diff --git a/a/ABySS/ABySS-2.0.3-foss-2018a-Py-2.7.eb b/a/ABySS/ABySS-2.0.3-foss-2018a-Py-2.7.eb new file mode 100644 index 00000000..17c61cd2 --- /dev/null +++ b/a/ABySS/ABySS-2.0.3-foss-2018a-Py-2.7.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '2.0.3' + +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] + +dependencies = [ + ('Boost', '1.66.0', '-Py-2.7'), + ('sparsehash', '2.0.3'), + ('SQLite', '3.21.0', '', True), + ('pigz', '2.4', '', ('GCC', '6.3.0-2.27')), + ('zsh', '5.2'), +] + +configopts = '--enable-maxk=256 --with-boost=$EBROOTBOOST/include ' +configopts += '--with-mpi=$EBROOTOPENMPI --with-sqlite=$EBROOTSQLITE3' + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/n/numpy/numpy-1.14.2-Py-2.7-test.eb b/n/numpy/numpy-1.14.2-Py-2.7-test.eb new file mode 100644 index 00000000..fd7abd8f --- /dev/null +++ b/n/numpy/numpy-1.14.2-Py-2.7-test.eb @@ -0,0 +1,33 @@ +# IT4Innovations 2018 + +easyblock = 'PythonPackage' + +name = 'numpy' +version = '1.14.2' +versionsuffix = '-test' + +homepage = 'http://www.numpy.org' +description = """NumPy is the fundamental package needed for scientific computing with Python.""" + +toolchain = {'name': 'Py', 'version': '2.7'} + +source_urls = ['https://github.com/numpy/numpy/releases/download/v%(version)s'] +sources = [SOURCE_TAR_GZ] + +patch = [ + 'numpy-1.8.1-mkl.patch', + 'numpy-1.11.0-sse42.patch' +] + +dependencies = [ + ('mkl', '2017.4.239', '', True), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python2.7/site-packages/%(name)s-%(version)s-py2.7-linux-x86_64.egg/numpy'], +} + +sanity_check_commands = [('python', '-c "import numpy; assert(numpy.__version__ == \'%(version)s\')"')] + +moduleclass = 'python' diff --git a/p/phono3py/phono3py-1.12.7.46-Py-2.7.eb b/p/phono3py/phono3py-1.11.13.35-Py-2.7-test.eb similarity index 80% rename from p/phono3py/phono3py-1.12.7.46-Py-2.7.eb rename to p/phono3py/phono3py-1.11.13.35-Py-2.7-test.eb index 623ad4d6..2d6ae632 100644 --- a/p/phono3py/phono3py-1.12.7.46-Py-2.7.eb +++ b/p/phono3py/phono3py-1.11.13.35-Py-2.7-test.eb @@ -3,15 +3,16 @@ easyblock = "PythonPackage" name = 'phono3py' -version = '1.12.7.46' +version = '1.11.13.35' +versionsuffix = '-test' homepage = 'http://phonopy.sourceforge.net/phono3py/index.html' description = """This software calculates phonon-phonon interaction related properties""" toolchain = {'name': 'Py', 'version': '2.7'} -source_urls = ['https://pypi.python.org/packages/a5/93/3a9cc9f134ba1f7aa246a27c8a02137e7f9a7311df87ae656bba9051c6df/'] -sources = ['%(name)s-%(version)s.tar.gz'] +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/phonopy/files/phono3py/'] prebuildopts = 'python setup.py build #' # notice the hash hack to override setup.py preinstallopts = 'python setup.py install --prefix=%(installdir)s #' # another hack diff --git a/p/phono3py/phono3py-1.11.13.35-Py-2.7.eb b/p/phono3py/phono3py-1.11.13.35-Py-2.7.eb new file mode 100644 index 00000000..0e265727 --- /dev/null +++ b/p/phono3py/phono3py-1.11.13.35-Py-2.7.eb @@ -0,0 +1,30 @@ +# IT4Innovations 2018 + +easyblock = "PythonPackage" + +name = 'phono3py' +version = '1.11.13.35' + +homepage = 'http://phonopy.sourceforge.net/phono3py/index.html' +description = """This software calculates phonon-phonon interaction related properties""" + +toolchain = {'name': 'Py', 'version': '2.7'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://sourceforge.net/projects/phonopy/files/phono3py/'] + +prebuildopts = 'python setup.py build #' # notice the hash hack to override setup.py +preinstallopts = 'python setup.py install --prefix=%(installdir)s #' # another hack +skipsteps = ['test'] +options = {'modulename': 'phonopy'} + +dependencies = [ + ('OpenBLAS', '0.2.19', '-GCC-6.3.0-2.27-LAPACK-3.7.0', True), + ('numpy', '1.13.3'), + ('h5py', '2.7.1'), + ('matplotlib', '2.1.1'), + ('PyYAML', '3.12'), + ('phonopy', '1.12.4.11'), +] + +moduleclass = 'phys' diff --git a/p/phono3py/phono3py-1.12.9.5-Py-2.7.eb b/p/phono3py/phono3py-1.12.9.5-Py-2.7.eb new file mode 100644 index 00000000..36528386 --- /dev/null +++ b/p/phono3py/phono3py-1.12.9.5-Py-2.7.eb @@ -0,0 +1,30 @@ +# IT4Innovations 2018 + +easyblock = "PythonPackage" + +name = 'phono3py' +version = '1.12.9.5' + +homepage = 'http://phonopy.sourceforge.net/phono3py/index.html' +description = """This software calculates phonon-phonon interaction related properties""" + +toolchain = {'name': 'Py', 'version': '2.7'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pypi.python.org/packages/81/fd/b2a3be820ff70af7ea88039e0ef36ed4e9c1df7d85e1b91c69339a503cf5/'] + +prebuildopts = 'python setup.py build #' # notice the hash hack to override setup.py +preinstallopts = 'python setup.py install --prefix=%(installdir)s #' # another hack +skipsteps = ['test'] +options = {'modulename': 'phonopy'} + +dependencies = [ + ('OpenBLAS', '0.2.19', '-GCC-6.3.0-2.27-LAPACK-3.7.0', True), + ('numpy', '1.14.2', '-test'), + ('h5py', '2.7.1'), + ('matplotlib', '2.1.1'), + ('PyYAML', '3.12'), + ('phonopy', '1.12.6.66'), +] + +moduleclass = 'phys' diff --git a/p/phonopy/phonopy-1.12.6.66-Py-2.7.eb b/p/phonopy/phonopy-1.12.6.66-Py-2.7.eb new file mode 100644 index 00000000..c6f4bb62 --- /dev/null +++ b/p/phonopy/phonopy-1.12.6.66-Py-2.7.eb @@ -0,0 +1,25 @@ +# IT4Innovations 2018 + +easyblock = 'PythonPackage' + +name = 'phonopy' +version = '1.12.6.66' + +homepage = 'https://atztogo.github.io/phonopy' +description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" + +toolchain = {'name': 'Py', 'version': '2.7'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('matplotlib', '2.1.1'), + ('lxml', '4.1.1'), + ('PyYAML', '3.12'), + ('numpy', '1.13.3'), + ('h5py', '2.7.1'), + ('scipy', '1.0.0') +] + +moduleclass = 'python' diff --git a/z/zsh/zsh-5.2-foss-2018b.eb b/z/zsh/zsh-5.2-foss-2018b.eb new file mode 100644 index 00000000..52e19675 --- /dev/null +++ b/z/zsh/zsh-5.2-foss-2018b.eb @@ -0,0 +1,20 @@ +# IT4Innovations 2018 + +easyblock = 'ConfigureMake' + +name = 'zsh' +version = '5.2' + +homepage = 'http://www.zsh.org/' +description = "Zsh is a shell designed for interactive use, although it is also a powerful scripting language." + +toolchain = {'name': 'foss', 'version': '2018a'} + +sources = [SOURCELOWER_TAR_XZ] +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] + +dependencies = [ + ('ncurses', '6.0', '', True), +] + +moduleclass = 'tools'