diff --git a/a/ABySS/ABySS-2.0.2-foss-2018a-Py-2.7.eb b/a/ABySS/ABySS-2.0.2-foss-2018a-Py-2.7.eb new file mode 100644 index 00000000..688f25ce --- /dev/null +++ b/a/ABySS/ABySS-2.0.2-foss-2018a-Py-2.7.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '2.0.2' + +homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d87b76edeac3a6fb48f24a1d63f243d8278a324c9a5eb29027b640f7089422df'] + +dependencies = [ + ('Boost', '1.66.0', '-Py-2.7'), + ('sparsehash', '2.0.3'), + ('SQLite', '3.21.0', '', True), +] + +configopts = " --enable-maxk=256 " + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/a/ASE/ASE-3.15.0-Python-2.7.13-base-test.eb b/a/ASE/ASE-3.15.0-Python-2.7.13-base-test.eb new file mode 100644 index 00000000..d880d098 --- /dev/null +++ b/a/ASE/ASE-3.15.0-Python-2.7.13-base-test.eb @@ -0,0 +1,31 @@ +# IT4Innovations 2017 + +easyblock = 'PythonPackage' + +name = 'ASE' +version = '3.15.0' +versionsuffix = '-Python-%(pyver)s-base-test' + +homepage = 'https://wiki.fysik.dtu.dk/ase/' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5e22d961b1311ef4ba2d83527f7cc7448abac8cf9bddd1593bee548459263fe8'] + +dependencies = [ + ('Python', '2.7.13'), +# ('numpy', '1.13.0', '-Python-2.7.13-base'), +# ('scipy', '0.19.1', '-Python-2.7.13-base'), +# ('matplotlib', '2.0.2', '-Python-2.7.13-base'), +] + +sanity_check_paths = { + 'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' diff --git a/a/ASE/ASE-3.15.0-Python-3.6.4-base-test.eb b/a/ASE/ASE-3.15.0-Python-3.6.4-base-test.eb new file mode 100644 index 00000000..f7774fa0 --- /dev/null +++ b/a/ASE/ASE-3.15.0-Python-3.6.4-base-test.eb @@ -0,0 +1,31 @@ +# IT4Innovations 2017 + +easyblock = 'PythonPackage' + +name = 'ASE' +version = '3.15.0' +versionsuffix = '-Python-%(pyver)s-base-test' + +homepage = 'https://wiki.fysik.dtu.dk/ase/' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language.""" + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5e22d961b1311ef4ba2d83527f7cc7448abac8cf9bddd1593bee548459263fe8'] + +dependencies = [ + ('Python', '3.6.1'), +# ('numpy', '1.13.0', '-Python-2.7.13-base'), +# ('scipy', '0.19.1', '-Python-2.7.13-base'), +# ('matplotlib', '2.0.2', '-Python-2.7.13-base'), +] + +sanity_check_paths = { + 'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' diff --git a/b/Bash/Bash-4.4-GCC-6.3.0-2.27.eb b/b/Bash/Bash-4.4-GCC-6.3.0-2.27.eb new file mode 100644 index 00000000..35eff52c --- /dev/null +++ b/b/Bash/Bash-4.4-GCC-6.3.0-2.27.eb @@ -0,0 +1,29 @@ +# IT4Innovations 2018 + +easyblock = 'ConfigureMake' + +name = 'Bash' +version = '4.4' + +homepage = 'http://www.gnu.org/software/bash' +description = """Bash is an sh-compatible command language interpreter that executes commands + read from the standard input or from a file. Bash also incorporates useful features from the + Korn and C shells (ksh and csh).""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libreadline', '7.0', '', True), +] + +configopts = " --enable-readline --enable-job-control --enable-history " + +sanity_check_paths = { + 'files': ["bin/bash"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/b/Bash/Bash-4.4-intel-2017b.eb b/b/Bash/Bash-4.4-intel-2017b.eb new file mode 100644 index 00000000..9ee6a9fc --- /dev/null +++ b/b/Bash/Bash-4.4-intel-2017b.eb @@ -0,0 +1,29 @@ +# IT4Innovations 2018 + +easyblock = 'ConfigureMake' + +name = 'Bash' +version = '4.4' + +homepage = 'http://www.gnu.org/software/bash' +description = """Bash is an sh-compatible command language interpreter that executes commands + read from the standard input or from a file. Bash also incorporates useful features from the + Korn and C shells (ksh and csh).""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = [GNU_SOURCE] + +dependencies = [ + ('libreadline', '7.0', '', True), +] + +configopts = " --enable-readline --enable-job-control --enable-history " + +sanity_check_paths = { + 'files': ["bin/bash"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/b/Boost/Boost-1.66.0-foss-2018a-Py-2.7.eb b/b/Boost/Boost-1.66.0-foss-2018a-Py-2.7.eb new file mode 100644 index 00000000..d544118c --- /dev/null +++ b/b/Boost/Boost-1.66.0-foss-2018a-Py-2.7.eb @@ -0,0 +1,28 @@ +# IT4Innovations 2018 + +name = 'Boost' +version = '1.66.0' +versionsuffix = '-Py-2.7' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] + + +dependencies = [ + ('bzip2', '1.0.6', '', True), + ('zlib', '1.2.11', '', True), + ('Py', '2.7', '', True) +] + +configopts = '--with-python=$EBROOTPYTHON/bin/python' + +# also build boost_mpi +boost_mpi = True + +moduleclass = 'devel' diff --git a/f/foss/foss-2018a.eb b/f/foss/foss-2018a.eb new file mode 100644 index 00000000..06399514 --- /dev/null +++ b/f/foss/foss-2018a.eb @@ -0,0 +1,33 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2018a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +gccver = '6.3.0-2.27' + +blaslib = 'OpenBLAS' +blasver = '0.2.20' +blas = '%s-%s' % (blaslib, blasver) + +# toolchain used to build foss dependencies +comp_mpi_tc_name = 'gompi' +comp_mpi_tc = (comp_mpi_tc_name, version) + +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds +dependencies = [ + ('GCC', gccver), + ('OpenMPI', '3.0.0', '', ('GCC', gccver)), + (blaslib, blasver, '', ('GCC', gccver)), + ('FFTW', '3.3.7', '', comp_mpi_tc), + ('ScaLAPACK', '2.0.2', '-%s' % blas, comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/n/numpy/numpy-1.14.1-Py-3.6.eb b/n/numpy/numpy-1.14.1-Py-3.6.eb new file mode 100644 index 00000000..19af713c --- /dev/null +++ b/n/numpy/numpy-1.14.1-Py-3.6.eb @@ -0,0 +1,35 @@ +# IT4Innovations 2018 + +easyblock = 'PythonPackage' + +name = 'numpy' +version = '1.14.1' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package needed for scientific computing with Python.""" + +toolchain = {'name': 'Py', 'version': '3.6'} + +source_urls = ['https://github.com/numpy/numpy/releases/download/v%(version)s'] +sources = ['%(name)s-%(version)s.tar.gz'] + +patches = [ + 'numpy-1.12.0-mkl.patch', +# 'numpy-1.14.1-mkl.patch' +] + +builddependencies = [ +# ('mkl', '2017.4.239', '', True), + ('intel', '2017a', '', True), +] + +#prebuildopts = 'mv site.cfg.example site.cfg && export MKL_THREADING_LAYER=GNU && ' # ' export CFLAGS="-fopenmp -m64 -mtune=native -O3 -Wl,--no-as-needed" && export CXXFLAGS="-fopenmp -m64 -mtune=native -O3 -Wl,--no-as-needed" && export LDFLAGS="-ldl -lm" && export FFLAGS="-fopenmp -m64 -mtune=native -O3" && ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python3.6/site-packages/numpy-%(version)s-py3.6-linux-x86_64.egg/numpy'], +} + +sanity_check_commands = [('python', '-c "import numpy; assert(numpy.__version__ == \'%(version)s\')"')] + +moduleclass = 'python' diff --git a/n/numpy/numpy-1.14.1-mkl.patch b/n/numpy/numpy-1.14.1-mkl.patch new file mode 100644 index 00000000..21350692 --- /dev/null +++ b/n/numpy/numpy-1.14.1-mkl.patch @@ -0,0 +1,19 @@ +--- site.cfg.example.old 2018-02-20 00:16:17.000000000 +0100 ++++ site.cfg.example 2018-03-09 10:47:51.496213510 +0100 +@@ -159,11 +159,11 @@ + # https://software.intel.com/en-us/articles/numpyscipy-with-intel-mkl + # Assuming you installed the mkl in /opt/intel/compilers_and_libraries_2018/linux/mkl, + # for 64 bits code at Linux: +-# [mkl] +-# library_dirs = /opt/intel/compilers_and_libraries_2018/linux/mkl/lib/intel64 +-# include_dirs = /opt/intel/compilers_and_libraries_2018/linux/mkl/include +-# mkl_libs = mkl_rt +-# lapack_libs =  ++[mkl] ++library_dirs = /apps/all/mkl/2017.4.239/mkl/lib/intel64 ++include_dirs = /apps/all/mkl/2017.4.239/mkl/include ++mkl_libs = mkl_def, mkl_intel_lp64, mkl_intel_thread, mkl_core ++lapack_libs = mkl_lapack95_lp64 + # + # For 32 bit code at Linux: + # [mkl] diff --git a/o/OpenMPI/OpenMPI-3.0.0-GCC-6.3.0-2.27.eb b/o/OpenMPI/OpenMPI-3.0.0-GCC-6.3.0-2.27.eb new file mode 100644 index 00000000..c723e6cf --- /dev/null +++ b/o/OpenMPI/OpenMPI-3.0.0-GCC-6.3.0-2.27.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'OpenMPI' +version = '3.0.0' + +homepage = 'http://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-2 implementation.""" + +toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'} + +source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0bbb279b88edc25bbded39520dab6d4b32020277a6088fb1456c9437a8231cf8'] + +builddependencies = [ + ('Java', '1.8.0_144', '', True) +] + +dependencies = [ + ('hwloc', '1.11.7'), + ('zlib', '1.2.11', '', True), +] + +configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs ' +configopts += '--enable-mpirun-prefix-by-default ' # suppress failure modes in relation to mpirun path +configopts += '--with-hwloc=$EBROOTHWLOC ' # hwloc support +#configopts += '--disable-dlopen ' # dont disable dlopen! https://github.com/open-mpi/ompi/issues/3630 +configopts += '--with-tm=/opt/pbs/default ' # Enable PBS +configopts += '--enable-mpi-java ' # Java support RT#4090 +configopts += '--enable-mpi-cxx ' # Enable building the C++ MPI bindings + +# for PBS Pro 13 +preconfigopts = 'export LIBS="-ldl" && ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +# needed for --with-verbs +osdependencies = [('libibverbs-dev', 'libibverbs-devel')] + +libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"] +sanity_check_paths = { + 'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] + + ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] + + ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]], + 'dirs': [], +} + +modextravars = {'OMPI_MCA_btl_openib_if_include': 'mlx4_0', + 'OMPI_MCA_oob_tcp_if_include': '10.0.0.0/8', +} + +moduleclass = 'mpi' diff --git a/s/SQLite/SQLite-3.21.0.eb b/s/SQLite/SQLite-3.21.0.eb new file mode 100644 index 00000000..ae6157a1 --- /dev/null +++ b/s/SQLite/SQLite-3.21.0.eb @@ -0,0 +1,33 @@ +# IT4Innovations 2018 + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.21.0' + +homepage = 'http://www.sqlite.org/' +description = 'SQLite: SQL Database Engine in a C Library' + +toolchain = {'name': 'dummy', 'version': ''} + +source_urls = ['http://www.sqlite.org/2017/'] +version_minor_etc = version.split('.')[1:] +version_minor_etc += '0' * (3 - len(version_minor_etc)) +version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version_minor_etc) +sources = [ + 'sqlite-autoconf-%s.tar.gz' % version_str, + 'sqlite-amalgamation-%s.zip' % version_str, +] + +dependencies = [ + ('libreadline', '7.0'), + ('Tcl', '8.6.6'), +] + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a', + 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel'