !! +exts_list = [ + ('RCurl', '1.95-4.5', ext_options), # requires cURL + ('XML', '3.98-1.1', ext_options), # requires libxml2 + # extensions below require one or more extensions that have an external dependency listed above + ('picante', '1.6-2', ext_options), + ('spacodiR', '0.13.0115', ext_options), + ('picante', '1.6-2', ext_options), + ('httr', '0.6.1', ext_options), + ('tkWidgets', '1.44.0', bioconductor_options), + ('Mfuzz', '2.26.0', bioconductor_options), + ('maSigPro', '1.38.0', bioconductor_options), + ('rtracklayer', '1.26.3', bioconductor_options), + ('BSgenome', '1.34.1', bioconductor_options), + ('GEOquery', '2.32.0', bioconductor_options), + ('biomaRt', '2.22.0', bioconductor_options), + ('annotate', '1.44.0', bioconductor_options), + ('GSEABase', '1.28.0', bioconductor_options), + ('genefilter', '1.48.1', bioconductor_options), + ('Category', '2.32.0', bioconductor_options), + ('GOstats', '2.32.0', bioconductor_options), + ('geneplotter', '1.44.0', bioconductor_options), + ('DESeq2', '1.6.3', bioconductor_options), + ('GenomicFeatures', '1.18.7', bioconductor_options), + ('VariantAnnotation', '1.12.9', bioconductor_options), + ('biovizBase', '1.14.1', bioconductor_options), + ('OrganismDbi', '1.8.1', bioconductor_options), + ('ggbio', '1.14.0', bioconductor_options), + ('ReportingTools', '2.6.0', bioconductor_options), + ('affycoretools', '1.38.0', bioconductor_options), + ('AgiMicroRna', '2.16.0', bioconductor_options), + ('DESeq', '1.18.0', bioconductor_options), + ('GenomeGraphs', '1.26.0', bioconductor_options), + ('geneLenDataBase', '1.1.1', bioconductor_options), + ('goseq', '1.18.0', bioconductor_options), + ('TxDb.Hsapiens.UCSC.hg19.knownGene', '3.0.0', bioconductor_options), + ('Homo.sapiens', '1.1.2', bioconductor_options), + ('KEGGgraph', '1.24.0', bioconductor_options), + ('KEGGREST', '1.6.4', bioconductor_options), + ('KEGGprofile', '1.8.2', bioconductor_options), + ('minfi', '1.12.0', bioconductor_options), + ('methylumi', '2.12.0', bioconductor_options), + ('lumi', '2.18.0', bioconductor_options), + ('Gviz', '1.10.11', bioconductor_options), + ('methyAnalysis', '1.8.0', bioconductor_options), + ('pathview', '1.6.0', bioconductor_options), + ('SPIA', '2.18.0', bioconductor_options), + ('cummeRbund', '2.8.2', bioconductor_options), + ('spliceR', '1.8.0', bioconductor_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['RCurl', 'XML', 'spliceR'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..dd2dee5fb47b0b515cc7cff2c35bd95bfdffbd0c --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-pbd/R-bundle-pbd-20150605-intel-2015a-R-3.1.3.eb @@ -0,0 +1,49 @@ +easyblock = 'Bundle' + +name = 'R-bundle-pbd' +version = '20150605' +rver = '3.1.3' +versionsuffix = '-R-%s' % rver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +# these are extensions for R +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +dependencies = [ + ('R', rver), +] + +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 !! +exts_list = [ + ('pbdMPI', '0.2-5', ext_options), + ('pbdSLAP', '0.2-0', ext_options), + ('pbdBASE', '0.2-3', dict(ext_options.items() + [('patches', ['pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch'])])), + ('pbdDMAT', '0.2-3', ext_options), + ('pbdDEMO', '0.2-0', ext_options), + ('pmclust', '0.1-6', ext_options), + ('EMCluster', '0.2-4', ext_options), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['EMCluster', 'pbdBASE', 'pbdDEMO', 'pbdDMAT', 'pbdMPI', 'pbdSLAP', 'pmclust'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R-bundle-pbd/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch b/easybuild/easyconfigs/r/R-bundle-pbd/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch new file mode 100644 index 0000000000000000000000000000000000000000..34eaf4da137f5c6683481e276bfdfb569dd2d5f8 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-pbd/pbdBASE-02.3-0_ignore-BI_COMM_GLOBAL-for-intel-mpi.patch @@ -0,0 +1,45 @@ +# Add support for intel mpi by removing references to BI_COMM_WORLD +# BI_COMM_WORLD just appears to shadow MPI_COMM_WORLD. +--- pbdBASE.orig/src/export_blacs/pkg_tools.c 2015-06-02 15:25:57.705288000 +0200 ++++ pbdBASE/src/export_blacs/pkg_tools.c 2015-06-02 15:25:29.470539000 +0200 +@@ -25,7 +25,9 @@ + BLACS_APTS.BI_AuxBuff = &BI_AuxBuff; + BLACS_APTS.BI_MyContxts = BI_MyContxts; + BLACS_APTS.BI_SysContxts = BI_SysContxts; ++#ifndef __INTEL_COMPILER + BLACS_APTS.BI_COMM_WORLD = BI_COMM_WORLD; ++#endif + BLACS_APTS.BI_Stats = BI_Stats; + + #if (BLACS_APTS_DEBUG & 1) == 1 +@@ -44,7 +46,9 @@ + BI_AuxBuff.nAops, BI_AuxBuff.N); + REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, + &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); ++#ifndef __INTEL_COMPILER + REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, ++#endif + BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); + REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, + BI_Stats); +@@ -89,7 +93,9 @@ + + BI_MyContxts = (BLACSCONTEXT**) BLACS_APTS_ptr->BI_MyContxts; + BI_SysContxts = (MPI_Comm*) BLACS_APTS_ptr->BI_SysContxts; ++#ifndef __INTEL_COMPILER + BI_COMM_WORLD = (int*) BLACS_APTS_ptr->BI_COMM_WORLD; ++#endif + BI_Stats = (MPI_Status*) BLACS_APTS_ptr->BI_Stats; + + #if (BLACS_APTS_DEBUG & 1) == 1 +@@ -109,7 +115,9 @@ + REprintf(" %s (a): %x %x %x %x %x.\n", __FILE__, &BI_MaxNCtxt, + &BI_MaxNSysCtxt, &BI_Iam, &BI_Np, &BI_AuxBuff); + REprintf(" %s (a): %x %x %x %x.\n", __FILE__, BI_ReadyB, ++#ifndef __INTEL_COMPILER + BI_ActiveQ, *BI_MyContxts, BI_COMM_WORLD); ++#endif + REprintf(" %s (a): %x %x.\n", __FILE__, BI_SysContxts, + BI_Stats); + } + diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/r/R/R-2.15.2-goalf-1.1.0-no-OFED.eb index 8468c6029d48b95356a6ec5b4b69077851ab3c3d..d91d0ca1fd74fcc71ba25fec3c243c3ee402447e 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-goalf-1.1.0-no-OFED.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb b/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb index 84d3f3e99e4cd3721ffb94da5b88340466aadc5a..517c6d157a2c637e40a2e872c3e60536a210b76f 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-goolf-1.4.10.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.10.eb b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.10.eb index 70126d1ce646d1164f3a3db5dce15962cbda6fc4..b2152142eb75d140691522fdb1639a06430174cd 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.10.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.10.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.6.eb b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.6.eb index 3a90cc17ebd491fb937ada5615441ffba09e2fd8..9414cfc682214bbba0707101af740483bbf9df0f 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-4.0.6.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb index 201aa6b6366582083a0ac2abbad003ac17555e93..4b3f70cab0d2d0b03ec611e5c23b346674bed388 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.2-ictce-5.3.0.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.11/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.3-goalf-1.1.0-no-OFED.eb b/easybuild/easyconfigs/r/R/R-2.15.3-goalf-1.1.0-no-OFED.eb index 65f22fa5a8ace751880dbc16022488cfe8afd763..4434fbdf2a657a68b6b66962ad07ed079d3b5024 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.3-goalf-1.1.0-no-OFED.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.3-goalf-1.1.0-no-OFED.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb b/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb index 2672165c5022be2bbea20fbe410c8ebc1e3897a4..174451bf4401e1e3127f1302e5c91da09aa6e283 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.3-goolf-1.4.10.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.3-ictce-4.1.13.eb b/easybuild/easyconfigs/r/R/R-2.15.3-ictce-4.1.13.eb index 2f2b2a553e91701f77a98285b8b62f8adceccbe1..cc29570d01a9016120d92e83e38fb77fc0fb36f2 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.3-ictce-4.1.13.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.3-ictce-4.1.13.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb b/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb index 2d510cfe36e70f1da082d2aa94f96b41608e54e5..4b201ba94793d80b7e983ea2c5f46def100dfe38 100644 --- a/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/r/R/R-2.15.3-ictce-5.3.0.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.12/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb b/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb index 3bc73c713b4d65c5d57e77dcb5f694091a03d544..5280f5e5c7c20071d99185a090142dbb754d15b0 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.2-goolf-1.4.10.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.13/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.13/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } diff --git a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb index 580cc3effdd735e0ff34a3693da1c7436b984413..8fababc35894f07a670966ee06bee0af35d74d1a 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.3.0.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.13/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.13/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } diff --git a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb index 1bda6f96bcf6640fa85698b5894b5ee74265e7c1..549134c6cc0531791eabfa4078c1a54a69a26bc3 100644 --- a/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/R/R-3.0.2-ictce-5.5.0.eb @@ -41,7 +41,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.13/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.13/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } diff --git a/easybuild/easyconfigs/r/R/R-3.1.0-ictce-5.5.0.eb b/easybuild/easyconfigs/r/R/R-3.1.0-ictce-5.5.0.eb index ba677bcf6dea4a02e7bac76203c7b364505ff8aa..e7c9c708cc66cb7322acc0a8e520e58144ceff2d 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.0-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.0-ictce-5.5.0.eb @@ -31,7 +31,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.14/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.14/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-3.1.1-intel-2014b.eb b/easybuild/easyconfigs/r/R/R-3.1.1-intel-2014b.eb index 37633fc50a2375c6b9a9c1850940b746fc15afe0..91ba061891d1a3ded8ff797335d435c0d2545196 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.1-intel-2014b.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.1-intel-2014b.eb @@ -32,7 +32,9 @@ ext_options = { } # Bioconductor packages have a different download url bioconductor_options = { - 'source_urls': ['http://www.bioconductor.org/packages/2.14/bioc/src/contrib/'], + 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/2.14/bioc/src/contrib/'], 'source_tmpl': name_tmpl, } # !! order of packages is important !! diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb index e60a4bb6fd1f0ddb298d3ada897ece1647772d38..bcd67f42d0f7f5ca9ee458da04019acf9368bb39 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-foss-2015a.eb @@ -34,6 +34,9 @@ ext_options = { # Bioconductor packages have a different download url bioconductor_options = { 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb b/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb index a73e438a8cdd87d1c1ebdd76c63392bb7ec7333c..467f0009f86710f027c19713434e26b7bfd052eb 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-goolf-1.5.14.eb @@ -34,6 +34,9 @@ ext_options = { # Bioconductor packages have a different download url bioconductor_options = { 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', diff --git a/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb index 99a39db56abaedc1857f6c47d8d73b84966d49ce..813bbd8f5db87fe114bd533379d39acc1a5436f5 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.2-intel-2015a.eb @@ -34,6 +34,9 @@ ext_options = { # Bioconductor packages have a different download url bioconductor_options = { 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb index 6af8bc63b208da9744faf3e49bba98516354873a..d82c3b8db250e2ae6d88b27bc4bd1401e27cd7cd 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-foss-2015a.eb @@ -20,6 +20,8 @@ dependencies = [ ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk ] name_tmpl = '%(name)s_%(version)s.tar.gz' @@ -34,6 +36,9 @@ ext_options = { # Bioconductor packages have a different download url bioconductor_options = { 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', @@ -42,7 +47,7 @@ bioconductor_options = { } # !! order of packages is important !! -# packages updated on January 8th 2015 +# packages updated on January 8th 2015 (last change for Bioconductor: June 25th 2015) exts_list = [ # default libraries, only here to sanity check their presence 'base', @@ -219,7 +224,7 @@ exts_list = [ ('Biobase', '2.26.0', bioconductor_options), ('S4Vectors', '0.4.0', bioconductor_options), ('IRanges', '2.0.1', bioconductor_options), - ('GenomeInfoDb', '1.2.4', bioconductor_options), + ('GenomeInfoDb', '1.2.5', bioconductor_options), ('AnnotationDbi', '1.28.2', bioconductor_options), ('XVector', '0.6.0', bioconductor_options), ('zlibbioc', '1.12.0', bioconductor_options), @@ -308,7 +313,7 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('affyio', '1.34.0', bioconductor_options), - ('BiocInstaller', '1.16.2', bioconductor_options), + ('BiocInstaller', '1.16.5', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), ('affy', '1.44.0', bioconductor_options), ('GO.db', '3.0.0', bioconductor_options), @@ -375,7 +380,12 @@ exts_list = [ ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), ('Rsubread', '1.16.1', bioconductor_options), + ('vegan', '2.2-1', ext_options), # requires Tcl/Tk + ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk + ('forecast', '6.1', ext_options), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), ] moduleclass = 'lang' - diff --git a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb index 6cdafd6edc35d86609fe83777ee2fcc484b5e931..53bd4b075109ffc77b6119b2495460fcea2e8ba0 100644 --- a/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb +++ b/easybuild/easyconfigs/r/R/R-3.1.3-intel-2015a.eb @@ -20,6 +20,8 @@ dependencies = [ ('libpng', '1.6.16'), # for plotting in R ('libjpeg-turbo', '1.4.0'), # for plottting in R ('Java', '1.8.0_25', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk ] name_tmpl = '%(name)s_%(version)s.tar.gz' @@ -34,6 +36,9 @@ ext_options = { # Bioconductor packages have a different download url bioconductor_options = { 'source_urls': [ + 'http://www.bioconductor.org/packages/release/bioc/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/annotation/src/contrib/', + 'http://www.bioconductor.org/packages/release/data/experiment/src/contrib/', 'http://www.bioconductor.org/packages/3.0/bioc/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/annotation/src/contrib/', 'http://www.bioconductor.org/packages/3.0/data/experiment/src/contrib/', @@ -42,7 +47,7 @@ bioconductor_options = { } # !! order of packages is important !! -# packages updated on January 8th 2015 +# packages updated on January 8th 2015 (last change for Bioconductor: June 25th 2015) exts_list = [ # default libraries, only here to sanity check their presence 'base', @@ -219,7 +224,7 @@ exts_list = [ ('Biobase', '2.26.0', bioconductor_options), ('S4Vectors', '0.4.0', bioconductor_options), ('IRanges', '2.0.1', bioconductor_options), - ('GenomeInfoDb', '1.2.4', bioconductor_options), + ('GenomeInfoDb', '1.2.5', bioconductor_options), ('AnnotationDbi', '1.28.2', bioconductor_options), ('XVector', '0.6.0', bioconductor_options), ('zlibbioc', '1.12.0', bioconductor_options), @@ -308,7 +313,7 @@ exts_list = [ ('klaR', '0.6-12', ext_options), ('neuRosim', '0.2-12', ext_options), ('affyio', '1.34.0', bioconductor_options), - ('BiocInstaller', '1.16.2', bioconductor_options), + ('BiocInstaller', '1.16.5', bioconductor_options), ('preprocessCore', '1.28.0', bioconductor_options), ('affy', '1.44.0', bioconductor_options), ('GO.db', '3.0.0', bioconductor_options), @@ -375,6 +380,12 @@ exts_list = [ ('xlsxjars', '0.6.1', ext_options), ('xlsx', '0.5.7', ext_options), ('Rsubread', '1.16.1', bioconductor_options), + ('vegan', '2.2-1', ext_options), # requires Tcl/Tk + ('widgetTools', '1.44.0', bioconductor_options), # requires Tcl/Tk + ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..6cf2221cfdeafcfaa0e081977c48dd57c59b461f --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.0-foss-2015a-bare.eb @@ -0,0 +1,27 @@ +name = 'R' +version = '3.2.0' +versionsuffix = '-bare' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +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', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.7.0_80', '', 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-3.2.0-goolf-1.7.20-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..d8c3392f6ae52d44eb6379aef14887692b8e628c --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20-bare.eb @@ -0,0 +1,27 @@ +name = 'R' +version = '3.2.0' +versionsuffix = '-bare' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +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', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.7.0_80', '', 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-3.2.0-goolf-1.7.20.eb b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..37f178514d9137b6c8cd7cdbcd41fa96b53ad9cc --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.0-goolf-1.7.20.eb @@ -0,0 +1,353 @@ +name = 'R' +version = '3.2.0' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +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', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk + ('cURL', '7.43.0'), # for RCurl + ('libxml2', '2.9.2'), # for XML +] + +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 8th 2015 +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 segfaults (on some systems) when built with goolf/1.7.20? + #('Rmpi', '0.6-5', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-5', ext_options), + ('bit', '1.1-12', ext_options), + ('filehash', '2.2-2', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.7.1', ext_options), + ('bootstrap', '2015.2', ext_options), + ('combinat', '0.0-8', ext_options), + ('deal', '1.2-37', ext_options), + ('fdrtool', '1.2.14', ext_options), + ('formatR', '1.2', ext_options), + ('gtools', '3.4.2', ext_options), + ('gdata', '2.13.3', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.5', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-20', ext_options), + ('mime', '0.3', ext_options), + ('markdown', '0.7.7', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-6', ext_options), + ('mclust', '5.0.1', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.1', ext_options), + ('som', '0.3-5', ext_options), + ('SuppDists', '1.1-9.1', ext_options), + ('stabledist', '0.6-6', ext_options), + ('survivalROC', '1.0.3', ext_options), + ('pspline', '1.0-16', ext_options), + ('timeDate', '3012.100', ext_options), + ('longmemo', '1.0-0', ext_options), + ('ADGofTest', '0.3', ext_options), + ('ade4', '1.7-2', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-2', ext_options), + ('BH', '1.55.0-3', ext_options), + ('brew', '1.0-6', ext_options), + ('Brobdingnag', '1.2-4', ext_options), + ('corpcor', '1.6.7', ext_options), + ('longitudinal', '1.1.11', ext_options), + ('checkmate', '1.5.2', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-2', ext_options), + ('digest', '0.6.8', ext_options), + ('fastmatch', '1.0-4', ext_options), + ('ffbase', '0.11.3', ext_options), + ('iterators', '1.0.7', ext_options), + ('maps', '2.3-9', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.0-1', ext_options), + ('subplex', '1.1-4', ext_options), + ('stringr', '0.6.2', ext_options), + ('evaluate', '0.7', ext_options), + ('logspline', '2.1.5', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.8-3', ext_options), + ('plotrix', '3.5-11', ext_options), + ('randomForest', '4.6-10', ext_options), + ('scatterplot3d', '0.3-35', ext_options), + ('SparseM', '1.6', ext_options), + ('tripack', '1.3-6', ext_options), + ('irace', '1.06', ext_options), + ('rJava', '0.9-6', ext_options), + ('lattice', '0.20-31', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-26', ext_options), + ('Matrix', '1.2-0', ext_options), + ('png', '0.1-7', ext_options), + ('Rcpp', '0.11.5', ext_options), + ('RcppArmadillo', '0.5.000.0', ext_options), + ('plyr', '1.8.2', ext_options), + ('pROC', '1.7.3', ext_options), + ('quadprog', '1.5-5', ext_options), + ('BB', '2014.10-1', ext_options), + ('BBmisc', '1.9', ext_options), + ('fail', '1.2', ext_options), + ('rlecuyer', '0.3-3', ext_options), + ('snow', '0.3-13', ext_options), + ('MASS', '7.3-40', ext_options), + ('tree', '1.0-35', ext_options), + ('pls', '2.4-3', ext_options), + ('class', '7.3-12', ext_options), + ('e1071', '1.6-4', ext_options), + ('nnet', '7.3-9', ext_options), + ('nlme', '3.1-120', ext_options), + ('minqa', '1.2.4', ext_options), + ('RcppEigen', '0.3.2.4.0', ext_options), + ('quantreg', '5.11', ext_options), + ('mgcv', '1.8-6', ext_options), + ('colorspace', '1.2-6', ext_options), + ('robustbase', '0.92-3', ext_options), + ('sp', '1.1-0', ext_options), + ('vcd', '1.3-2', ext_options), + ('snowfall', '1.84-6', ext_options), + ('rpart', '4.1-9', ext_options), + ('mice', '2.22', ext_options), + ('urca', '1.2-8', ext_options), + ('fracdiff', '1.4-2', ext_options), + ('logistf', '1.21', ext_options), + ('akima', '0.5-11', ext_options), + ('bitops', '1.0-6', ext_options), + ('boot', '1.3-15', ext_options), + ('mixtools', '1.0.3', ext_options), + ('cluster', '2.0.1', ext_options), + ('gclus', '1.3.1', ext_options), + ('coda', '0.17-1', ext_options), + ('codetools', '0.2-11', ext_options), + ('foreach', '1.4.2', ext_options), + ('doMC', '1.3.3', ext_options), + ('DBI', '0.3.1', ext_options), + ('foreign', '0.8-63', ext_options), + ('survival', '2.38-1', ext_options), + ('gam', '1.09.1', ext_options), + ('gamlss.data', '4.2-7', ext_options), + ('gamlss.dist', '4.3-4', ext_options), + ('hwriter', '1.3.2', ext_options), + ('KernSmooth', '2.23-14', ext_options), + ('zoo', '1.7-12', ext_options), + ('xts', '0.9-7', ext_options), + ('TTR', '0.22-0', ext_options), + ('quantmod', '0.4-4', ext_options), + ('lmtest', '0.9-33', ext_options), + ('mnormt', '1.5-2', ext_options), + ('mvtnorm', '1.0-2', ext_options), + ('pcaPP', '1.9-60', ext_options), + ('numDeriv', '2012.9-1', ext_options), + ('lava', '1.4.0', ext_options), + ('prodlim', '1.5.1', ext_options), + ('pscl', '1.4.9', ext_options), + ('RSQLite', '1.0.0', ext_options), + ('BatchJobs', '1.6', ext_options), + ('sandwich', '2.3-3', ext_options), + ('sfsmisc', '1.0-27', ext_options), + ('spatial', '7.3-9', ext_options), + ('VGAM', '0.9-7', ext_options), + ('waveslim', '1.7.5', ext_options), + ('xtable', '1.7-4', ext_options), + ('profileModel', '0.5-9', ext_options), + ('brglm', '0.5-9', ext_options), + ('deSolve', '1.11', 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', '1.1.33', ext_options), + ('R.utils', '2.0.1', ext_options), + ('R.matlab', '3.2.0', 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', '0.2.4', ext_options), + ('proto', '0.3-10', ext_options), + ('ggplot2', '1.0.1', ext_options), + ('Hmisc', '3.15-0', ext_options), + ('fastcluster', '1.1.16', ext_options), + ('chron', '2.3-45', ext_options), + ('data.table', '1.9.4', ext_options), + ('igraph', '0.7.1', ext_options), + ('GeneNet', '1.2.12', ext_options), + ('ape', '3.2', ext_options), + ('htmltools', '0.2.6', ext_options), + ('RJSONIO', '1.3-0', ext_options), + ('caTools', '1.17.1', ext_options), + ('gplots', '2.16.0', ext_options), + ('ROCR', '1.0-7', ext_options), + ('httpuv', '1.3.2', ext_options), + ('R6', '2.0.1', ext_options), + ('shiny', '0.11.1', ext_options), + ('adegenet', '1.4-2', ext_options), + ('phylobase', '0.6.8', ext_options), + ('adephylo', '1.1-6', ext_options), + ('animation', '2.3', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.4.6', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.3-40', ext_options), + ('dismo', '1.0-12', ext_options), + ('expm', '0.99-1.1', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.3', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.2-1', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.3', ext_options), + ('glmnet', '2.0-2', ext_options), + ('labdsv', '1.6-1', ext_options), + ('MatrixModels', '0.4-0', ext_options), + ('stabs', '0.5-1', ext_options), + ('mboost', '2.4-2', ext_options), + ('msm', '1.5', ext_options), + ('nor1mix', '1.2-0', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-8', ext_options), + ('quantreg', '5.11', ext_options), + ('polspline', '1.1.9', ext_options), + ('TH.data', '1.0-6', ext_options), + ('multcomp', '1.4-0', ext_options), + ('gridExtra', '0.9.1', ext_options), + ('rms', '4.3-0', ext_options), + ('RWekajars', '3.7.12-1', ext_options), + ('RWeka', '0.4-24', ext_options), + ('slam', '0.1-32', ext_options), + ('tm', '0.6', ext_options), + ('TraMineR', '1.8-9', ext_options), + ('chemometrics', '1.3.9', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-4', ext_options), + ('yaml', '2.1.13', ext_options), + ('knitr', '1.10', ext_options), + ('statmod', '1.4.21', ext_options), + ('miscTools', '0.6-16', ext_options), + ('maxLik', '1.2-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('reshape', '0.8.5', ext_options), + ('optparse', '1.3.0', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), + ('locfit', '1.5-9.1', ext_options), + ('GGally', '0.5.0', ext_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('matrixStats', '0.14.0', 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', '1.1-8', ext_options), + ('pbkrtest', '0.4-2', ext_options), + ('car', '2.0-25', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.29', 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', '0.75-6', ext_options), + ('trimcluster', '0.1-2', ext_options), + ('fpc', '2.1-9', ext_options), + ('BiasedUrn', '1.06.1', ext_options), + ('TeachingDemos', '2.9', ext_options), + ('jsonlite', '0.9.16', ext_options), + ('kohonen', '2.0.18', ext_options), + ('base64', '1.1', ext_options), + ('registry', '0.2', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doRNG', '1.6', ext_options), + ('nleqslv', '2.7', ext_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '1.0.2', ext_options), + ('openxlsx', '2.4.0', ext_options), + ('pvclust', '1.3-2', ext_options), + ('RCircos', '1.1.2', ext_options), + ('VennDiagram', '1.6.9', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('vegan', '2.3-0', ext_options), + ('forecast', '6.1', ext_options), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), + ('XML', '3.98-1.1', ext_options), + ('memoise', '0.2.1', ext_options), + ('crayon', '1.3.1', ext_options), + ('testthat', '0.10.0', ext_options), + ('rmarkdown', '0.7', ext_options), + ('curl', '0.9.1', ext_options), + ('RCurl', '1.95-4.7', ext_options), + ('httr', '0.6.1', ext_options), + ('maptools', '0.8-36', ext_options), + ('deldir', '0.1-9', ext_options), + ('tensor', '1.5', ext_options), + ('polyclip', '1.3-0', ext_options), + ('goftest', '1.0-2', ext_options), + ('spatstat', '1.41-1', ext_options), + ('gdalUtils', '0.3.1', ext_options), + ('pracma', '1.8.3', ext_options), + ('bio3d', '2.2-2', ext_options), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..fb021535855eab46b5739ba0527c953ab5721cc7 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.0-ictce-7.3.5-bare.eb @@ -0,0 +1,29 @@ +name = 'R' +version = '3.2.0' +versionsuffix = '-bare' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'ictce', 'version': '7.3.5'} + +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', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.7.0_80', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk +] + +exts_list = [] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015a-bare.eb b/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015a-bare.eb new file mode 100644 index 0000000000000000000000000000000000000000..f4f7ec9970020dd0c263b55795788596befe4292 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.0-intel-2015a-bare.eb @@ -0,0 +1,27 @@ +name = 'R' +version = '3.2.0' +versionsuffix = '-bare' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +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', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.0'), # for plottting in R + ('Java', '1.7.0_80', '', 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-3.2.1-intel-2015a.eb b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..2c0d70505808d7cc3335941f74568ad6e4ceb8cb --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.2.1-intel-2015a.eb @@ -0,0 +1,369 @@ +name = 'R' +version = '3.2.1' + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +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', '5.9'), + ('libpng', '1.6.17'), # for plotting in R + ('libjpeg-turbo', '1.4.1'), # for plottting in R + ('Java', '1.8.0_45', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.4'), # for tcltk + ('Tk', '8.6.4', '-no-X11'), # for tcltk + ('cURL', '7.43.0'), # for RCurl + ('libxml2', '2.9.2'), # for XML +] + +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 8th 2015 +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', dict(ext_options.items() + [('patches', ['Rmpi-0.6-5_impi5.patch'])])), + ('abind', '1.4-3', ext_options), + ('magic', '1.5-6', ext_options), + ('geometry', '0.3-5', dict(ext_options.items() + [('patches', ['geometry-0.3-4-icc.patch'])])), + ('bit', '1.1-12', ext_options), + ('filehash', '2.2-2', ext_options), + ('ff', '2.2-13', ext_options), + ('bnlearn', '3.8.1', 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', ext_options), + ('gtools', '3.5.0', ext_options), + ('gdata', '2.17.0', ext_options), + ('GSA', '1.03', ext_options), + ('highr', '0.5', ext_options), + ('infotheo', '1.2.0', ext_options), + ('lars', '1.2', ext_options), + ('lazy', '1.2-15', ext_options), + ('kernlab', '0.9-20', ext_options), + ('mime', '0.3', ext_options), + ('markdown', '0.7.7', ext_options), + ('mlbench', '2.1-1', ext_options), + ('NLP', '0.1-8', ext_options), + ('mclust', '5.0.2', ext_options), + ('RANN', '2.5', ext_options), + ('rmeta', '2.16', ext_options), + ('segmented', '0.5-1.1', 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', '1.7-2', ext_options), + ('AlgDesign', '1.1-7.3', ext_options), + ('base64enc', '0.1-2', ext_options), + ('BH', '1.58.0-1', 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', '1.6.0', ext_options), + ('cubature', '1.1-2', ext_options), + ('DEoptimR', '1.0-2', ext_options), + ('digest', '0.6.8', ext_options), + ('fastmatch', '1.0-4', ext_options), + ('ffbase', '0.12.1', ext_options), + ('iterators', '1.0.7', ext_options), + ('maps', '2.3-10', ext_options), + ('nnls', '1.4', ext_options), + ('sendmailR', '1.2-1', ext_options), + ('spam', '1.0-1', ext_options), + ('subplex', '1.1-6', ext_options), + ('stringi', '0.5-5', ext_options), + ('magrittr', '1.5', ext_options), + ('stringr', '1.0.0', ext_options), + ('evaluate', '0.7', ext_options), + ('logspline', '2.1.8', ext_options), + ('ncbit', '2013.03.29', ext_options), + ('permute', '0.8-4', ext_options), + ('plotrix', '3.5-12', ext_options), + ('randomForest', '4.6-10', ext_options), + ('scatterplot3d', '0.3-35', ext_options), + ('SparseM', '1.6', ext_options), + ('tripack', '1.3-6', ext_options), + ('irace', '1.06', ext_options), + ('rJava', '0.9-6', ext_options), + ('lattice', '0.20-31', ext_options), + ('RColorBrewer', '1.1-2', ext_options), + ('latticeExtra', '0.6-26', ext_options), + ('Matrix', '1.2-2', ext_options), + ('png', '0.1-7', ext_options), + ('Rcpp', '0.11.6', ext_options), + ('RcppArmadillo', '0.5.200.1.0', 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', '1.2', ext_options), + ('rlecuyer', '0.3-3', ext_options), + ('snow', '0.3-13', ext_options), + ('MASS', '7.3-42', ext_options), + ('tree', '1.0-36', ext_options), + ('pls', '2.4-3', ext_options), + ('class', '7.3-13', ext_options), + ('e1071', '1.6-4', ext_options), + ('nnet', '7.3-10', ext_options), + ('nlme', '3.1-121', ext_options), + ('minqa', '1.2.4', ext_options), + ('RcppEigen', '0.3.2.4.0', ext_options), + ('quantreg', '5.11', ext_options), + ('mgcv', '1.8-6', ext_options), + ('colorspace', '1.2-6', ext_options), + ('robustbase', '0.92-4', ext_options), + ('sp', '1.1-1', ext_options), + 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'0.9-7', ext_options), + ('TTR', '0.23-0', ext_options), + ('quantmod', '0.4-4', ext_options), + ('mnormt', '1.5-3', ext_options), + ('mvtnorm', '1.0-2', ext_options), + ('pcaPP', '1.9-60', ext_options), + ('numDeriv', '2014.2-1', ext_options), + ('lava', '1.4.1', ext_options), + ('prodlim', '1.5.1', ext_options), + ('pscl', '1.4.9', ext_options), + ('RSQLite', '1.0.0', ext_options), + ('BatchJobs', '1.6', ext_options), + ('sandwich', '2.3-3', ext_options), + ('sfsmisc', '1.0-27', ext_options), + ('spatial', '7.3-10', ext_options), + ('VGAM', '0.9-8', ext_options), + ('waveslim', '1.7.5', ext_options), + ('xtable', '1.7-4', 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', '1.1.33', ext_options), + ('R.utils', '2.1.0', ext_options), + ('R.matlab', '3.2.0', 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', '0.2.5', ext_options), + ('proto', '0.3-10', ext_options), + ('ggplot2', '1.0.1', ext_options), + ('gridExtra', '0.9.1', ext_options), + ('Hmisc', '3.16-0', ext_options), + ('fastcluster', '1.1.16', ext_options), + ('chron', '2.3-47', ext_options), + ('data.table', '1.9.4', ext_options), + ('registry', '0.3', ext_options), + ('pkgmaker', '0.22', ext_options), + ('rngtools', '1.2.4', ext_options), + ('doParallel', '1.0.8', ext_options), + ('gridBase', '0.4-7', ext_options), + ('NMF', '0.20.6', ext_options), + ('irlba', '1.0.3', ext_options), + ('igraph', '1.0.1', ext_options), + ('GeneNet', '1.2.12', ext_options), + ('ape', '3.3', ext_options), + ('htmltools', '0.2.6', 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', '1.3.2', ext_options), + ('R6', '2.1.0', ext_options), + ('jsonlite', '0.9.16', ext_options), + ('shiny', '0.12.1', ext_options), + ('seqinr', '3.1-3', ext_options), + ('LearnBayes', '2.15', ext_options), + ('deldir', '0.1-9', ext_options), + ('spdep', '0.5-88', ext_options), + ('assertthat', '0.1', ext_options), + ('lazyeval', '0.1.10', ext_options), + ('dplyr', '0.4.2', ext_options), + ('adegenet', '2.0.0', ext_options), + ('phylobase', '0.6.8', ext_options), + ('adephylo', '1.1-6', ext_options), + ('animation', '2.3', ext_options), + ('bigmemory.sri', '0.1.3', ext_options), + ('bigmemory', '4.4.6', ext_options), + ('calibrate', '1.7.2', ext_options), + ('clusterGeneration', '1.3.4', ext_options), + ('raster', '2.4-15', ext_options), + ('dismo', '1.0-12', ext_options), + ('expm', '0.99-1.1', ext_options), + ('extrafontdb', '1.0', ext_options), + ('Rttf2pt1', '1.3.3', ext_options), + ('extrafont', '0.17', ext_options), + ('fields', '8.2-1', ext_options), + ('shapefiles', '0.7', ext_options), + ('fossil', '0.3.7', ext_options), + ('geiger', '2.0.3', ext_options), + ('glmnet', '2.0-2', ext_options), + ('rgl', '0.95.1247', ext_options), + ('labdsv', '1.7-0', ext_options), + ('MatrixModels', '0.4-0', ext_options), + ('stabs', '0.5-1', ext_options), + ('mboost', '2.4-2', ext_options), + ('msm', '1.5', ext_options), + ('nor1mix', '1.2-0', ext_options), + ('np', '0.60-2', ext_options), + ('polynom', '1.3-8', ext_options), + ('quantreg', '5.11', ext_options), + ('polspline', '1.1.11', ext_options), + ('TH.data', '1.0-6', ext_options), + ('multcomp', '1.4-0', ext_options), + ('rms', '4.3-1', 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', '1.8-9', ext_options), + ('chemometrics', '1.3.9', ext_options), + ('FNN', '1.1', ext_options), + ('ipred', '0.9-4', ext_options), + ('yaml', '2.1.13', ext_options), + ('knitr', '1.10.5', ext_options), + ('statmod', '1.4.21', ext_options), + ('miscTools', '0.6-16', ext_options), + ('maxLik', '1.2-4', ext_options), + ('mlogit', '0.2-4', ext_options), + ('getopt', '1.20.0', ext_options), + ('gsalib', '2.1', ext_options), + ('reshape', '0.8.5', ext_options), + ('optparse', '1.3.0', ext_options), + ('klaR', '0.6-12', ext_options), + ('neuRosim', '0.2-12', ext_options), + ('locfit', '1.5-9.1', ext_options), + ('GGally', '0.5.0', ext_options), + ('beanplot', '1.2', ext_options), + ('clValid', '0.6-6', ext_options), + ('matrixStats', '0.14.2', 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', '1.1-8', ext_options), + ('pbkrtest', '0.4-2', ext_options), + ('car', '2.0-25', ext_options), + ('flashClust', '1.01-2', ext_options), + ('FactoMineR', '1.31.3', 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', '2.1-9', ext_options), + ('BiasedUrn', '1.06.1', ext_options), + ('TeachingDemos', '2.9', ext_options), + ('jsonlite', '0.9.16', ext_options), + ('kohonen', '2.0.18', ext_options), + ('base64', '1.1', ext_options), + ('doRNG', '1.6', ext_options), + ('nleqslv', '2.8', ext_options), + ('RGCCA', '2.0', ext_options), + ('pheatmap', '1.0.7', ext_options), + ('openxlsx', '3.0.0', ext_options), + ('pvclust', '1.3-2', ext_options), + ('RCircos', '1.1.2', ext_options), + ('VennDiagram', '1.6.9', ext_options), + ('xlsxjars', '0.6.1', ext_options), + ('xlsx', '0.5.7', ext_options), + ('vegan', '2.3-0', ext_options), + ('forecast', '6.1', dict(ext_options.items() + [('patches', ['forecast-6.1_icpc-wd308.patch'])])), + ('fma', '2.01', ext_options), + ('expsmooth', '2.3', ext_options), + ('fpp', '0.5', ext_options), + ('XML', '3.98-1.3', ext_options), + ('memoise', '0.2.1', ext_options), + ('crayon', '1.3.1', ext_options), + ('testthat', '0.10.0', ext_options), + ('rmarkdown', '0.7', ext_options), + ('curl', '0.9.1', ext_options), + ('httr', '1.0.0', ext_options), + ('maptools', '0.8-36', 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', '1.42-2', ext_options), + ('gdalUtils', '0.3.1', ext_options), + ('pracma', '1.8.3', ext_options), + ('RCurl', '1.95-4.7', ext_options), + ('bio3d', '2.2-2', ext_options), + ('AUC', '0.3.0', ext_options), + ('interpretR', '0.2.3', ext_options), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch b/easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch new file mode 100644 index 0000000000000000000000000000000000000000..8582ea93aeaac9b2adab311e43a9f8c6eb115d04 --- /dev/null +++ b/easybuild/easyconfigs/r/R/forecast-6.1_icpc-wd308.patch @@ -0,0 +1,9 @@ +ignore warning/error when building with Intel C++ compiler by including -wd308 flag in $CXXFLAGS +author: Kenneth Hoste (HPC-UGent) +--- forecast/src/Makevars.orig 2015-05-12 11:56:10.000000000 +0200 ++++ forecast/src/Makevars 2015-05-28 10:53:13.878100139 +0200 +@@ -1,2 +1,4 @@ + ## Use the R_HOME indirection to support installations of multiple R version + PKG_LIBS=$(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS) ++# disable Intel C++ compiler (icpc) warning/error #308, to avoid 'member "std::complex::_M_value" is inaccessible' ++PKG_CXXFLAGS = -wd308 diff --git a/easybuild/easyconfigs/r/RELION/RELION-1.3-foss-2014b.eb b/easybuild/easyconfigs/r/RELION/RELION-1.3-foss-2014b.eb index 5101540bd39ba4e272aeb9e2269aea6438dca0d6..0ad7f07069a17f142675d597d13b84b38fc422ff 100644 --- a/easybuild/easyconfigs/r/RELION/RELION-1.3-foss-2014b.eb +++ b/easybuild/easyconfigs/r/RELION/RELION-1.3-foss-2014b.eb @@ -32,7 +32,7 @@ dependencies = [ # RELION expects FLTK to be in external/fltk-1.3.0 configopts = ['--enable-mpi --enable-openmp && ln -s $EBROOTFLTK/include external/fltk-1.3.0'] buildopts = 'LIBS="-lfftw3_threads -lfftw3 -lm -lpthread -lfltk -lX11 -lXft -lfontconfig -lXext -lXinerama" ' -installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/relion " +installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/%(namelower)s " sanity_check_paths = { 'files': ['bin/relion'], diff --git a/easybuild/easyconfigs/r/RELION/RELION-1.3-intel-2014b.eb b/easybuild/easyconfigs/r/RELION/RELION-1.3-intel-2014b.eb index 7b003f1cbf188be766c193f8b77f15077203d1ec..25abcbdcb90c23421ab7a3b6b631747aba5d6213 100644 --- a/easybuild/easyconfigs/r/RELION/RELION-1.3-intel-2014b.eb +++ b/easybuild/easyconfigs/r/RELION/RELION-1.3-intel-2014b.eb @@ -34,7 +34,7 @@ dependencies = [ configopts = ['--enable-mpi --enable-openmp && ln -s $EBROOTFLTK/include external/fltk-1.3.0'] buildopts = 'LIBS="-lfftw3_threads -lfftw3 -lm -lpthread -lfltk -lX11 -lXft -lfontconfig -lXext -lXinerama" ' # users expect the maingui binary to be called relion -installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/relion " +installopts = " && cp %(installdir)s/bin/relion_maingui %(installdir)s/bin/%(namelower)s " moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-ictce-4.0.6.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-ictce-4.0.6.eb index fb2d4796614c8627848364e7c0fee23050245341..55aab9105bb4ba04c0f61cdd8149937dcd468165 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-ictce-4.0.6.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-ictce-4.0.6.eb @@ -32,7 +32,7 @@ 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-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-libdir=$EBROOTIMKL/mkl/lib/intel64' configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb index 6fd56a833caf614ef5936479356127008852f784..c0e1e4e91ecf6043c611b3321f00e8db5a8bf421 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.01-intel-2015a.eb @@ -32,7 +32,7 @@ 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-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-libdir=$EBROOTIMKL/mkl/lib/intel64' configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' diff --git a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb index 74c34689f1fb7452c243a3a8ed7eeb45fa115cd3..cc50539ec7d09cd80d6dfcec20518e34d41fc165 100644 --- a/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb +++ b/easybuild/easyconfigs/r/ROOT/ROOT-v5.34.18-ictce-5.5.0.eb @@ -36,7 +36,7 @@ configopts = ' --disable-xft --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-fftw3-incdir=$EBROOTIMKL/mkl/include/fftw --with-fftw3-libdir=$EBROOTIMKL/mkl/lib/intel64' configopts += ' --with-xml-incdir=$EBROOTLIBXML2/include/libxml2/libxml --with-xml-libdir=$EBROOTLIBXML2/lib' configopts += ' --with-python-libdir=$EBROOTPYTHON/lib' diff --git a/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb b/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb index 355b27d3e62b51bdfb109ec069fc67ba9795f823..418cc4118e796b57dd7cc5000bbb036aee8a3506 100644 --- a/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/r/RSEQtools/RSEQtools-0.6-goolf-1.4.10.eb @@ -53,7 +53,7 @@ sanity_check_paths = { } modextravars = { - 'BIOINFOCONFDIR': '$root/bios/conf', + 'BIOINFOCONFDIR': '%(installdir)s/bios/conf', } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.1.6.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.6.eb new file mode 100644 index 0000000000000000000000000000000000000000..b2e22e2b135e26c65e67e1b1281f6988723e9cc1 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.1.6.eb @@ -0,0 +1,38 @@ +# 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 = '2.1.6' + +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', '1.9.8', ext_options), + ('childprocess', '0.5.6', ext_options), + ('json', '1.8.2', ext_options), + ('cabin', '0.7.1', ext_options), + ('backports', '3.6.4', ext_options), + ('arr-pm', '0.0.10', ext_options), + ('clamp', '0.6.5', ext_options), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b1d493612160c91e60b7fcce5028a0979d756d47 --- /dev/null +++ b/easybuild/easyconfigs/r/renderproto/renderproto-0.11-intel-2015a.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'renderproto' +version = '0.11' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = "Xrender protocol and ancillary headers" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'optarch': True} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/proto/'] + +sanity_check_paths = { + 'files' : ['include/X11/extensions/%s' % x for x in ['render.h', 'renderproto.h']], + 'dirs' : [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/requests/requests-2.6.2-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/r/requests/requests-2.6.2-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..c8c3ba972031422fb76cce466aeb445d6f2948a8 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.6.2-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.6.2' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/requests-%s-py%s.egg' % (pyshortver, version, pyshortver)], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/requests/requests-2.7.0-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/r/requests/requests-2.7.0-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..d4e3a34ddb4077bba27fd17eea91ca0003d17631 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.7.0-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.7.0' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/requests-%s-py%s.egg' % (pyshortver, version, pyshortver)], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/requests/requests-2.7.0-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/r/requests/requests-2.7.0-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..f8a41a318c69b51939836fd182a23f118206f411 --- /dev/null +++ b/easybuild/easyconfigs/r/requests/requests-2.7.0-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'requests' +version = '2.7.0' + +homepage = 'https://pypi.python.org/pypi/requests/2.6.0' +description = """Python http for humans""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pyshortver = '.'.join(pythonversion.split('.')[:2]) + +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/requests-%s-py%s.egg' % (pyshortver, version, pyshortver)], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..aeaed8d595cd5202614d143a4a6f6511ae129f97 --- /dev/null +++ b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'rpy2' +version = '2.4.3' + +homepage = 'http://rpy.sourceforge.net/' +description = """rpy2 is a redesign and rewrite of rpy. It is providing a low-level +interface to R from Python, a proposed high-level interface, including wrappers to +graphical libraries, as well as R-like structures and functions. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://pypi.python.org/packages/source/r/%(name)s'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '2.7.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('R', '2.15.2'), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..6d5edb8ec20d3183e0caf28dae5298f1a2f016a3 --- /dev/null +++ b/easybuild/easyconfigs/r/rpy2/rpy2-2.4.3-goolf-1.4.10-Python-3.2.3.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'rpy2' +version = '2.4.3' + +homepage = 'http://rpy.sourceforge.net/' +description = """rpy2 is a redesign and rewrite of rpy. It is providing a low-level +interface to R from Python, a proposed high-level interface, including wrappers to +graphical libraries, as well as R-like structures and functions. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://pypi.python.org/packages/source/r/%(name)s'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pyver = '3.2.3' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [ + (python, pyver), + ('R', '2.15.2'), +] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..c7a055062ea6d5e726004229a88aaec1fcd2320c --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-foss-2015a.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': '2015a'} +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', '5.9'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..cb7232a3fb1298973ce3fdb7def4ba575588775d --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.7.20.eb @@ -0,0 +1,22 @@ +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': 'goolf', 'version': '1.7.20'} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [('http://sourceforge.net/projects/samtools/files/%(namelower)s/%(version)s', 'download')] + +checksums = ['ff8b46e6096cfb452003b1ec5091d86a'] + +patches = ['SAMtools-%(version)s_Makefile-ncurses.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..91e58c27f084775489ef7213be45f4e4df14f20a --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.1-intel-2015a.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 +## + +name = 'SAMtools' +version = '1.1' + +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': '2015a'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = [SOURCEFORGE_SOURCE] + +patches = ['SAMtools-1.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..695f8c6b45dd56a582adb2f1b0dfbbaee8e29bf9 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.2-goolf-1.7.20.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$ +# +## + +name = 'SAMtools' +version = '1.2' + +homepage = 'http://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_BZ2] +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] + +patches = ['SAMtools-1.1_Makefile.patch'] + +dependencies = [ + ('ncurses', '5.9'), + ('zlib', '1.2.8'), +] + +parallel = 1 + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..88fe827b030bb2923ea49a7f9d70f5cb87edfeef --- /dev/null +++ b/easybuild/easyconfigs/s/SCANMS/SCANMS-2.02-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,43 @@ +# 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 = 'PerlModule' + +name = 'SCANMS' +version = '2.02' + +homepage = 'http://compbio.ucmerced.edu/ardell/software/scanms/' +description = """SCANMS is an open source utility written in Perl that works in + conjunction with Richard Hudson’s coalescent simulator MS to do parametric + bootstrapping of a sliding window analysis of neutrality test statistics. + Currently supported statistics are Tajima’s D and Fu and Li’s D* and F*. + Its output of a joint distribution of window minima and maxima may then be + used to correct for multiple comparisons in such analyses.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['http://compbio.ucmerced.edu/'] +sources = [SOURCELOWER_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), +] + +# override the default sanity check for perl packages which tries to load Perl module +exts_filter = ('scanms -v 2>&1 | grep version', "") + +sanity_check_paths = { + 'files': ["bin/scanms"], + 'dirs': [] +} + +# copy all the documentation provided in the tarball to install directory +postinstallcmds = ["cp -r %(builddir)s/*/{README,SCANMS.pdf,scanms.doc.html} %(installdir)s"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..f5bdd9828b42f190729fe1fb0bdf05f2b1156633 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.0.4-foss-2015.05.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': '2015.05'} +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/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..e745733edd78f7e99ad23e8e5fd7d5565e4d327a --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +# 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 = '4.16.8' + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +configopts = "configure.py" + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..87b18fbf3c5f01f32cc2e6c1748efe96825a36d2 --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-4.16.8-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,25 @@ +# 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 = '4.16.8' + +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': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/pyqt/files/sip/sip-%(version)s'] + +python = 'Python' +pyver = '2.7.9' +versionsuffix = '-%s-%s' % (python, pyver) + +dependencies = [(python, pyver)] + +configopts = "configure.py" + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..0f01678e280d373ac118eff9d1f16d5713941dd7 --- /dev/null +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.5.3-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,21 @@ +name = 'SLEPc' +version = '3.5.3' +versionsuffix = '-Python-2.7.9' + +homepage = 'http://www.grycap.upv.es/slepc/' +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of + large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either + standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial + SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://www.grycap.upv.es/slepc/download/download.php?filename='] +sources = [SOURCELOWER_TAR_GZ] + +dependencies = [('PETSc', '3.5.3', versionsuffix)] + +petsc_arch = 'arch-linux2-c-opt' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SOBAcl/SOBAcl-r18-intel-2014b-Perl-5.20.0.eb b/easybuild/easyconfigs/s/SOBAcl/SOBAcl-r18-intel-2014b-Perl-5.20.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..e58e9e902a4720e96177b0342bfce4b2dc4477d2 --- /dev/null +++ b/easybuild/easyconfigs/s/SOBAcl/SOBAcl-r18-intel-2014b-Perl-5.20.0.eb @@ -0,0 +1,22 @@ +easyblock = "Tarball" + +name = 'SOBAcl' +version = 'r18' + +homepage = 'http://www.sequenceontology.org/software/sobacl.html' +description = """SOBAcl is a command line tool for analyzing GFF3 annotations. +GFF3 is a standard file format for genomic annotation data. SOBAcl gathers +statistics from GFF3 files and can generate a wide variety of tables +and graphs.""" + +toolchain = {'name': 'intel', 'version': '2014b'} +sources = [('SOBA_%s.tar.gz' % (version))] +source_urls = ['http://www.sequenceontology.org/software/SOBA_Code/'] + +perl = 'Perl' +perlver = '5.20.0' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [('GraphViz', '2.18', versionsuffix)] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-foss-2015a.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..31a4eb409aa8870a08588b24ae192ac81239e16c --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-foss-2015a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'SPIDER' +version = '22.10' + +homepage = 'http://spider.wadsworth.org/spider_doc/spider/docs/spider.html' +description = """SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is + an image processing system for electron microscopy.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'static': True} + +source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] +sources = ['spiderweb.%(version)s.tar.gz'] + +patches = [ + 'SPIDER-%(version)s_fix-syntax-ifort.patch', + 'SPIDER-%(version)s_gfortran49.patch', +] + +start_dir = 'spider/src' + +buildininstalldir = True + +parallel = 1 + +skipsteps = ['configure', 'install'] + +prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " +buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_GFORTRAN -cpp -dM -c" LF="$F90FLAGS"' + +modextrapaths = {'PATH': ['spider/bin']} + +sanity_check_paths = { + 'files': ['spider/bin/spider'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb new file mode 100644 index 0000000000000000000000000000000000000000..cdcacc46310bdf3fb79cbe27197742c00658f2a6 --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mpi.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'SPIDER' +version = '22.10' +versionsuffix = '-mpi' + +homepage = 'http://spider.wadsworth.org/spider_doc/spider/docs/spider.html' +description = """SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is + an image processing system for electron microscopy.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'usempi': True} + +source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] +sources = ['spiderweb.%(version)s.tar.gz'] + +patches = ['SPIDER-%(version)s_fix-syntax-ifort.patch'] + +dependencies = [('FFTW', '3.3.4')] + +start_dir = 'spider/src' + +buildininstalldir = True + +parallel = 1 + +skipsteps = ['configure', 'install'] + +prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " +buildopts = '-f Makefile_linux_mp COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DUSE_MPI" LF="$F90FLAGS -ldl -lpthread"' + +modextrapaths = {'PATH': ['spider/bin']} + +sanity_check_paths = { + 'files': ['spider/bin/spider'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb new file mode 100644 index 0000000000000000000000000000000000000000..a747562bcb644866afb681fbfc94d22e88c60531 --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a-mt.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'SPIDER' +version = '22.10' +versionsuffix = '-mt' + +homepage = 'http://spider.wadsworth.org/spider_doc/spider/docs/spider.html' +description = """SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is + an image processing system for electron microscopy.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'static': True, 'openmp': True} + +source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] +sources = ['spiderweb.%(version)s.tar.gz'] + +patches = ['SPIDER-%(version)s_fix-syntax-ifort.patch'] + +dependencies = [('FFTW', '3.3.4')] + +start_dir = 'spider/src' + +buildininstalldir = True + +parallel = 1 + +skipsteps = ['configure', 'install'] + +prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " +buildopts = '-f Makefile_linux_mp COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c -DSP_MP" LF="$F90FLAGS"' + +modextrapaths = {'PATH': ['spider/bin']} + +sanity_check_paths = { + 'files': ['spider/bin/spider'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..cf9bac0479914f784a929fd34fe848d4a4f5c112 --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10-intel-2015a.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'SPIDER' +version = '22.10' + +homepage = 'http://spider.wadsworth.org/spider_doc/spider/docs/spider.html' +description = """SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is + an image processing system for electron microscopy.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'static': True} + +source_urls = ['http://spider.wadsworth.org/spider_doc/spider/download/'] +sources = ['spiderweb.%(version)s.tar.gz'] + +patches = ['SPIDER-%(version)s_fix-syntax-ifort.patch'] + +dependencies = [('FFTW', '3.3.4')] + +start_dir = 'spider/src' + +buildininstalldir = True + +parallel = 1 + +skipsteps = ['configure', 'install'] + +prebuildopts = "rm ../bin/spider* && rm ../src/spider*.[ao] && " +buildopts = '-f Makefile_linux COMP="$F90" EXE=spider FFTWLIBDIR=$EBROOTFFTW/lib ' +buildopts += 'FFLAGS="$F90FLAGS -DSP_LIBFFTW3 -DSP_LINUX -DSP_IFC -fpp -c" LF="$F90FLAGS"' + +modextrapaths = {'PATH': ['spider/bin']} + +sanity_check_paths = { + 'files': ['spider/bin/spider'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch new file mode 100644 index 0000000000000000000000000000000000000000..957ed589cf4a903a5545b1be859bbb2dadff78a5 --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_fix-syntax-ifort.patch @@ -0,0 +1,202 @@ +fix syntax issues that trip Intel Fortran compiler (ifort) +author: Kenneth Hoste (HPC-UGent) +--- spider/src/copyfromtif.f.orig 2014-11-20 17:31:58.000000000 +0100 ++++ spider/src/copyfromtif.f 2015-05-21 12:04:17.049891641 +0200 +@@ -88,7 +88,7 @@ + INTEGER(KIND=1), ALLOCATABLE :: I1VALS(:) + INTEGER(KIND=4), ALLOCATABLE :: I4VALS(:) + +- CHARACTER(LEN=1), ALLOCATABLE :: CVAL(:) ++ CHARACTER(LEN=:), ALLOCATABLE :: CVAL + + CHARACTER(LEN=24) :: CDATE + +@@ -290,7 +290,7 @@ + IF ( ICOUNT > ICVAL_LEN) THEN + IF (ALLOCATED(CVAL)) DEALLOCATE(CVAL) + ICVAL_LEN = ICOUNT +- ALLOCATE(CVAL(1)(ICVAL_LEN), STAT=IRTFLG) ++ ALLOCATE(CHARACTER(LEN=ICVAL_LEN) :: CVAL, STAT=IRTFLG) + + IF (IRTFLG .NE. 0) THEN + CALL ERRT(46,'COPYFROMTIF; CVAL...',ICVAL_LEN) +@@ -432,9 +432,9 @@ + GOTRESU = .TRUE. + + ELSEIF (ITAG == 306) THEN +- CDATE = CVAL(1)(1:22) ++ CDATE = CVAL(1:22) + c IF (DEBUG) WRITE(NOUT,'(2X,A,1X,200A)')'DATE & TIME:', +-c & CVAL(1)(1:ICOUNT) ++c & CVAL(1:ICOUNT) + GOTDATE = .TRUE. + + ELSE +--- spider/src/copypos.f.orig 2015-05-20 21:21:12.693293000 +0200 ++++ spider/src/copypos.f 2015-05-20 21:21:37.499077116 +0200 +@@ -269,7 +269,7 @@ + ENDIF + + C GREATER OF (0 AND (THE SMALLER OF RVAL AND 255)) +- IVAL = MAX(0,MIN(RVAL, 255.)) ++ IVAL = MAX(0.,MIN(RVAL, 255.)) + + IF (FLIP) THEN + IVAL = 255 - IVAL +--- spider/src/hisd.f.orig 2015-05-20 21:30:04.788208000 +0200 ++++ spider/src/hisd.f 2015-05-20 21:30:29.848221000 +0200 +@@ -146,9 +146,7 @@ + & 'OUTPUT DOC FILE (OR * IF NONE)',ISOLD,APPEND,MESSAGE, + & NEWFILE,IRTFLG) + +- WANTDOC = (IRTFLG == 0) +- +- IF (WANTDOC) THEN ++ IF (IRTFLG == 0) THEN + C OUTPUT TO DOC FILE + + C 123456789 123456789 123456789 123456789 123456789 +--- spider/src/star2doc.f.orig 2015-05-20 21:41:24.588241000 +0200 ++++ spider/src/star2doc.f 2015-05-20 21:41:50.069338858 +0200 +@@ -82,6 +82,7 @@ + CHARACTER(LEN=1) :: CDUM + INTEGER :: LUNDOCT,ILOC,IT,NLIST,ILAST + INTEGER :: IHI,I,IKEY,IRTFLG,LENREC,IVAR,ITOK ++ INTEGER :: NSPI + + LOGICAL :: ISOPEN,EX,CALLERRT,ASKNAM + LOGICAL :: ADDEXT,GETNAME +--- spider/src/Makebody.inc.orig 2015-05-21 09:53:57.937621000 +0200 ++++ spider/src/Makebody.inc 2015-05-21 09:52:36.558197000 +0200 +@@ -14,4 +14,4 @@ + .f.a: + $(COMP) $(FFLAGS) $< + $(AR) $(AFLAGS) $(LIB) $*.o +- @\rm $*.o ++# @\rm $*.o +--- spider/src/four_fq.f.orig 2015-05-21 10:37:01.109541000 +0200 ++++ spider/src/four_fq.f 2015-05-21 10:36:37.703908871 +0200 +@@ -1028,13 +1028,11 @@ + C BUTTERWORTH ELLIPTIC LOWPASS FILTER ********* + CALL ERRT(101, + & 'OPTION NOT IMPLEMENTED FOR VOLUMES',IOPT) +- RETURN + + ELSEIF (IOPT == 12) THEN + C BUTTERWORTH ELLIPTIC HIGHPASS FILTER ********* + CALL ERRT(101, + & 'OPTION NOT IMPLEMENTED FOR VOLUMES',IOPT) +- RETURN + + + ELSEIF (IOPT == 13) THEN +--- spider/src/spider.f.orig 2015-04-21 15:30:40.000000000 +0200 ++++ spider/src/spider.f 2015-05-21 15:03:36.159704166 +0200 +@@ -195,9 +195,15 @@ + + #ifndef USE_MPI + #ifndef __APPLE__ ++#ifdef SP_IFC ++ isiz1 = kmp_get_stacksize() ++ CALL kmp_set_stacksize(65536) ++ isiz2 = kmp_get_stacksize() ++#else + isiz1 = omp_get_stack_size() + CALL omp_set_stack_size(65536) + isiz2 = omp_get_stack_size() ++#endif + !write(6,*) ' OMP Stack size: ',isiz1,' -->',isiz2 + + #endif +--- spider/src/lundoc.f.orig 2015-03-27 14:08:10.000000000 +0100 ++++ spider/src/lundoc.f 2015-05-21 15:26:30.008871936 +0200 +@@ -1252,7 +1252,7 @@ + INCLUDE 'CMBLOCK.INC' + + INTEGER :: NDOC,MAXKEYT,MAXREGT,KEYSINUSE,IRTFLG +- LOGICAL :: SAYIT ++ LOGICAL :: SAYIT, EOF + + REAL, POINTER :: IPQ(:) + CHARACTER(LEN=80) :: RECLIN ! ONLY NEEDS START +@@ -1319,15 +1319,15 @@ + BACKSPACE(NDOC) ! REREAD LINE + READ(NDOC,*,END=100,IOSTAT=IER) RECLIN + +- ENDFILE = .TRUE. ++ EOF = .TRUE. + READ(NDOC,*,END=100,IOSTAT=IER) NKEY,NREGPLINE +- ENDFILE = .FALSE. ++ EOF = .FALSE. + ENDIF + + +- 100 CALL BCAST_MPI('LUNDOCINFO','ENDFILE',ENDFILE,1,'L',ICOMM) ++ 100 CALL BCAST_MPI('LUNDOCINFO','EOF',EOF,1,'L',ICOMM) + CALL BCAST_MPI('LUNDOCINFO','IER',IER,1,'I',ICOMM) +- IF (ENDFILE) GOTO 799 ++ IF (EOF) GOTO 799 + + CALL BCAST_MPI('LUNDOCINFO','NKEY',NKEY,1,'I',ICOMM) + CALL BCAST_MPI('LUNDOCINFO','NREGPLINE',NREGPLINE,1, +@@ -1434,7 +1434,7 @@ + + REAL :: PLIST(*) + CHARACTER(LEN=180) :: RECLIN +- LOGICAL :: TILLEND ++ LOGICAL :: TILLEND, EOF, ERRFILE + + CALL SET_MPI(ICOMM,MYPID,MPIERR) ! SETS ICOMM AND MYPID + +@@ -1464,18 +1464,18 @@ + 10 CONTINUE + IF (MYPID == 0) THEN + ERRFILE = .TRUE. +- ENDFILE = .TRUE. ++ EOF = .TRUE. + READ (LUNDOC,81,ERR=100,END=200) RECLIN + 81 FORMAT(A120) + ERRFILE = .FALSE. +- ENDFILE = .FALSE. ++ EOF = .FALSE. + ENDIF + + 100 CALL BCAST_MPI('LUNDOCGETCOM','ERRFILE',ERRFILE,1,'L',ICOMM) + IF (ERRFILE) GOTO 998 + +-200 CALL BCAST_MPI('LUNDOCGETCOM','ENDFILE',ENDFILE,1,'L',ICOMM) +- IF (ENDFILE) GOTO 997 ++200 CALL BCAST_MPI('LUNDOCGETCOM','EOF',EOF,1,'L',ICOMM) ++ IF (EOF) GOTO 997 + + CALL BCAST_MPI('LUNDOCGETCOM','RECLIN',RECLIN,180,'C',ICOMM) + +@@ -1580,7 +1580,7 @@ + CHARACTER *120 RECLIN + #ifdef USE_MPI + include 'mpif.h' +- LOGICAL ENDFILE, ERRFILE ++ LOGICAL EOF, ERRFILE + ICOMM = MPI_COMM_WORLD + CALL MPI_COMM_RANK(ICOMM, MYPID, MPIERR) + #else +@@ -1595,15 +1595,15 @@ + #ifdef USE_MPI + 10 IF (MYPID == 0) THEN + ERRFILE = .TRUE. +- ENDFILE = .TRUE. ++ EOF = .TRUE. + READ (LUNDOC,81,ERR=100,END=100) RECLIN + ERRFILE = .FALSE. +- ENDFILE = .FALSE. ++ EOF = .FALSE. + ENDIF + +-100 CALL BCAST_MPI('LUNDOCSAYHDR','ENDFILE',ENDFILE,1,'L',ICOMM) ++100 CALL BCAST_MPI('LUNDOCSAYHDR','EOF',EOF,1,'L',ICOMM) + CALL BCAST_MPI('LUNDOCSAYHDR','ERRFILE',ERRFILE,1,'L',ICOMM) +- IF (ENDFILE .OR. ERRFILE) GOTO 999 ++ IF (EOF .OR. ERRFILE) GOTO 999 + + CALL BCAST_MPI('LUNDOCSAYHDR','RECLIN',RECLIN,120,'C',ICOMM) + #else diff --git a/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_gfortran49.patch b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_gfortran49.patch new file mode 100644 index 0000000000000000000000000000000000000000..3ffd0417381235daae10cf5dd78cc3a30e9b265b --- /dev/null +++ b/easybuild/easyconfigs/s/SPIDER/SPIDER-22.10_gfortran49.patch @@ -0,0 +1,22 @@ +--- spider/src/copy1.f.orig 2015-06-16 18:11:37.000000000 +0300 ++++ spider/src/copy1.f 2015-06-16 18:12:12.000000000 +0300 +@@ -72,6 +72,8 @@ + INTEGER, PARAMETER :: LUNXM1 = 83 + INTEGER, PARAMETER :: LUNXM2 = 84 + ++ LOGICAL :: VERBOSET ++ + C FROM/'AS','MR','PD','RA','NI','TE','VA','EM','NT','XP'/ + + C TO/'AS','BR','MR','PO','RA','TI','XP','OP','JPG'/ +--- spider/src/pr3d.f.orig 2015-06-16 18:49:45.000000000 +0300 ++++ spider/src/pr3d.f 2015-06-16 18:50:05.000000000 +0300 +@@ -75,7 +75,7 @@ + + CALL SET_MPI(ICOMM,MYPID,MPIERR) + +- WANTSQRTS = (FSCOP == .TRUE.) ++ WANTSQRTS = (FSCOP .eqv. .TRUE.) + + C INPUT FIRST IMAGE + MAXIM = 0 diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..fbe46bacc9c1bd8179973683d6bd7b48e215c4a8 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-foss-2015a.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 = '3.8.10.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'foss', 'version': '2015a'} + +# 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', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..03c9b50fbabb2dd183ad3118fd064f74afdd885f --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.10.2-intel-2015a.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 = '3.8.10.2' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'intel', 'version': '2015a'} + +# 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', '8.6.4'), +] + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', 'lib/libsqlite3.so'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..5e77859d0758dc3e6880c242b90029237e0552a9 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-foss-2015.05.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': 'foss', 'version': '2015.05'} + +# 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-3.8.8.1-goolf-1.7.20.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..ee10abf94853081b471a6cfaae6b205fd191a6bc --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.8.8.1-goolf-1.7.20.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': 'goolf', 'version': '1.7.20'} + +# 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/STAR/STAR-2.3.0e-goolf-1.4.10.eb b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-goolf-1.4.10.eb new file mode 100644 index 0000000000000000000000000000000000000000..c428723fec1ce476f55b4e38b9936cec7f7566cc --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.3.0e-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 +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.3.0e' + +homepage = 'https://code.google.com/p/rna-star/' +description = """ STAR aligns RNA-seq reads to a reference genome using + uncompressed suffix arrays. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://rna-star.googlecode.com/files/'] +sources = ['%(name)s_%(version)s.tgz'] + +patches = ['STAR_missing_includes.patch'] + +# a binary is provided with the source files. We delete it +prebuildopts = 'rm STAR && ' + +parallel = 1 + +files_to_copy = [(["STAR"], "bin"), "README.txt"] + +sanity_check_paths = { + 'files': ["bin/STAR"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb b/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..01b05100cc626639dfe354e5aa778f1ca67bbbd3 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.3.1z12-goolf-1.7.20.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.3.1z12' + +homepage = 'https://code.google.com/p/rna-star/' +description = """STAR: ultrafast universal RNA-seq aligner""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/alexdobin/%(name)s/archive/'] +sources = ['%(name)s_%(version)s.tar.gz'] + +checksums = ['c1e5b36a02011a73f9461f5bdc4dacaa'] + +buildopts = 'CXX="$CXX"' + +executables = [name, 'STARstatic'] +files_to_copy = [(executables, 'bin')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/STAR/STAR_missing_includes.patch b/easybuild/easyconfigs/s/STAR/STAR_missing_includes.patch new file mode 100644 index 0000000000000000000000000000000000000000..82d8f2d8e0a94105119f7bf8923219b53e1cd319 --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR_missing_includes.patch @@ -0,0 +1,10 @@ +--- STAR_2.3.0e.orig/Genome.cpp 2013-01-22 21:51:14.000000000 +0100 ++++ STAR_2.3.0e/Genome.cpp 2014-08-23 22:06:02.954503545 +0200 +@@ -6,6 +6,7 @@ + #include "streamFuns.h" + #include + #include ++#include + + #define SHM_sizeG 0 + #define SHM_sizeSA 8 diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-2.0.12-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SWIG/SWIG-2.0.12-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..f049ac6af01f063544d0d0f223ea39d3b1bbf0ea --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-2.0.12-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,23 @@ +name = 'SWIG' +version = '2.0.12' + +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': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('PCRE', '8.36'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SWIG/SWIG-3.0.5-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.5-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..31935853750ee2b12d04320deadd4d413cb4221e --- /dev/null +++ b/easybuild/easyconfigs/s/SWIG/SWIG-3.0.5-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,23 @@ +name = 'SWIG' +version = '3.0.5' + +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': '2015a'} +toolchainopts = {'pic': True, 'opt': True, 'optarch': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +versionsuffix = '-%s-%s' % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + ('PCRE', '8.36'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..6edbc50c07514978a9b6c2e75b70ad5a1bc96e1b --- /dev/null +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW-20150315-intel-2015a.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'SaguaroGW' +version = '20150315' + +homepage = 'http://sourceforge.net/projects/saguarogw/' +description = """Saguaro Genome-Wide is a program to detect signatures of selection within populations, strains, + or species. It takes SNPs or nucleotides as input, and creates statistical local phylogenies for each region in +the genome.""" + +toolchain = {'name': 'intel', 'version': '2015a'} +toolchainopts = {'openmp': True} + +# SVN revision r29, download via http://sourceforge.net/p/saguarogw/code/29/tree/ ('Download Snapshot' link) +sources = ['%(namelower)s-code-29.zip'] + +patches = ['SaguaroGW_icpc-drop-const.patch'] + +buildopts = 'CPLUSPLUS="$CXX" CC="$CC" OPEN_MP=yes' + +files_to_copy = [(['checkLock', 'CactiCorrelate', 'ChromoPaintCacti', 'ClusterCacti', 'Fasta2HMMFeature', + 'Genotype2HMMFeature', 'FilterCacti', 'HMMClassify', 'HMMTrain', 'HeatMaps', 'LocalTrees', + 'Maf2HMMFeature', 'PullFromFasta', 'Saguaro', 'Saguaro2Phylip', 'VCF2HMMFeature'], 'bin')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW_icpc-drop-const.patch b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW_icpc-drop-const.patch new file mode 100644 index 0000000000000000000000000000000000000000..193b028341e0e2c379a01910e90fe6f66492e72f --- /dev/null +++ b/easybuild/easyconfigs/s/SaguaroGW/SaguaroGW_icpc-drop-const.patch @@ -0,0 +1,15 @@ +fix issue with Intel compilers: 'the object has cv-qualifiers that are not compatible with the member function' +author: Kenneth Hoste (Ghent University) +--- /tmp/vsc40023/easybuild_build/SaguaroGW/20150315/intel-2015a/saguarogw-code-29/base/CommandLineParser.h.orig 2012-05-16 15:40:12.000000000 +0200 ++++ /tmp/vsc40023/easybuild_build/SaguaroGW/20150315/intel-2015a/saguarogw-code-29/base/CommandLineParser.h 2015-05-12 21:54:40.830166431 +0200 +@@ -39,8 +39,8 @@ + string GetName() { return mName; } + string GetDescription() { return mDesc; } + +-friend bool operator< (const commandArg &lhs, +- const commandArg &rhs) ++friend bool operator< (commandArg &lhs, ++ commandArg &rhs) + { + if ( lhs.GetName() < rhs.GetName() ) + return true; diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb new file mode 100644 index 0000000000000000000000000000000000000000..b8fe958616c29288e29e6ab3e6c0abdcd4e2d94a --- /dev/null +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.6.3-foss-2014b-Python-2.7.8.eb @@ -0,0 +1,34 @@ +name = 'Sailfish' +version = '0.6.3' +easyblock = 'CMakeMake' + +homepage = 'http://www.cs.cmu.edu/~ckingsf/software/sailfish/' +description = """Sailfish is a software tool that implements a novel, alignment-free algorithm for the estimation of + isoform abundances directly from a set of reference sequences and RNA-seq reads. """ + +toolchain = {'name': 'foss', 'version': '2014b'} + +source_urls = ['https://github.com/kingsfordgroup/sailfish/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.8' +versionsuffix = '-%s-%s' % (python, pyver) + +builddependencies = [ + ('CMake', '3.0.0'), +] + +dependencies = [ + ('Boost', '1.55.0', versionsuffix), + ('tbb', '4.0.5.339', '', True), + ('Jellyfish', '2.1.3'), + ('g2log', '1.0'), +] + +preconfigopts = "export CMAKE_INCLUDE_PATH=$CMAKE_INCLUDE_PATH:$EBROOTTBB/tbb/include &&" +configopts = "-DBOOST_ROOT=$EBROOTBOOST -DTBB_INSTALL_DIR=$EBROOTTBB" + +parallel = 1 +moduleclass = 'bio' + diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..a52473e7ffedd519f37acacfd370df8c95defd6c --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-1.5.16-OpenBLAS-0.2.13-LAPACK-3.5.0.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': '1.5.16'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.13' +blassuff = '-LAPACK-3.5.0' + +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-2015.05-OpenBLAS-0.2.14-LAPACK-3.5.0.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.05-OpenBLAS-0.2.14-LAPACK-3.5.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..e8390ed236603791e0d1281349dae16f551179a6 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.0.2-gompi-2015.05-OpenBLAS-0.2.14-LAPACK-3.5.0.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': '2015.05'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] + +blaslib = 'OpenBLAS' +blasver = '0.2.14' +blassuff = '-LAPACK-3.5.0' + +versionsuffix = "-%s-%s%s" % (blaslib, blasver, blassuff) + +dependencies = [(blaslib, blasver, blassuff, ('GNU', '4.9.2-2.25'))] + +## parallel build tends to fail, so disabling it +parallel = 1 + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.0-gompi-1.4.12-no-OFED.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.0-gompi-1.4.12-no-OFED.eb index 1f62732cc171343f44ace416337dd866362459c7..b4c09a0c490a87ad6a1fed26d6589b74b9b01523 100644 --- a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.0-gompi-1.4.12-no-OFED.eb +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.0-gompi-1.4.12-no-OFED.eb @@ -26,9 +26,8 @@ dependencies = [ ('OTF2', '1.2.1'), ] -# http://apps.fz-juelich.de/scalasca/releases/scalasca/2.0/dist/scalasca-2.0.tar.gz sources = [SOURCELOWER_TAR_GZ] -source_urls = ['http://apps.fz-juelich.de/scalasca/releases/scalasca/2.0/dist'] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/scalasca/%(version_major_minor)s/dist'] sanity_check_paths = { 'files': ["bin/scalasca", ("lib64/libpearl.replay.a", "lib/libpearl.replay.a")], diff --git a/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..55d127b2f7d9b73bbcce60e64867ab0c60e3fba1 --- /dev/null +++ b/easybuild/easyconfigs/s/Scalasca/Scalasca-2.2-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/ +## +easyblock = 'EB_Score_minus_P' + +name = "Scalasca" +version = "2.2" + +homepage = 'http://www.scalasca.org/' +description = """Scalasca is a software tool that supports the performance optimization of + parallel programs by measuring and analyzing their runtime behavior. The analysis identifies + potential performance bottlenecks -- in particular those concerning communication and + synchronization -- and offers guidance in exploring their causes.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {"usempi": True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://apps.fz-juelich.de/scalasca/releases/scalasca/%(version_major_minor)s/dist'] + +checksums = [ + '06e0380c612811a1ff9c183fed9331a9', # scalasca-2.2.tar.gz +] + +dependencies = [ + ('Cube', '4.3'), + ('OTF2', '1.5.1'), +] + +sanity_check_paths = { + 'files': ["bin/scalasca", ("lib64/libpearl.replay.a", "lib/libpearl.replay.a")], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..0170615e9cd30b1f399f51cf88b1b6ba9fc605dc --- /dev/null +++ b/easybuild/easyconfigs/s/ScientificPython/ScientificPython-2.9.4-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,36 @@ +easyblock = "PythonPackage" + +name = 'ScientificPython' +version = '2.9.4' + +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': '2015a'} + +source_urls = ['https://sourcesup.renater.fr/frs/download.php/4570'] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [ + (python, pythonversion), + # 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%s/site-packages/Scientific' % pythonshortversion], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb new file mode 100644 index 0000000000000000000000000000000000000000..137bacee9cab4f55cbfc869ca4330c81a0c97e92 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.2.3-goolf-1.5.14.eb @@ -0,0 +1,40 @@ +# This is an easyconfig file for EasyBuild, see https://github.com/hpcugent/easybuild +# Authors:: Jordi Blasco +# License:: New BSD +# +# make sure we don't fall back to the ConfigureMake easyblock + +easyblock = 'EB_Score_minus_P' + +name = "Score-P" +version = "1.2.3" + +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 = [ + ('binutils', '2.22'), + ('Cube', '4.2.3'), + ('OPARI2', '1.1.2'), + ('OTF2', '1.2.1'), + ('PAPI', '5.2.0'), + ('PDT', '3.20'), +] + +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/Score-P/Score-P-1.4-foss-2015a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..91b0941367ae6df6439ce4d8d3a890e732f8a3f3 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-1.4-foss-2015a.eb @@ -0,0 +1,46 @@ +# 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/ +## +# make sure we don't fall back to the ConfigureMake easyblock +easyblock = 'EB_Score_minus_P' + +name = 'Score-P' +version = '1.4' + +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': 'foss', 'version': '2015a'} +toolchainopts = {"usempi": True} + +sources = ["scorep-%(version)s.tar.gz"] +source_urls = ['http://www.vi-hps.org/upload/packages/scorep/'] + +checksums = [ + '17bd732cf54097d35157bf0d8284ad78', # scorep-1.4.tar.gz +] + +# compiler toolchain depencies +dependencies = [ + ('binutils', '2.25', '', ('GCC', '4.9.2')), + ('Cube', '4.3'), + ('OPARI2', '1.1.2'), + ('OTF2', '1.5.1'), + ('PAPI', '5.4.0'), + ('PDT', '3.20'), +] + +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/Seaborn/Seaborn-0.6.0-goolf-1.4.10-Python-2.7.5.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-goolf-1.4.10-Python-2.7.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..63cb8346ded5af12407a0316d177c20b52e8990b --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.6.0-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 (SIB) +# Biozentrum - University of Basel + +easyblock = "PythonPackage" + +name = 'Seaborn' +version = '0.6.0' + +homepage = 'http://stanford.edu/~mwaskom/software/seaborn/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://github.com/mwaskom/seaborn/archive/'] +sources = ['v%(version)s.tar.gz'] + +python = 'Python' +pyver = '2.7.5' +pyshortver = '.'.join(pyver.split('.')[:2]) + +versionsuffix = "-%s-%s" % (python, pyver) + +dependencies = [ + (python, pyver), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb new file mode 100644 index 0000000000000000000000000000000000000000..fae61083b0ea89060a719ec6368d46977f3260d5 --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-1.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'Spark' +version = '1.3.0' + +homepage = 'http://spark.apache.org' +description = """Spark is Hadoop MapReduce done in memory""" + +toolchain = {'name': 'dummy', 'version': ''} + +sources = ['%(namelower)s-%(version)s-bin-hadoop2.3.tgz'] +source_urls = [ + 'http://apache.belnet.be/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.eu.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', + 'http://www.us.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s/', +] + +dependencies = [('Java', '1.7.0_76')] + +sanity_check_paths = { + 'files': ['bin/spark-shell'], + 'dirs': ['lib', 'python'] +} + +modextrapaths = {'PYTHONPATH': 'python'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..dfcda740abf749e3526172aa9d71843c075f6bfb --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.1.29.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': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True, 'dynamic': 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/Szip/Szip-2.1-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..0772f31b941fc2ede2b6aa53ad18ff9219221e4e --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.25.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': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'dynamic': 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/Szip/Szip-2.1-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..d98933db4b77e10a3b372b457b2863986e4fb218 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-CrayGNU-5.2.40.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': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True, 'dynamic': 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/Szip/Szip-2.1-foss-2014b.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..9d1f75c5eb86da7db35e3da92c6efccddcfa985a --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-foss-2014b.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': '2014b'} +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/Szip/Szip-2.1-ictce-6.1.5.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-6.1.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..d90d48702e0469fa4f0aa9cf1081706f00641106 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1-ictce-6.1.5.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': 'ictce', 'version': '6.1.5'} +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-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..8b997036dd3d105b2ad03a19cf8e61af6ffedf51 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-0.16.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'scikit-learn' +version = '0.16.1' + +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': '2015a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonversion = '2.7.9' +pythonshortversion = ".".join(pythonversion.split(".")[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) +dependencies = [ + (python, pythonversion), + ('matplotlib', '1.4.3', versionsuffix), +] + +options = {'modulename': "sklearn"} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.1.29-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.1.29-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..d6c03f828cc2bd68723d57341873f1a8191cfc2a --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.1.29-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +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': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..be06b3e90748364a0510988c8634683a439b8d2b --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.25-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +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': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..adb35688b359f69ea64a185ea7a641195468a338 --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-CrayGNU-5.2.40-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +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': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'pic': True} + +source_urls = [('http://sourceforge.net/projects/scipy/files/scipy/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('numpy', '1.9.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scipy/scipy-0.15.1-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..f67514e5916421bfda3e3fa28c545750721b5eee --- /dev/null +++ b/easybuild/easyconfigs/s/scipy/scipy-0.15.1-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,19 @@ +name = 'scipy' +version = '0.15.1' +versionsuffix = '-Python-2.7.9' + +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', '1.9.2', versionsuffix), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goalf-1.1.0-no-OFED-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goalf-1.1.0-no-OFED-Python-2.7.3.eb index 5e2b080c59dc4ce83a7ef19afa2d3f5bcbc7ff9a..637462ec29ff5f2a63cdecc706337677342fd364 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goalf-1.1.0-no-OFED-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goalf-1.1.0-no-OFED-Python-2.7.3.eb @@ -3,12 +3,12 @@ easyblock = "PythonPackage" name = "setuptools" version = "0.6c11" -homepage = "http://pypi.python.org/pypi/setuptools/" +homepage = "https://pypi.python.org/pypi/setuptools/" description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" toolchain = {'name': 'goalf', 'version': '1.1.0-no-OFED'} -source_urls = ['http://pypi.python.org/packages/source/s/%s/' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goolf-1.4.10-Python-2.7.3.eb index ca5228d480c75f4316ecddd08120ec083c550381..517404e7700ec39ba6b9ef51f08d33f00768d730 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goolf-1.4.10-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-goolf-1.4.10-Python-2.7.3.eb @@ -3,12 +3,12 @@ easyblock = "PythonPackage" name = "setuptools" version = "0.6c11" -homepage = "http://pypi.python.org/pypi/setuptools/" +homepage = "https://pypi.python.org/pypi/setuptools/" description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" toolchain = {'name': 'goolf', 'version': '1.4.10'} -source_urls = ['http://pypi.python.org/packages/source/s/%s/' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-4.0.6-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-4.0.6-Python-2.7.3.eb index d34f8f5f649f3f3786437bd7c11aa98d5647a907..62aa6e2bbcc7bdd1432818377a253e881197ea17 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-4.0.6-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-4.0.6-Python-2.7.3.eb @@ -3,12 +3,12 @@ easyblock = "PythonPackage" name = "setuptools" version = "0.6c11" -homepage = "http://pypi.python.org/pypi/setuptools/" +homepage = "https://pypi.python.org/pypi/setuptools/" description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" toolchain = {'name': 'ictce', 'version': '4.0.6'} -source_urls = ['http://pypi.python.org/packages/source/s/%s/' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-5.3.0-Python-2.7.3.eb index 612cf670c02d28ee9a97d7fa5d5292f0b0838b0a..82de605fe3249e36e71ce7db371b19c2ec0d74e2 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-5.3.0-Python-2.7.3.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-0.6c11-ictce-5.3.0-Python-2.7.3.eb @@ -3,13 +3,12 @@ easyblock = "PythonPackage" name = "setuptools" version = "0.6c11" -homepage = "http://pypi.python.org/pypi/setuptools/" +homepage = "https://pypi.python.org/pypi/setuptools/" description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" - toolchain = {'name': 'ictce', 'version': '5.3.0'} -source_urls = ['http://pypi.python.org/packages/source/s/%s/' % name] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] python = "Python" diff --git a/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb b/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb index 87db02a9faa43ba673e00b5cf4175b13c6f89847..f08e79381b75e694f1f5c99c093b5cae4fd7c0de 100644 --- a/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb +++ b/easybuild/easyconfigs/s/setuptools/setuptools-1.4.2.eb @@ -3,12 +3,12 @@ easyblock = "VersionIndependentPythonPackage" name = "setuptools" version = "1.4.2" -homepage = "http://pypi.python.org/pypi/setuptools/" +homepage = "https://pypi.python.org/pypi/setuptools/" description = """Download, build, install, upgrade, and uninstall Python packages -- easily!""" toolchain = {'name': 'dummy', 'version': 'dummy'} -source_urls = ['http://pypi.python.org/packages/source/s/%(name)s/'] +source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.2-GCC-4.9.2.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-GCC-4.9.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..551924427db6983d92bab23312dfba6e75b0a384 --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.2-GCC-4.9.2.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'snappy' +version = '1.1.2' + +# snappy was migrated from code.google.com to github.com and this commit +# corresponds to release 1.1.2 (which they haven't tagged). +# see https://github.com/google/snappy/commit/1ff9be9 +commit = '1ff9be9' + +homepage = 'http://code.google.com/p/snappy/' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'GCC', 'version': '4.9.2'} + +source_urls = ['https://github.com/google/snappy/archive'] +sources = ['%s.tar.gz' % commit] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['lib/libsnappy.so'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb new file mode 100644 index 0000000000000000000000000000000000000000..eb194cd37cc756f5b9ea0038082aa08ff50e90f0 --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-3.6-Java-1.7.0_80.eb @@ -0,0 +1,28 @@ +easyblock = 'PackedBinary' + +name = 'snpEff' +version = '3.6' + +homepage = 'http://sourceforge.net/projects/snpeff/' +description = """SnpEff is a variant annotation and effect prediction tool. + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) + +source_urls = [SOURCEFORGE_SOURCE] +sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] + +dependencies = [(java, javaver)] + +checksums = ['f4571413833df913261ff76b6f40bb76'] + +sanity_check_paths = { + 'files': ['snpEff.jar', 'SnpSift.jar'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb b/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb new file mode 100644 index 0000000000000000000000000000000000000000..8b1570a18150845687b89346f1c32f6eeb2a6e47 --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-4.1d-Java-1.7.0_80.eb @@ -0,0 +1,28 @@ +easyblock = 'PackedBinary' + +name = 'snpEff' +version = '4.1d' + +homepage = 'http://sourceforge.net/projects/snpeff/' +description = """SnpEff is a variant annotation and effect prediction tool. + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +java = 'Java' +javaver = '1.7.0_80' +versionsuffix = '-%s-%s' % (java, javaver) + +source_urls = [SOURCEFORGE_SOURCE] +sources = [('%s_v%s_core.zip' % (name, version.replace('.', '_')))] + +dependencies = [(java, javaver)] + +checksums = ['23b48ebe02288c1e3c5c0391949eea5a'] + +sanity_check_paths = { + 'files': ['snpEff.jar', 'SnpSift.jar'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/spglib/spglib-1.7.3-intel-2015a.eb b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..f6b34ab67040f9b8b01e2071dd256ddba174c843 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib/spglib-1.7.3-intel-2015a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'spglib' +version = '1.7.3' + +homepage = 'http://spglib.sourceforge.net/' +description = """Spglib is a C library for finding and handling crystal symmetries.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] + +start_dir = '%(name)s-%(version)s' + +sanity_check_paths = { + 'files': ['lib/libsymspg.a', 'lib/libsymspg.so'], + 'dirs': ['include/spglib'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb b/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb index 04c3e479884ed83d5d1fa558bd40362afa36de7c..241a1d5fbffd4c00660499cb945886844c5d629f 100644 --- a/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb +++ b/easybuild/easyconfigs/s/stemming/stemming-1.0-ictce-5.5.0-Python-2.7.6.eb @@ -3,7 +3,7 @@ easyblock = "PythonPackage" name = "stemming" version = "1.0" -homepage = "http://pypi.python.org/pypi/stemming/" +homepage = "https://pypi.python.org/pypi/stemming/" description = """Python implementations of the Porter, Porter2, Paice-Husk, and Lovins stemming algorithms for English.""" toolchain = {'name': 'ictce', 'version': '5.5.0'} diff --git a/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb b/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb new file mode 100644 index 0000000000000000000000000000000000000000..4722866acfba5f7a604033484922154903cdf825 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-0.7.6-intel-2015a-Python-2.7.9.eb @@ -0,0 +1,32 @@ +easyblock = "PythonPackage" + +name = 'sympy' +version = '0.7.6' + +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': '2015a'} + +source_urls = ['https://github.com/sympy/sympy/releases/download/sympy-%(version)s/'] +sources = [SOURCE_TAR_GZ] + +python = "Python" +pythonversion = '2.7.9' +pythonshortversion = '.'.join(pythonversion.split('.')[:-1]) + +versionsuffix = "-%s-%s" % (python, pythonversion) + +dependencies = [(python, pythonversion)] + +runtest = 'python setup.py test' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages/sympy' % pythonshortversion], +} + +moduleclass = 'math' 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 new file mode 100644 index 0000000000000000000000000000000000000000..bd202e0e1bf8a43b6fd3ea50ee862a587774a3e8 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-foss-2015.05.eb @@ -0,0 +1,25 @@ +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': 'foss', 'version': '2015.05'} + +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-goolf-1.7.20.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..41060701af9d916894364e98bb050cbfe6e2e6ed --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.3-goolf-1.7.20.eb @@ -0,0 +1,25 @@ +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': 'goolf', 'version': '1.7.20'} + +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-foss-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..d1a6b6efb26e8bf4f455a9d38d6b9aec575cc312 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-foss-2015a.eb @@ -0,0 +1,25 @@ +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': 'foss', 'version': '2015a'} + +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-goolf-1.7.20.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..e2124cc24dd1bd2fd38f2e70acc86afe3d7ba90f --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-goolf-1.7.20.eb @@ -0,0 +1,25 @@ +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': 'goolf', 'version': '1.7.20'} + +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-ictce-7.3.5.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-ictce-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..ab1bbc53d31b00003a7e6f78f26dedd3ebaa3230 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-ictce-7.3.5.eb @@ -0,0 +1,25 @@ +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': 'ictce', 'version': '7.3.5'} + +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-intel-2015a.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..b2673863fdd00046885a98f13efe2283adfbd6ad --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.4-intel-2015a.eb @@ -0,0 +1,25 @@ +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': 'intel', 'version': '2015a'} + +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/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..335241b80726b196c98de41bb1409b9db0df06ee --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-goolf-1.4.10-Python-2.7.3.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'Theano' +version = '0.6.0' + +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': 'goolf', 'version': '1.4.10'} + +source_urls = ['https://pypi.python.org/packages/source/T/%s' % name] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'lib/python%s/site-packages/%s-%s-py%s.egg' + % (pythonshortver, name, version, pythonshortver)], + 'dirs': [] +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..a9aa394aab847d79036b6f808f6ed0476689fee3 --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-0.6.0-ictce-5.3.0-Python-2.7.3.eb @@ -0,0 +1,28 @@ +easyblock = "PythonPackage" + +name = 'Theano' +version = '0.6.0' + +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': 'ictce', 'version': '5.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/T/%s' % name] +sources = [SOURCE_TAR_GZ] + +python = 'Python' +pythonver = '2.7.3' +pythonshortver = '.'.join(pythonver.split('.')[0:2]) +versionsuffix = '-%s-%s' % (python, pythonver) + +dependencies = [(python, pythonver)] + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'lib/python%s/site-packages/%s-%s-py%s.egg' + % (pythonshortver, name, version, pythonshortver)], + 'dirs': [] +} + +moduleclass = 'math' 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 new file mode 100644 index 0000000000000000000000000000000000000000..602101704ac40739961538d102c4e94d3d2da717 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-GCC-4.9.2-no-X11.eb @@ -0,0 +1,24 @@ +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': '4.9.2'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +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-foss-2015.05-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..8ff29d34a28dd637d9b8ea3b684e3144f2ae75c4 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015.05-no-X11.eb @@ -0,0 +1,24 @@ +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': 'foss', 'version': '2015.05'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +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-foss-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..c34f24fd99b7d222605dc64889c19d9310eb082e --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-foss-2015a-no-X11.eb @@ -0,0 +1,24 @@ +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': 'foss', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +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-gompi-1.5.16-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..a292e06eb8d354f8f350dd93a00f2cdba642f757 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-gompi-1.5.16-no-X11.eb @@ -0,0 +1,24 @@ +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': 'gompi', 'version': '1.5.16'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +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-goolf-1.5.14-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..cd4da6afb65ea2c76938a0a1ab28ece42f2ed959 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.5.14-no-X11.eb @@ -0,0 +1,24 @@ +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': 'goolf', 'version': '1.5.14'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +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-goolf-1.7.20-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..025f5e64769cc609b4615df61b60138d4101d5cf --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-goolf-1.7.20-no-X11.eb @@ -0,0 +1,24 @@ +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': 'goolf', 'version': '1.7.20'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +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-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..d841e7bd84c473523c5a9279634389b6e9572d7b --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.3-intel-2015a-no-X11.eb @@ -0,0 +1,24 @@ +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': 'intel', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +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-foss-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..fee35bd216f5d347a3b2c3dffd9d79d6d18da047 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-foss-2015a-no-X11.eb @@ -0,0 +1,24 @@ +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': 'foss', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +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-goolf-1.7.20-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..5d72cc8d790953b40950a662062b17a3c547e1e9 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-goolf-1.7.20-no-X11.eb @@ -0,0 +1,24 @@ +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': 'goolf', 'version': '1.7.20'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +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-ictce-7.3.5-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..2363e89fc918cbdd0f68d3b8cf4811bb6e42be1e --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-ictce-7.3.5-no-X11.eb @@ -0,0 +1,24 @@ +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': 'ictce', 'version': '7.3.5'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +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-intel-2015a-no-X11.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb new file mode 100644 index 0000000000000000000000000000000000000000..39ccca9596c474a28981fb45da38dba7155449b0 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.4-intel-2015a-no-X11.eb @@ -0,0 +1,24 @@ +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': 'intel', 'version': '2015a'} + +source_urls = ["http://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] + +dependencies = [ + ('Tcl', version), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib --without-x CFLAGS="-I$EBROOTTCL/include"' + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..d99d70b100c2417eddd9b9f880f16acc2a59ca79 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.13-goolf-1.7.20.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 = 'TopHat' +version = '2.0.13' + +homepage = 'http://ccb.jhu.edu/software/tophat/' +description = """TopHat is a fast splice junction mapper for RNA-Seq reads.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] + +patches = ['tophat-%(version)s-zlib.patch'] + +dependencies = [ + ('Boost', '1.55.0'), + ('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/TopHat/TopHat-2.0.14-goolf-1.7.20.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..6743572399208ab0950369ed77f5e3a8357cfc1a --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.14-goolf-1.7.20.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 = 'TopHat' +version = '2.0.14' + +homepage = 'http://ccb.jhu.edu/software/tophat/' +description = """TopHat is a fast splice junction mapper for RNA-Seq reads.""" + +toolchain = {'name': 'goolf', 'version': '1.7.20'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://ccb.jhu.edu/software/tophat/downloads/'] + +patches = ['tophat-2.0.13-zlib.patch'] + +dependencies = [ + ('Boost', '1.58.0'), + ('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/TopHat/tophat-2.0.13-zlib.patch b/easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch new file mode 100644 index 0000000000000000000000000000000000000000..6021cbe107fb5f9f9b25ebfe6dbff72ec0eb3038 --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/tophat-2.0.13-zlib.patch @@ -0,0 +1,12 @@ +diff -ru tophat-2.0.13.orig/src/samtools-0.1.18/Makefile tophat-2.0.13/src/samtools-0.1.18/Makefile +--- tophat-2.0.13.orig/src/samtools-0.1.18/Makefile 2014-09-25 04:38:49.000000000 +0200 ++++ tophat-2.0.13/src/samtools-0.1.18/Makefile 2015-06-03 18:10:39.588554000 +0200 +@@ -12,7 +12,7 @@ + PROG= samtools_0.1.18 + INCLUDES= -I. + SUBDIRS= . bcftools +-LIBPATH= ++LIBPATH= -L$(EBROOTZLIB)/lib + LIBCURSES= -lcurses + + .SUFFIXES:.c .o 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 new file mode 100644 index 0000000000000000000000000000000000000000..4ab3c4b882088688322a148927a4bae7ce718c7b --- /dev/null +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-goolf-1.4.10.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': 'goolf', 'version': '1.4.10'} + +source_urls = [('http://sourceforge.net/projects/samtools/files/', 'download')] +sources = [SOURCE_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +buildopts = '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-intel-2014b.eb b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..355e0eb0ad04f64903e2d076425ac06aa09873d3 --- /dev/null +++ b/easybuild/easyconfigs/t/tabix/tabix-0.2.6-intel-2014b.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': '2014b'} + +source_urls = [('http://sourceforge.net/projects/samtools/files/', 'download')] +sources = [SOURCE_TAR_BZ2] + +dependencies = [('zlib', '1.2.8')] + +buildopts = '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/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..b62190e55f4ee003cc0f723aa4ddedcdf960d91c --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.1.29.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/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..c678adaf683a57839c16531ca33c276f4031143b --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.25.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/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..171465e133945344b370cb31c81e9ce2b73c8938 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-CrayGNU-5.2.40.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/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'dynamic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..4b5f7237ff41083d2d456bc2eae3cb1bbc8daef7 --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.18.01-foss-2015a.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/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.18.01' + +homepage = 'http://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [ + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] + +dependencies = [('ncurses', '5.9')] + +sanity_check_paths = { + 'files': ["bin/tcsh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb new file mode 100644 index 0000000000000000000000000000000000000000..40607b696078338253ed8b22aea8d9883ced9f7a --- /dev/null +++ b/easybuild/easyconfigs/t/tecplot360ex/tecplot360ex-linux64.eb @@ -0,0 +1,24 @@ +easyblock = 'Binary' + +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. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# fi. http://www.tecplot.com/my/product-releases/ +installername = '%(name)s_%(version)s.sh' +sources = [installername] + +sanity_check_paths = { + 'files': ['bin/tec360'], + 'dirs': [] +} +install_cmd = 'chmod +x %s && ./%s --skip-license --prefix=%%(installdir)s' % (installername, installername) + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..dc874b1a62fe2986c85058a879b4b7232dfc0a43 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.26.1-foss-2015a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.26.1' + +homepage = 'http://www.kernel.org/pub/linux/utils/util-linux' +description = """Set of Linux utilities""" + +toolchain = {'name': 'foss', 'version': '2015a'} + +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', '5.9')] + +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/Vampir/Vampir-8.4.1-demo.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb new file mode 100644 index 0000000000000000000000000000000000000000..44f692903f0e41917736d8694c88fc073ec3a934 --- /dev/null +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1-demo.eb @@ -0,0 +1,44 @@ +## +# 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 = 'Binary' + +name = "Vampir" +version = "8.4.1" +versionsuffix = "-demo" +variant = "linux-x86_64" + +homepage = 'http://www.vampir.eu' +description = """The Vampir software tool provides an easy-to-use framework that enables + developers to quickly display and analyze arbitrary program behavior at any level of detail. + The tool suite implements optimized event analysis algorithms and customizable displays that + enable fast and interactive rendering of very complex performance monitoring data.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['vampir-%s%s-%s-setup.bin' % (version, versionsuffix, variant)] + +# Adjust this variable to point to the location of your Vampir license file +license_file = '/example/licenses/path/vampir.license' + +install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" + +sanity_check_paths = { + 'files': ["bin/vampir", "doc/vampir-manual.pdf"], + 'dirs': [] +} + +modextravars = { + 'VAMPIR_LICENSE': license_file, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb new file mode 100644 index 0000000000000000000000000000000000000000..5596a89f02442f10f19bf1942e7d6af6aab59965 --- /dev/null +++ b/easybuild/easyconfigs/v/Vampir/Vampir-8.4.1.eb @@ -0,0 +1,47 @@ +## +# 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 = 'Binary' + +name = "Vampir" +version = "8.4.1" +variant = "linux-x86_64" + +homepage = 'http://www.vampir.eu' +description = """The Vampir software tool provides an easy-to-use framework that enables + developers to quickly display and analyze arbitrary program behavior at any level of detail. + The tool suite implements optimized event analysis algorithms and customizable displays that + enable fast and interactive rendering of very complex performance monitoring data.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['vampir-%s-%s-setup.bin' % (version, variant)] + +checksums = [ + '471840910cd552a5a788df3b69251d29', # vampir-8.4.1-linux-x86_64-setup.bin +] + +# Adjust this variable to point to the location of your Vampir license file +license_file = '/example/licenses/path/vampir.license' + +install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s --no-icon --no-menu-items --no-trace-file-association" + +sanity_check_paths = { + 'files': ["bin/vampir", "doc/vampir-manual.pdf"], + 'dirs': [] +} + +modextravars = { + 'VAMPIR_LICENSE': license_file, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5b068e3cf704aa9f792ebf374f73eb95d57caa6c --- /dev/null +++ b/easybuild/easyconfigs/v/VampirServer/VampirServer-8.4.1-gompi-2015a.eb @@ -0,0 +1,48 @@ +## +# 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 = 'Binary' + +name = "VampirServer" +version = "8.4.1" +variant = "linux-x86_64" + +homepage = 'http://www.vampir.eu' +description = """The Vampir software tool provides an easy-to-use framework that enables + developers to quickly display and analyze arbitrary program behavior at any level of detail. + The tool suite implements optimized event analysis algorithms and customizable displays that + enable fast and interactive rendering of very complex performance monitoring data.""" + +toolchain = {'name': 'gompi', 'version': '2015a'} +toolchainopts = {"usempi": True} + +sources = ['vampirserver-%s-%s-setup.bin' % (version, variant)] + +checksums = [ + '2a2236bb071168b7d488c83363c30ac8', # vampirserver-8.4.1-linux-x86_64-setup.bin +] + +# Adjust this variable to point to the location of your Vampir license file +license_file = '/example/licenses/path/vampir.license' + +install_cmd = "./" + sources[0] + " --silent --instdir=%(installdir)s && %(installdir)s/bin/vampirserver config --silent" + +sanity_check_paths = { + 'files': ["bin/vampirserver", "doc/vampirserver-manual.pdf", "lib/vampirserver-driver.so"], + 'dirs': [] +} + +modextravars = { + 'VAMPIR_LICENSE': license_file, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb new file mode 100644 index 0000000000000000000000000000000000000000..1d1bbb0d8acf0a4cc7e9f088a437da70d9127115 --- /dev/null +++ b/easybuild/easyconfigs/v/verifyBamID/verifyBamID-1.1.2-goolf-1.7.20.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'verifyBamID' +version = '1.1.2' + +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': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/statgen/%(name)s/releases/download/v%(version)s'] +sources = ['%(name)sLibStatGen.%(version)s.tgz'] + +checksums = ['fafc6fa58ba2bd51d0324ae616f5b29e'] + +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-2.0.4.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.0.4.eb new file mode 100644 index 0000000000000000000000000000000000000000..24862f2519145bfb1257355b62a091a4d89d81c7 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.0.4.eb @@ -0,0 +1,17 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'vsc-base' +version = '2.0.4' + +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.""" + +# we build this to work with every python version +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +options = {'modulename': 'vsc.utils'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-base/vsc-base-2.1.2.eb b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.1.2.eb new file mode 100644 index 0000000000000000000000000000000000000000..b0db50051eb15dbfe604a073d9fb78eb81e2cf90 --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-base/vsc-base-2.1.2.eb @@ -0,0 +1,17 @@ +easyblock = 'VersionIndependentPythonPackage' + +name = 'vsc-base' +version = '2.1.2' + +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.""" + +# we build this to work with every python version +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_SOURCE] + +options = {'modulename': 'vsc.utils'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb new file mode 100755 index 0000000000000000000000000000000000000000..e24521bcf5d389fad7aaf9e7ad6389842529435d --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-3.4.2.eb @@ -0,0 +1,25 @@ +easyblock = 'VSCPythonPackage' + +name = 'vsc-mympirun' +version = '3.4.2' + +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.""" + +# we build this to work with every python version +toolchain = {'name': 'dummy', 'version': ''} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/hpcugent/vsc-mympirun/archive/'] + +dependencies = [ + ('vsc-base', '2.1.2'), + ('setuptools', '1.4.2'), +] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +options = {'modulename': 'vsc.mympirun'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2014b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2014b.eb new file mode 100644 index 0000000000000000000000000000000000000000..9a8f71d9ca8e939815707671b685d6e483d14fc2 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2014b.eb @@ -0,0 +1,46 @@ +name = 'WIEN2k' +version = '14.1' + +homepage = 'http://www.wien2k.at/' +description = """The program package WIEN2k allows to perform electronic structure calculations of solids +using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave +((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. +WIEN2k is an all-electron scheme including relativistic effects and has many features.""" + +toolchain = {'name': 'intel', 'version': '2014b'} + +sources = ['%(name)s_%(version)s.tar'] +checksums = ['b926596ea86d505120af8829cec4814e'] + +patches = [ + 'WIEN2k-%(version)s_lapw5-main-accuracy-fix.patch', + 'WIEN2k-%(version)s_fix-tetra.patch', + 'WIEN2k-%(version)s_fix-x_lapw.patch', +] + +dependencies = [('FFTW', '3.3.4')] + +osdependencies = ['glib-devel'] # required for libpthread.a + +remote = 'pbsssh' +wien_mpirun = 'mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_' +use_remote = True +mpi_remote = False +wien_granularity = True +taskset = 'no' + +tests = [ + # test case 1: NaCl + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1227', r'^:ENE.*-1248.1427']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [ + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*14.63.*total forces', + ]), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2015a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..a5d641a90f9785c8324c4cdf0f45a475be8ceaa8 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1-intel-2015a.eb @@ -0,0 +1,46 @@ +name = 'WIEN2k' +version = '14.1' + +homepage = 'http://www.wien2k.at/' +description = """The program package WIEN2k allows to perform electronic structure calculations of solids +using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave +((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. +WIEN2k is an all-electron scheme including relativistic effects and has many features.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['%(name)s_%(version)s.tar'] +checksums = ['b926596ea86d505120af8829cec4814e'] + +patches = [ + 'WIEN2k-%(version)s_lapw5-main-accuracy-fix.patch', + 'WIEN2k-%(version)s_fix-tetra.patch', + 'WIEN2k-%(version)s_fix-x_lapw.patch', +] + +dependencies = [('FFTW', '3.3.4')] + +osdependencies = ['glib-devel'] # required for libpthread.a + +remote = 'pbsssh' +wien_mpirun = 'mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_' +use_remote = True +mpi_remote = False +wien_granularity = True +taskset = 'no' + +tests = [ + # test case 1: NaCl + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1227', r'^:ENE.*-1248.1427']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [ + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*14.63.*total forces', + ]), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-tetra.patch b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-tetra.patch new file mode 100644 index 0000000000000000000000000000000000000000..ef8bc83ba2a31323f868a63a562c13d666ecedf4 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-tetra.patch @@ -0,0 +1,57 @@ +see http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg11178.html +--- WIEN2k_14.orig/SRC_tetra/tetra.f 2014-09-19 13:30:20.757390463 +0200 ++++ WIEN2k_14/SRC_tetra/tetra.f 2014-09-19 13:30:37.671774186 +0200 +@@ -165,7 +165,7 @@ + SO=1.d0 + NSORT=1 + KLMAX=1 +- allocate( TEXT(Nsort+1),QTL(Nsort+1,klmax+1),xqtl(nsort,lxdos2*(lxdos2+1)) ) ++ allocate( TEXT(0:Nsort+1),QTL(Nsort+1,klmax+1),xqtl(nsort,lxdos2*(lxdos2+1)) ) + IDOS(1,1)=0 + IDOS(1,2)=0 + DOSTYP(1)='TOTAL' +@@ -220,7 +220,7 @@ + READ(4,1010) ALAT1,ALAT2,ALAT3,EFERM + READ(4,1020) MINWAV,MAXWAV,KSPIN,NSORT,kso,kLmax + if(klmax.eq.0) klmax=14 +- allocate( TEXT(Nsort+1),QTL(Nsort+1,klmax+1),xqtl(nsort,lxdos2*(lxdos2+1)) ) ++ allocate( TEXT(0:Nsort+1),QTL(Nsort+1,klmax+1),xqtl(nsort,lxdos2*(lxdos2+1)) ) + ! INCREASE NSORT BY ONE FOR THE INTERSTITIAL DOS (OUT) + NSORT=NSORT+1 + WRITE(6,2000) SYSTEM +@@ -240,7 +240,7 @@ + DO 107 ISORT=1,NSORT + IF(ISORT.EQ.NSORT) GOTO 107 + READ(4,1030) JATOM,NEQU,isplit,text(isort) +- WRITE(6,2030) JATOM,NEQU,isplit,text(isort) ++ WRITE(6,2030) JATOM,NEQU,isplit,text(isort) + 107 CONTINUE + nndos_save=nndos + DO 90 JCASE=1,NNDOS +@@ -364,7 +364,11 @@ + if(nst.eq.1.and.ibrsw.eq.-1) then ! for one k-point calculate the DOS with broadening + ibrsw=1 + print*,'Only 1 k-point, switching to Gauss-broadening with',br +- endif ++ if(br.lt.1.d-6) then ++ br=0.002 ++ print*,' No broadening specified, increasing broadening to',br ++ endif ++ endif + if(ibrsw.ne.-1) then + CALL broadDOS (ibrsw,br,brlor,NNDOS,1,JEND,EMIN,EMAX,NYMIN,NYMAX,DE,ebs,fc,nst,densty) + endif +@@ -523,7 +527,7 @@ + 1000 FORMAT(1X,A70,/) + 1010 FORMAT(1X,15X,3F8.5,16X,F10.5) + 1020 FORMAT(1X,I4,10X,I4,8X,I1,7X,I3,8x,i2,6x,i3) +- 1030 FORMAT(6X,I3,7X,I2,9x,i2,2x,a200) ++ 1030 FORMAT(6X,I3,7X,I2,9x,i2,2x,a96) + 1040 FORMAT(6X,I4) + 1041 FORMAT(5X,I5) + 1050 FORMAT(F10.5,I3,F8.5,3X,(40F8.5)) +@@ -532,3 +536,4 @@ + 2020 FORMAT(1X,I4,' < NMAT < ',I4,3X,'SPIN=',I1,3X,'NATO=',I4) + 2030 FORMAT(1X,'JATOM',I3,2X,'MULT=',I2,2x,'ISPLIT=',i2,2x,a96) + END ++ diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-x_lapw.patch b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-x_lapw.patch new file mode 100644 index 0000000000000000000000000000000000000000..a17c8dbe5829412b32d7d512b6a74b4dbae0f94d --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_fix-x_lapw.patch @@ -0,0 +1,461 @@ +see http://zeus.theochem.tuwien.ac.at/pipermail/wien/2014-September/021667.html +--- x_lapw.orig 2014-10-09 15:03:02.181799391 +0200 ++++ x_lapw 2014-10-09 15:08:25.254125143 +0200 +@@ -4,28 +4,28 @@ + set running = ".running.$$.`hostname`.`date +%d%m%H%M%S`" + echo $$ >$running + onintr clear +-alias error 'echo ">>> ($name) \!* -> exit"; goto error' ++alias error 'echo ">>> ($name) \!* -> exit"; goto error' + +-set name = $0 #full name of script-file +-set bin = $name:h #default directory for WIEN-executables ++set name = $0 #full name of script-file ++set bin = $name:h #default directory for WIEN-executables + if !(-d $bin) set bin = . +-set name = $name:t ++set name = $name:t + +-set def = def #def-file +-set tmp = ( ) #tmp-files, to be deleted before exit +-set log = :log #log-file +-set t = time # +-set updn # spinpolarization switch +-set dnup = 'dn' # spinpolarization switch ++set def = def #def-file ++set tmp = ( ) #tmp-files, to be deleted before exit ++set log = :log #log-file ++set t = time # ++set updn # spinpolarization switch ++set dnup = 'dn' # spinpolarization switch + set spin=1 # for -it in lapw1 + #set ne_it=1.1 # for -it in lapw1 + set emin=-999.0 # for -emin XX in lapw2 + set emax=999.0 # for -all XX YY in lapw2 + set settol=0.00001 # tol parameter for sgroup + set wf=0 # wplot: WF to plot (0 = read from file) +-set sc # semicore-switch +-set so # spinorbit-switch +-set sodum # spinorbit-switch ++set sc # semicore-switch ++set so # spinorbit-switch ++set sodum # spinorbit-switch + #set cmplx + set cmplx1 + set cmplx2 +@@ -62,12 +62,12 @@ + unset efg # regular run in lapw2 + unset emin1 # regular run in lapw2 + unset emax1 # regular run in lapw2 +-unset command #command +-unset file #file-head +-unset deffile_only #create just def file +-unset fftstop #for dstart +-unset vresp #for lapw2 +-unset help_files #for lapw2 ++unset command #command ++unset file #file-head ++unset deffile_only #create just def file ++unset fftstop #for dstart ++unset vresp #for lapw2 ++unset help_files #for lapw2 + unset super # for dstart, creates new.clmsum + unset rxes # for tetra, uses rxes-weight file + unset rxesw # for tetra, writes rxes-weight file +@@ -88,9 +88,9 @@ + + if ( $?SCRATCH && $SCRATCH != '') then + set scratch=`echo $SCRATCH | sed -e 's/\/$//'`/ # we are afraid +- # different settings in different +- # computing centers +- #use global variable for scratch if set ++ # different settings in different ++ # computing centers ++ #use global variable for scratch if set + endif + set argv1=($argv) + +@@ -138,16 +138,16 @@ + shift; breaksw + case -it: + set iter +- shift; breaksw ++ shift; breaksw + case -noHinv: + set iter + unset readHinv +- shift; breaksw ++ shift; breaksw + case -noHinv0: + set iter + unset readHinv + set writeHinv +- shift; breaksw ++ shift; breaksw + # case -ne_it: + # shift;set ne_it=$1 + # shift; breaksw +@@ -169,36 +169,36 @@ + shift; breaksw + case -help_files: + set help_files +- shift; breaksw ++ shift; breaksw + case -vresp: + set vresp +- shift; breaksw ++ shift; breaksw + case -eece: + set eece=eece +- shift; breaksw ++ shift; breaksw + case -grr: + set grr=grr +- shift; breaksw ++ shift; breaksw + case -orb: + set orb +- shift; breaksw ++ shift; breaksw + case -nmat_only: + set nmat_only +- shift; breaksw ++ shift; breaksw + case -nohns: + set nohns +- shift; breaksw ++ shift; breaksw + case -enefile: + set enefile +- shift; breaksw ++ shift; breaksw + case -rxes: + set rxes +- shift; breaksw ++ shift; breaksw + case -rxesw: + set rxesw + shift;set rxese1 = $1 + shift;set rxese2 = $1 +- shift; breaksw ++ shift; breaksw + case -so: + set so = 'so' + set sodum = 'dum' +@@ -313,7 +313,7 @@ + endif + shift; breaksw + ## w2w stuff ## +- case -pp: # passed on to Wannier90 ++ case -pp: # passed on to Wannier90 + shift; breaksw + case -wf: + shift; set wf = $1 +@@ -338,7 +338,7 @@ + + if !($?file) then + set file = `pwd` +-set file = $file:t #tail of file-names ++set file = $file:t #tail of file-names + endif + + touch $file.struct +@@ -409,7 +409,7 @@ + #echo "`date`> ($name) $command $argv1[2-]" >> $log + echo "`date`> ($name) $argv1" >> $log + +-set def = $updn$command$sc.def ++set def = $updn$command$sc.def + #touch $def + + switch ($command) +@@ -1200,7 +1200,7 @@ + cat << theend > $def + 6,'$file.outputst', 'unknown','formatted' + 7,'$file.tmpden', 'unknown','formatted' +-10,'$file.tmp', 'unknown','unformatted' ++10,'$file.tmp', 'unknown','unformatted' + 11,'$file.vsp_st', 'unknown','formatted' + 12,'$file.vspdn_st', 'unknown','formatted' + 13,'$file.sigma', 'unknown','formatted' +@@ -1268,7 +1268,7 @@ + + case mixer_vresp: + set exe = mixer +- if !(-e $file.clmvalup || -z $file.clmvalup) then ++ if !(-e $file.clmvalup || -z $file.clmvalup) then + cat << theend > $def + 5,'$file.inm_vresp', 'old', 'formatted',0 + 6,'$file.outputm_vresp', 'unknown','formatted',0 +@@ -1283,7 +1283,7 @@ + 32,'$file.vrespbroyd2', 'unknown','unformatted',164896 + 51,'$file.vrespsum', 'unknown','formatted',0 + theend +- else ++ else + cat << theend > $def + 5,'$file.inm_vresp', 'old', 'formatted',0 + 6,'$file.outputm_vresp', 'unknown','formatted',0 +@@ -1304,7 +1304,7 @@ + 52,'$file.vrespdn', 'unknown','formatted',0 + 11,'$file.vrespsum', 'unknown','formatted',0 + theend +- endif ++ endif + breaksw + + +@@ -1318,7 +1318,7 @@ + cp $file.struct $file.struct_old + endif + set exe = $command +- if !(-e $file.clmvalup || -z $file.clmvalup) then ++ if !(-e $file.clmvalup || -z $file.clmvalup) then + cat << theend > $def + 5,'$file.inm', 'old', 'formatted',0 + 6,'$file.outputm', 'unknown','formatted',0 +@@ -1334,7 +1334,7 @@ + 32,'$file.broyd2', 'unknown','unformatted',164896 + 51,'$file.clmsum', 'unknown','formatted',0 + theend +- else ++ else + cat << theend > $def + 5,'$file.inm', 'old', 'formatted',0 + 6,'$file.outputm', 'unknown','formatted',0 +@@ -1364,7 +1364,7 @@ + echo "75,'$file.dmatdn_old','unknown','formatted',0" >> $def + echo "76,'$file.dmatud_old','unknown','formatted',0" >> $def + endif +- endif ++ endif + + if($eece == 'eece') then + echo "71,'$file.vorbup','unknown','formatted',0" >> $def +@@ -1557,16 +1557,16 @@ + if($para == para) then + set cnum=0 + if(-f .processes) then +- @ cnum=`grep -ce "^[0-9][0-9]* :" .processes` +-# @ cnum+=1 ++ @ cnum=`grep -ce "^[0-9][0-9]* :" .processes` ++# @ cnum+=1 + endif + #the original file will only be removed if there are sources to concat + if(-f "$file.output$typ$updnso" && $cnum>0) then +- rm "$file.output$typ$updnso" ++ rm "$file.output$typ$updnso" + endif + unset irr + if(-f "$file.irrep$hf$so${updn}_$cnum" && $cnum>0) then +- if(-f "$file.irrep$hf$so${updn}" ) rm "$file.irrep$hf$so${updn}" ++ if(-f "$file.irrep$hf$so${updn}" ) rm "$file.irrep$hf$so${updn}" + head -2 "$file.irrep$hf$so${updn}_$cnum" >"$file.irrep$hf$so${updn}" + set irr + endif +@@ -1574,9 +1574,9 @@ + while($count <= $cnum) + if($?irr) then + tail -n +3 $file.irrep$hf$so${updn}_$count >>$file.irrep$hf$so${updn} +- endif ++ endif + cat "$file.output$typ${updnso}_$count" >>"$file.output$typ$updnso" +- @ count++ ++ @ count++ + end + echo $file.output$typ$updnso created from $cnum parallel files + endif +@@ -2251,10 +2251,10 @@ + 7,'$file.amn$w90updn', 'unknown','formatted', 0 + 8,'$file.mmn$w90updn', 'unknown','formatted', 0 + 9,'${scratch}$file.vector$sc$hf$soupdn', 'unknown','unformatted',9000 +- 10,'$file.nnkp', 'old', 'formatted', 0 +- 12,'$file.eig$updn', 'unknown','formatted', 0 ++ 10,'$file.nnkp', 'old', 'formatted', 0 ++ 12,'$file.eig$updn', 'unknown','formatted', 0 + 18,'$file.vsp$updn', 'old', 'formatted', 0 +- 20,'$file.struct', 'old', 'formatted', 0 ++ 20,'$file.struct', 'old', 'formatted', 0 + 50,'$file.energy$soupdn', 'old', 'formatted', 0 + 51,'$file.fermi$updn' 'old', 'formatted', 0 + EOF +@@ -2296,23 +2296,23 @@ + if ($para == para) then + set cnum=0 + if(-f .processes) then +- @ cnum=`grep -ce "^[0-9][0-9]* :" .processes` ++ @ cnum=`grep -ce "^[0-9][0-9]* :" .processes` + endif + #the original file will only be removed if there are sources to concat + if(-f "$file.output$typ$updnso" && $cnum>0) then +- rm "$file.output$typ$updnso" ++ rm "$file.output$typ$updnso" + endif + set count=1 + while($count <= $cnum) + cat "$file.output$typ${updnso}_$count" >>"$file.output$typ$updnso" +- @ count++ ++ @ count++ + end + echo $file.output$typ$updnso created from $cnum parallel files + endif + cat >$def <$def + 4,'$file.klist', 'old', 'formatted', 0 + 10,'${scratch}$file.vector$sc$hf$so$updn', 'old', 'unformatted',0 +- 11,'$file.vector$sc$hf$so$updn', 'unknown','unformatted',0 +- 20,'$file.struct', 'old', 'formatted', 0 ++ 11,'$file.vector$sc$hf$so$updn', 'unknown','unformatted',0 ++ 20,'$file.struct', 'old', 'formatted', 0 + 50,'$file.energy$so$updn', 'old', 'formatted', 0 + 51,'$file.energy$so$updn', 'unknown','formatted', 0 + EOF +@@ -2402,7 +2402,7 @@ + ### end w2w ### + + default: +-error command $command does not exist ++error command $command does not exist + breaksw + + endsw +@@ -2445,10 +2445,11 @@ + if ($gw == 'gw') then + set exe = ($exe -gw) + endif +-endif ++endif + + echo $exe >>$running + $t $bin/$exe $def ++ + if($status != 0) then + echo "error: command $bin/$exe $def failed" + if ($?qtl || $?alm || $?almd || $?qdmft || $?band || $?fermi || $?efg || $?emin1 || $?emax1 ) then +@@ -2468,28 +2469,28 @@ + + set lapw2test=`echo $exe | cut -c 1-5` + if("$lapw2test" == 'lapw2') then ++ if ($?qtl || $?alm || $?almd || $?qdmft || $?band || $?fermi || $?efg || $?emin1 || $?emax1 ) then ++ if( -e .oldin2 ) mv .oldin2 $file.in2$cmplx ++ endif + if(! $?in1orig & ! $?band & ! $?emin1 & ! $?emax1) then +- if( -e $file.scf2$sc$updn && ! -z $file.scf2$sc$updn) then +- if($cmplx == 'c') then ++ if( -e $file.scf2$sc$updn && ! -z $file.scf2$sc$updn) then ++ if($cmplx == 'c') then + if(! (-e $file.in1$cmplx$sc && ! -z $file.in1$cmplx$sc)) set cmplx + endif +- set eferm=`grep ':FER :' $file.scf2$sc$updn|cut -f 2 -d=` +- set efold=`head -1 $file.in1$cmplx${sc}|cut -c11-17 | sed -e "s/[a-zA-Z(,=]//g"` ++ set eferm=`grep ':FER :' $file.scf2$sc$updn|cut -f 2 -d=` ++ set efold=`head -1 $file.in1$cmplx${sc}|cut -c11-17 | sed -e "s/[a-zA-Z(,=]//g"` + if($#efold == 0 ) set efold=0.5 +- set eferm=`echo " if($eferm > $efold) {if ($eferm > $efold + 0.2) {$efold + 0.2} else {$eferm} } else {if($eferm < $efold - 0.2) {$efold - 0.2} else ($eferm*0.75+$efold*0.25) }" | bc -l` # allow for max change of ef-old +- 0.2, pratt mix +- set modus=`head -1 $file.in1$cmplx${sc} | cut -c1-5` +- echo "$modus EF=$eferm (WFFIL, WFPRI, ENFIL, SUPWF) " >$file.in1$cmplx${sc}_tmp +- tail -n +2 $file.in1$cmplx${sc} >> $file.in1$cmplx${sc}_tmp +- mv $file.in1$cmplx${sc}_tmp $file.in1$cmplx${sc} +- endif ++ set eferm=`echo " if($eferm > $efold) {if ($eferm > $efold + 0.2) {$efold + 0.2} else {$eferm} } else {if($eferm < $efold - 0.2) {$efold - 0.2} else ($eferm*0.75+$efold*0.25) }" | bc -l` # allow for max change of ef-old +- 0.2, pratt mix ++ set modus=`head -1 $file.in1$cmplx${sc} | cut -c1-5` ++ echo "$modus EF=$eferm (WFFIL, WFPRI, ENFIL, SUPWF) " >$file.in1$cmplx${sc}_tmp ++ tail -n +2 $file.in1$cmplx${sc} >> $file.in1$cmplx${sc}_tmp ++ mv $file.in1$cmplx${sc}_tmp $file.in1$cmplx${sc} ++ endif + endif + endif + + clear: + #cleanup +-if ($?qtl || $?alm || $?almd || $?qdmft || $?band || $?fermi || $?efg || $?emin1 || $?emax1 ) then +- if( -e .oldin2 ) mv .oldin2 $file.in2$cmplx +-endif + if ($?rxesw ) then + if( -e .oldint ) mv .oldint $file.int + endif +@@ -2499,10 +2500,10 @@ + error: + rm $running + +-help: #help exit ++help: #help exit + cat << theend + +-USAGE: $0 PROGRAMNAME [flags] ++USAGE: $0 PROGRAMNAME [flags] + + PURPOSE:runs WIEN executables: afminput,aim,arrows,broadening,cif2struct, + clmaddsub,clmcopy,clminter,convham,conv2prim,dftd3,dipan,dmftproj, +@@ -2514,30 +2515,30 @@ + symmetso,telnes3,tetra,txspec,wannier90,w2w,w2waddsp,wplot,xspec + + FLAGS: +--f FILEHEAD -> FILEHEAD for path of struct & input-files +--t/-T -> suppress output of running time +--h/-H -> help +--d -> create only the def-file +--up -> runs up-spin +--dn -> runs dn-spin +--du -> runs up/dn-crossterm +--sc -> runs semicore calculation +--c -> complex calculation (no inversion symmetry present) ++-f FILEHEAD -> FILEHEAD for path of struct & input-files ++-t/-T -> suppress output of running time ++-h/-H -> help ++-d -> create only the def-file ++-up -> runs up-spin ++-dn -> runs dn-spin ++-du -> runs up/dn-crossterm ++-sc -> runs semicore calculation ++-c -> complex calculation (no inversion symmetry present) + -p -> run lapw0/1/2/hf/so/dm/optic in parallel (needs .machines or .processes file) + -scratch dir/ ->defines (and makes) $SCRATCH variable + -grr -> lapw0 for mBJ or hf (using $file.in0_grr) + -eece -> for hybrid-functionals (lapw0,lapw2,mixer,orb,sumpara) + -band -> for lapw1/2/hf bandstructures: uses *klist_band +--orb -> runs lapw1 with LDA+U/OP or B-ext correction, mixer with dmat +--it -> runs lapw1 with iterative diagonalization +--noHinv -> runs lapw1 with iterative diag. without Hinv +--noHinv0 -> runs lapw1 with iterative diag. writing new Hinv +--nohns -> runs lapw1 without HNS +--nmat_only-> runs lapw1 and yields only the matrixsize +--nmr -> runs lapw1 in NMR mode +--in1orig -> runs lapw2 but does not modify case.in1 +--emin X -> runs lapw2 with EMIN=X (in $file.in2$cmplx) +--all X Y -> runs lapw2 with ALL and E-window X-Y (in $file.in2$cmplx) ++-orb -> runs lapw1 with LDA+U/OP or B-ext correction, mixer with dmat ++-it -> runs lapw1 with iterative diagonalization ++-noHinv -> runs lapw1 with iterative diag. without Hinv ++-noHinv0 -> runs lapw1 with iterative diag. writing new Hinv ++-nohns -> runs lapw1 without HNS ++-nmat_only-> runs lapw1 and yields only the matrixsize ++-nmr -> runs lapw1 in NMR mode ++-in1orig -> runs lapw2 but does not modify case.in1 ++-emin X -> runs lapw2 with EMIN=X (in $file.in2$cmplx) ++-all X Y -> runs lapw2 with ALL and E-window X-Y (in $file.in2$cmplx) + -qtl -> runs lapw2 and calculates QTL + -alm -> runs lapw2 and calculates ALM,BLM + -almd -> runs lapw2 and calculates ALM,BLM in lapw2 for DMFT (Aichhorn) +@@ -2546,11 +2547,11 @@ + -vresp-> runs lapw2 and creates case.vrespval (for TAU/meta-GGA) + -fermi-> runs lapw2 with FERMI switch + -efg -> runs lapw2 with EFG switch +--so -> runs lapw2/optic/spaghetti with def-file for spin-orbit calc. ++-so -> runs lapw2/optic/spaghetti with def-file for spin-orbit calc. + -hf -> runs lapw2 with Hartree-Fock/hybrid vectors + -diaghf -> calculates only the diagonal elements of HF Hamiltonian + -nonself -> calculates hf with Ex only (no eigenvalues/vectors) +--fbz -> runs kgen and generates a full mesh in the BZ ++-fbz -> runs kgen and generates a full mesh in the BZ + -fft -> runs dstart only up to case.in0_std creation + -super-> runs dstart and creates new_super.clmsum (and not $file.clmsum) + -lcore-> runs dstart with $file.rsplcore (produces $file.clmsc) diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_lapw5-main-accuracy-fix.patch b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_lapw5-main-accuracy-fix.patch new file mode 100644 index 0000000000000000000000000000000000000000..3800834f1bcd9b82d28fce05699b8045ee2035d5 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.1_lapw5-main-accuracy-fix.patch @@ -0,0 +1,22 @@ +http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg11158.html +--- WIEN2k_14.orig/SRC_lapw5/main1.f 2014-09-19 13:30:20.757390463 +0200 ++++ WIEN2k_14/SRC_lapw5/main1.f 2014-09-19 13:30:37.671774186 +0200 +@@ -346,7 +346,7 @@ + if(addsub.eq.' ADD') fadd=1.d0 + if(addsub.eq.' SUB') fadd=-1.d0 + +- IF(IUNIT.EQ.'ANG ') FAK=Bohr**3 ++ IF(IUNIT.EQ.'ANG ') FAK=1.D0/Bohr**3 ! Change to avoid altering lapw5 output (fix to WIEN2k 14.1): Was 6.7551d0 in WIEN2k 13.1 (and likely in verisons < 13.1) but changed to increase accuracy + R=VNORM(VX) + RELX=R + R=VNORM(VY) +@@ -373,7 +373,7 @@ + ! + ! Correct TCharge for units + if(UseSTM)then +- if(IUNIT.EQ.'ANG ')CTarget=CTarget/FAK ++ if(IUNIT.EQ.'ANG ')CTarget=CTarget*FAK ! Change to avoid altering output + ! Array for STM (LDM) + allocate(STM(NPX,NPY)) + endif + diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.2-intel-2015a.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.2-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..5149928839f335388946ffc422ca9f1faca0e75a --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-14.2-intel-2015a.eb @@ -0,0 +1,40 @@ +name = 'WIEN2k' +version = '14.2' + +homepage = 'http://www.wien2k.at/' +description = """The program package WIEN2k allows to perform electronic structure calculations of solids +using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave +((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. +WIEN2k is an all-electron scheme including relativistic effects and has many features.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +sources = ['%(name)s_%(version)s.tar'] +checksums = ['1179be3b3bcb021af4c65fefea579ca6'] + +dependencies = [('FFTW', '3.3.4')] + +osdependencies = ['glib-devel'] # required for libpthread.a + +remote = 'pbsssh' +wien_mpirun = 'mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_' +use_remote = True +mpi_remote = False +wien_granularity = True +taskset = 'no' + +tests = [ + # test case 1: NaCl + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1227', r'^:ENE.*-1248.1427']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [ + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*14.63.*total forces', + ]), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb new file mode 100644 index 0000000000000000000000000000000000000000..cfdc17ab696c0e197eba66e03f6ebcb89b46f528 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.1.29-dmpar.eb @@ -0,0 +1,42 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.1.29'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# use tcsh provided by system, using an EB-provided tcsh results in a hanging build command on some Cray systems +osdependencies = ['tcsh'] +#builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb new file mode 100644 index 0000000000000000000000000000000000000000..b4103d924fa83df6ee36da7a05352da7ae1474f4 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.25-dmpar.eb @@ -0,0 +1,42 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# use tcsh provided by system, using an EB-provided tcsh results in a hanging build command on some Cray systems +osdependencies = ['tcsh'] +#builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb new file mode 100644 index 0000000000000000000000000000000000000000..4f97a286839880f07e25d069896b5f2c8175ff43 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-CrayGNU-5.2.40-dmpar.eb @@ -0,0 +1,41 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'CrayGNU', 'version': '5.2.40'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('cray-netcdf/4.3.2', EXTERNAL_MODULE), + ('cray-hdf5-parallel/1.8.13', EXTERNAL_MODULE), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +runtest = False + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb new file mode 100644 index 0000000000000000000000000000000000000000..5e773ca4e846ed36d1220b28794f644615a4aee9 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-3.6.1-foss-2015a-dmpar.eb @@ -0,0 +1,40 @@ +name = 'WRF' +version = '3.6.1' + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2015a'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +sources = ['%(name)sV%(version)s.TAR.gz'] +source_urls = [ + 'http://www2.mmm.ucar.edu/wrf/src/', + 'http://www.mmm.ucar.edu/wrf/src/', +] + +# csh is used by WRF install scripts +builddependencies = [('tcsh', '6.18.01')] + +dependencies = [ + ('JasPer', '1.900.1'), + ('netCDF', '4.3.2'), + ('netCDF-Fortran', '4.4.0'), +] + +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRF-3.6.1_netCDF-Fortran_separate_path.patch', + 'WRF-3.6.1_known_problems.patch', + 'WRF_tests_limit-runtimes.patch', +] + +# limit parallel build to 20 +maxparallel = 20 + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..5248d49efab9267ee27a60942ad990d6ffa62b66 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Parser/XML-Parser-2.41-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,24 @@ +easyblock = 'PerlModule' + +name = 'XML-Parser' +version = '2.41' + +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': 'goolf', 'version': '1.4.10'} +source_urls = ['http://cpan.metacpan.org/authors/id/T/TO/TODDR/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ('expat', '2.1.0') +] + +options = {'modulename': 'XML::Parser'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb b/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb new file mode 100644 index 0000000000000000000000000000000000000000..acd24ee88386363874c13db535fd36b27b70e4cf --- /dev/null +++ b/easybuild/easyconfigs/x/XML-Twig/XML-Twig-3.48-goolf-1.4.10-Perl-5.16.3.eb @@ -0,0 +1,24 @@ +easyblock = 'PerlModule' + +name = 'XML-Twig' +version = '3.48' + +homepage = 'http://search.cpan.org/~mirod/XML-Twig-3.48/' +description = """XML::Twig is (yet another!) XML transformation module.""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} +source_urls = ['http://cpan.metacpan.org/authors/id/M/MI/MIROD/'] +sources = [SOURCE_TAR_GZ] + +perl = 'Perl' +perlver = '5.16.3' +versionsuffix = '-%s-%s' % (perl, perlver) + +dependencies = [ + (perl, perlver), + ('XML-Parser', '2.41', versionsuffix) +] + +options = {'modulename': 'XML::Twig'} + +moduleclass = 'data' 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 fad6a95d952964d69defda099f851efd254579cb..3d54b29efd3f8e5025a8ca701c921aab5ee0d7c7 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 @@ -6,12 +6,13 @@ version = '5.0.5' homepage = 'http://tukaani.org/xz/' description = "xz: XZ utilities" +toolchain = {'name': 'GCC', 'version': '4.8.2'} + sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] -toolchain = {'name': 'GCC', 'version': '4.8.2'} - -# configopts = ' --disable-assembler ' # may become useful in non-x86 archs +# may become useful in non-x86 archs +#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 171e02c46b23a78b4e822c229801b1fe0f4db022..e60568da6efb51ea8badca0ae8d6b0148b95214d 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 @@ -6,12 +6,13 @@ version = '5.0.5' homepage = 'http://tukaani.org/xz/' description = "xz: XZ utilities" +toolchain = {'name': 'goolf', 'version': '1.4.10'} + sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] -toolchain = {'name': 'goolf', 'version': '1.4.10'} - -# configopts = ' --disable-assembler ' # may become useful in non-x86 archs +# may become useful in non-x86 archs +#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 c7b17522590816f7c467197afeabf43f1925467e..6f7148a406a89fecde26a47a660497697bbbbf78 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 @@ -6,12 +6,13 @@ version = '5.0.5' homepage = 'http://tukaani.org/xz/' description = "xz: XZ utilities" +toolchain = {'name': 'ictce', 'version': '5.3.0'} + sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] -toolchain = {'name': 'ictce', 'version': '5.3.0'} - -# configopts = ' --disable-assembler ' # may become useful in non-x86 archs +# may become useful in non-x86 archs +#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 5a6ed9b1225b2a7c9e67733bcd0329272729b46c..99b4d29f28dcda07be4ea7b3f1a039383fdb5c4c 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 @@ -6,10 +6,13 @@ version = '5.2.0' homepage = 'http://tukaani.org/xz/' description = "xz: XZ utilities" +toolchain = {'name': 'GCC', 'version': '4.9.2'} + sources = [SOURCELOWER_TAR_BZ2] source_urls = ['http://tukaani.org/xz/'] -toolchain = {'name': 'GCC', 'version': '4.9.2'} +# may become useful in non-x86 archs +#configopts = ' --disable-assembler ' sanity_check_paths = { 'files': ["bin/xz", "bin/lzmainfo"], 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 new file mode 100644 index 0000000000000000000000000000000000000000..fc928c6c5783657b8fd914d7e699b5a76da73e86 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-foss-2015a-Python-2.7.9.eb @@ -0,0 +1,32 @@ +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." + +source_urls = ['http://xmipp.cnb.csic.es/Downloads/'] +sources = ['Xmipp-%(version)s-src.tar.gz'] + +toolchain = {'name': 'foss', 'version': '2015a'} + +patches = [ + 'Xmipp-%(version)s_fix-sqlite-includes.patch', + 'Xmipp-%(version)s_fix-library-includes.patch', + 'Xmipp_install-script.patch', +] + +pyver = '2.7.9' +versionsuffix = '-Python-%s' % pyver + +dependencies = [ + ('Java', '1.8.0_40', '', True), + ('Python', pyver), # should have a working sqlite, and provide numpy/mpi4py + ('LibTIFF', '4.0.4beta'), + ('HDF5', '1.8.14'), + ('libjpeg-turbo', '1.4.0'), + ('FFTW', '3.3.4', '', ('gompi', '2015a')), + ('SQLite', '3.8.8.1'), # must match SQLite used by Python + ('matplotlib', '1.4.3', versionsuffix), +] + +moduleclass = 'vis' 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 new file mode 100644 index 0000000000000000000000000000000000000000..c1f4fa485c8a52d3abe146c463fab96e0ccb498b --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-goolf-1.4.10-with-incl-deps.eb @@ -0,0 +1,16 @@ +name = 'Xmipp' +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." + +source_urls = ['http://xmipp.cnb.csic.es/Downloads/'] +sources = ['Xmipp-%(version)s-src.tar.gz'] + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +# note: all other dependencies are taken care of by Xmipp itself +dependencies = [('Java', '1.7.0_80', '', True)] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb similarity index 61% rename from easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb rename to easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb index bd7faf390987c3efa8b5d675d087ecd6a437f64b..82d76eef0e88122546444a7d5e09fae201a18931 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1-intel-2015a-Python-2.7.9.eb @@ -9,17 +9,24 @@ sources = ['Xmipp-%(version)s-src.tar.gz'] toolchain = {'name': 'intel', 'version': '2015a'} -patches = ['sqlite_imports.patch', 'library_imports.patch'] +patches = [ + 'Xmipp-%(version)s_fix-sqlite-includes.patch', + 'Xmipp-%(version)s_fix-library-includes.patch', + 'Xmipp_install-script.patch', +] + +pyver = '2.7.9' +versionsuffix = '-Python-%s' % pyver dependencies = [ ('Java', '1.8.0_40', '', True), - ('Python', '2.7.9'), # should have a working sqlite, and provide numpy - ('freetype', '2.5.5'), + ('Python', pyver), # should have a working sqlite, and provide numpy/mpi4py ('LibTIFF', '4.0.4beta'), - ('HDF5', '1.8.14', '-gpfs'), + ('HDF5', '1.8.14'), ('libjpeg-turbo', '1.4.0'), ('FFTW', '3.3.4'), ('SQLite', '3.8.8.1'), # must match SQLite used by Python + ('matplotlib', '1.4.3', versionsuffix), ] moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/Xmipp/library_imports.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1_fix-library-includes.patch similarity index 100% rename from easybuild/easyconfigs/x/Xmipp/library_imports.patch rename to easybuild/easyconfigs/x/Xmipp/Xmipp-3.1_fix-library-includes.patch diff --git a/easybuild/easyconfigs/x/Xmipp/sqlite_imports.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.1_fix-sqlite-includes.patch similarity index 100% rename from easybuild/easyconfigs/x/Xmipp/sqlite_imports.patch rename to easybuild/easyconfigs/x/Xmipp/Xmipp-3.1_fix-sqlite-includes.patch diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp_install-script.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp_install-script.patch new file mode 100644 index 0000000000000000000000000000000000000000..c79477e52b65c151f432a870d4043a29f0c479c2 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp_install-script.patch @@ -0,0 +1,13 @@ +--- install.sh.orig 2014-04-03 10:46:46.000000000 +0300 ++++ install.sh 2015-06-17 10:09:32.000000000 +0300 +@@ -820,8 +820,8 @@ + DO_PYTHON=1 + DO_PYMOD=1 + elif [ "${WITH_PYTHON}" = "false" ]; then +- DO_PYTHON=1 +- DO_PYMOD=1 ++ DO_PYTHON=0 ++ DO_PYMOD=0 + else + echoRed "Parameter --python only accept true or false values. Ignored and assuming default value." + fi diff --git a/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..159e636639b246048dd97fed9ed755c8e0815588 --- /dev/null +++ b/easybuild/easyconfigs/x/xbitmaps/xbitmaps-1.1.1-intel-2015a.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': 'intel', 'version': '2015a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://xorg.freedesktop.org/archive/individual/data/'] + +sanity_check_paths = { + 'files' : ['include/X11/bitmaps/gray'], + 'dirs' : [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-foss-2015a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-foss-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..537ac748fee1b628be5ac893fc9ffb85a660ad10 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-foss-2015a.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '3.2.5' + +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': 'foss', 'version': '2015a'} + +source_urls = ['http://download.zeromq.org/'] +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$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.26.1'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-intel-2015a.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-intel-2015a.eb new file mode 100644 index 0000000000000000000000000000000000000000..19243eab21929639d393a570ffb061db30487553 --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-3.2.5-intel-2015a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '3.2.5' + +homepage = 'http://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'intel', 'version': '2015a'} + +source_urls = ['http://download.zeromq.org/'] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['ZeroMQ-3.2.2_icc.patch'] + +# --with-pgm will use shipped OpenPGM (in foreign subdir) +configopts = '--with-pic --with-system-pgm ' +configopts += 'OpenPGM_CFLAGS="-I$EBROOTOPENPGM/include/pgm-${EBVERSIONOPENPGM%.*}" ' +configopts += 'OpenPGM_LIBS="-L$EBROOTOPENPGM/lib -lpgm -lrt -lpthread -lm" ' + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('util-linux', '2.26.1'), +] + +sanity_check_paths = { + 'files': ['lib/libzmq.so', 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-6.1.5.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-6.1.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..62b9777b1c06b1fbded08b09b802f5041d09927e --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.7-ictce-6.1.5.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.2.7' + +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': 'ictce', 'version': '6.1.5'} +toolchainopts = {'optarch': True, '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.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.eb new file mode 100644 index 0000000000000000000000000000000000000000..f6714bc2c14f4a912545c40bdd9d01a116640c8c --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.1.29.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': '5.1.29'} +toolchainopts = {'pic': True, 'dynamic': 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.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..17db62ce981b6853924d35a91df9acb6b937870d --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.25.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': 'CrayGNU', 'version': '5.2.25'} +toolchainopts = {'pic': True, 'dynamic': 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.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.eb new file mode 100644 index 0000000000000000000000000000000000000000..736d7b43ce9634350228d1ea50eab4fa7c6ed67e --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-CrayGNU-5.2.40.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': '5.2.40'} +toolchainopts = {'pic': True, 'dynamic': 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.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..71c0cc0f498681bf6df37c060e3e3ab549974584 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-4.9.2-binutils-2.25.eb @@ -0,0 +1,24 @@ +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': '4.9.2-binutils-2.25'} + +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.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb new file mode 100644 index 0000000000000000000000000000000000000000..797739b09af41b607bd1bf405893e3e62f0700b4 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-GCC-5.1.0-binutils-2.25.eb @@ -0,0 +1,24 @@ +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': '5.1.0-binutils-2.25'} + +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.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.eb new file mode 100644 index 0000000000000000000000000000000000000000..76686828729cfb404785d90a97c2cee8133a5f89 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-foss-2015.05.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': '2015.05'} +toolchainopts = {'optarch': True, '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.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.16.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.16.eb new file mode 100644 index 0000000000000000000000000000000000000000..9b56c2bffb789bcf6da6637e14a3b70771dc9bed --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-goolf-1.5.16.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': 'goolf', 'version': '1.5.16'} +toolchainopts = {'optarch': True, '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.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-7.3.5.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-7.3.5.eb new file mode 100644 index 0000000000000000000000000000000000000000..8254f78ac9a7ff9d394f3ab2f42d0495f54523bc --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-ictce-7.3.5.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': 'ictce', 'version': '7.3.5'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [('http://sourceforge.net/projects/libpng/files/zlib/%s' % version, 'download')] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014.06.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014.06.eb new file mode 100644 index 0000000000000000000000000000000000000000..24f9e69fb82cad29785d3d60863d862662a94249 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8-intel-2014.06.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': '2014.06'} +toolchainopts = {'optarch': True, '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.so'], + '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 new file mode 100644 index 0000000000000000000000000000000000000000..50f8b33ec885626b8da6c7f9f47b798c61f2897c --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.8.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': 'dummy', 'version': 'dummy'} + +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.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/setup.py b/setup.py index e23ed2d782da22c56275b243c819df2eb1167810..d3563514accad0dee687abede6a63e80c9af0a8c 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,5 @@ ## -# Copyright 2012-2013 Ghent University +# Copyright 2012-2015 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), @@ -41,7 +41,7 @@ from distutils import log # note: release candidates should be versioned as a pre-release, e.g. "1.1rc1" # 1.1-rc1 would indicate a post-release, i.e., and update of 1.1, so beware! -VERSION = "2.1.0dev" +VERSION = '2.3.0dev' 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 5d7ca772792c7d88e95c16216d60d29783d2500d..a8b8f5a2f26c4ec7bb3ab21d882d468cbd9a1591 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -32,10 +32,11 @@ import copy import glob import os import re +import shutil import sys import tempfile from distutils.version import LooseVersion -from vsc import fancylogger +from vsc.utils import fancylogger from vsc.utils.missing import nub from unittest import TestCase, TestLoader, main @@ -48,8 +49,10 @@ from easybuild.framework.easyconfig.easyconfig import get_easyblock_class from easybuild.framework.easyconfig.parser import 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.filetools import write_file from easybuild.tools.module_naming_scheme import GENERAL_CLASS 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 @@ -66,7 +69,9 @@ class EasyConfigTest(TestCase): config.init(eb_go.options, eb_go.get_options_by_section('config')) build_options = { 'check_osdeps': False, + 'external_modules_metadata': {}, 'force': True, + 'optarch': 'test', 'robot_path': get_paths_for("easyconfigs")[0], 'suffix_modules_path': GENERAL_CLASS, 'valid_module_classes': config.module_classes(), @@ -75,8 +80,14 @@ class EasyConfigTest(TestCase): config.init_build_options(build_options=build_options) config.set_tmpdir() del eb_go - + + # put dummy 'craype-test' module in place, which is required for parsing easyconfigs using Cray* toolchains + TMPDIR = tempfile.mkdtemp() + os.environ['MODULEPATH'] = TMPDIR + write_file(os.path.join(TMPDIR, 'craype-test'), '#%Module\n') + log = fancylogger.getLogger("EasyConfigTest", fname=False) + # make sure a logger is present for main main._log = log ordered_specs = None @@ -93,7 +104,16 @@ class EasyConfigTest(TestCase): for spec in specs: self.parsed_easyconfigs.extend(process_easyconfig(spec)) - self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs) + # filter out external modules + for ec in self.parsed_easyconfigs: + for dep in ec['dependencies'][:]: + if dep.get('external_module', False): + ec['dependencies'].remove(dep) + for dep in ec['unresolved_deps'][:]: + if dep.get('external_module', False): + ec['unresolved_deps'].remove(dep) + + self.ordered_specs = resolve_dependencies(self.parsed_easyconfigs, retain_all_deps=True) def test_dep_graph(self): """Unit test that builds a full dependency graph.""" @@ -209,6 +229,10 @@ class EasyConfigTest(TestCase): if not (dirpath.endswith('/easybuild/easyconfigs') and filenames == ['TEMPLATE.eb']): self.assertTrue(False, "List of easyconfig files in %s is empty: %s" % (dirpath, filenames)) + def test_zzz_cleanup(self): + """Dummy test to clean up global temporary directory.""" + shutil.rmtree(self.TMPDIR) + def template_easyconfig_test(self, spec): """Tests for an individual easyconfig: parsing, instantiating easyblock, check patches, ...""" @@ -217,7 +241,7 @@ def template_easyconfig_test(self, spec): prev_single_tests_ok = single_tests_ok single_tests_ok = False - # parse easyconfig + # parse easyconfig ecs = process_easyconfig(spec) if len(ecs) == 1: ec = ecs[0]['ec'] @@ -226,13 +250,13 @@ def template_easyconfig_test(self, spec): # check easyconfig file name expected_fn = '%s-%s.eb' % (ec['name'], det_full_ec_version(ec)) - msg = "Filename '%s' of parsed easconfig matches expected filename '%s'" % (spec, expected_fn) + msg = "Filename '%s' of parsed easyconfig matches expected filename '%s'" % (spec, expected_fn) self.assertEqual(os.path.basename(spec), expected_fn, msg) name, easyblock = fetch_parameters_from_easyconfig(ec.rawtxt, ['name', 'easyblock']) # sanity check for software name - self.assertTrue(ec['name'], name) + self.assertTrue(ec['name'], name) # instantiate easyblock with easyconfig file app_class = get_easyblock_class(easyblock, name=name) @@ -279,6 +303,25 @@ def template_easyconfig_test(self, spec): app.close_log() os.remove(app.logfile) + # dump the easyconfig file + handle, test_ecfile = tempfile.mkstemp() + os.close(handle) + + ec.dump(test_ecfile) + dumped_ec = EasyConfig(test_ecfile) + os.remove(test_ecfile) + + # inject dummy values for templates that are only known at a later stage + dummy_template_values = { + 'builddir': '/dummy/builddir', + '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]) + # cache the parsed easyconfig, to avoid that it is parsed again self.parsed_easyconfigs.append(ecs[0]) diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index 65497da038f366e6c3aa544afc3b63bdb06b98e2..6afbd6ffb15accfe319e11c510c9e60e6131d8ba 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -36,7 +36,8 @@ import shutil import sys import tempfile import unittest -from vsc import fancylogger + +from vsc.utils import fancylogger import easybuild.tools.build_log # initialize EasyBuild logging, so we disable it import test.easyconfigs.easyconfigs as e