.add code.it4i.cz backup

a/ABAQUS/ABAQUS-6.12.1-linux-x86_64.eb

@@ -0,0 +1,16 @@
+name = 'ABAQUS'
+version = '6.12.1'
+versionsuffix = '-linux-x86_64'
+
+homepage = 'http://www.simulia.com/products/abaqus_fea.html'
+description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA."
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+sources = [SOURCE_TGZ]
+
+builddependencies = [('Java', '1.7.0_60')]
+
+preinstallopts = "export CHECK_DISK_SPACE=OFF && "
+
+moduleclass = 'cae'

a/ABAQUS/ABAQUS-6.13.5-linux-x86_64.eb

@@ -0,0 +1,16 @@
+name = 'ABAQUS'
+version = '6.13.5'
+versionsuffix = '-linux-x86_64'
+
+homepage = 'http://www.simulia.com/products/abaqus_fea.html'
+description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA."
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+sources = [SOURCE_TGZ]
+
+builddependencies = [('Java', '1.7.0_60')]
+
+preinstallopts = "export CHECK_DISK_SPACE=OFF && "
+
+moduleclass = 'cae'

a/ABAQUS/ABAQUS-6.14.1-linux-x86_64.eb

@@ -0,0 +1,16 @@
+name = 'ABAQUS'
+version = '6.14.1'
+versionsuffix = '-linux-x86_64'
+
+homepage = 'http://www.simulia.com/products/abaqus_fea.html'
+description = "Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA."
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+sources = [SOURCE_TGZ]
+
+builddependencies = [('Java', '1.7.0_60')]
+
+preinstallopts = "export CHECK_DISK_SPACE=OFF && "
+
+moduleclass = 'cae'

a/ABINIT/ABINIT-7.10.1-foss-2015b.eb

@@ -0,0 +1,30 @@
+# ABINIT recipe
+# 2015 Martin Stachon <martin.stachon@vsb.cz>
+##
+
+easyblock = "ConfigureMake"
+
+name = 'ABINIT'
+version = '7.10.1'
+
+homepage = 'http://www.abinit.org/'
+description = """Abinit is a plane wave pseudopotential code for doing
+ condensed phase electronic structure calculations using DFT."""
+
+toolchain = {'name': 'foss', 'version': '2015b'}
+
+# eg. http://ftp.abinit.org/abinit-7.10.1.tar.gz
+sources = [('abinit-%s.tar.gz' % (version), 'tar xfz %s')]
+source_urls = ['http://ftp.abinit.org/']
+
+#sanity_check_paths = {
+#                      'files': ["bin/abinit"], 
+#                      'dirs': []
+#                     }
+
+moduleclass = 'chem'
+
+configopts = '''CC=mpicc CXX=mpicxx FC=mpif90 --enable-mpi --enable-mpi-io --enable-64bit-flags --enable-optim="yes" --enable-clib="yes"''' + \
+ ''' --enable-gw-dpc="yes" --enable-memory-profiling="no" --enable-openmp="no" --enable-maintainer-checks="no"''' + \
+ ''' --enable-debug="no" ''' + \
+ ''' --with-trio-flavor="netcdf+etsf_io+fox" --with-dft-flavor="atompaw+bigdft+libxc+wannier90"'''

a/ABINIT/ABINIT-7.10.1-goolf-1.5.16.eb

@@ -0,0 +1,32 @@
+##
+# ABINIT recipe
+# 2015 Martin Stachon <martin.stachon@vsb.cz>
+##
+
+easyblock = "ConfigureMake"
+
+name = 'ABINIT'
+version = '7.10.1'
+
+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': '1.5.16'}
+
+# eg. http://ftp.abinit.org/abinit-7.10.1.tar.gz
+sources = [('abinit-%s.tar.gz' % (version), 'tar xfz %s')]
+source_urls = ['http://ftp.abinit.org/']
+
+#sanity_check_paths = {
+#                      'files': ["bin/abinit"], 
+#                      'dirs': []
+#                     }
+
+moduleclass = 'chem'
+
+configopts = '''CC=mpicc CXX=mpicxx FC=mpif90 --enable-mpi --enable-mpi-io --enable-64bit-flags --enable-optim="yes" --enable-clib="yes"''' + \
+ ''' --enable-gw-dpc="yes" --enable-memory-profiling="no" --enable-openmp="no" --enable-maintainer-checks="no"''' + \
+ ''' --enable-debug="no" ''' + \
+ ''' --with-trio-flavor="netcdf+etsf_io+fox" --with-dft-flavor="atompaw+bigdft+libxc+wannier90"'''
+

a/ADF/ADF-2014.02.eb

@@ -0,0 +1,31 @@
+easyblock = 'Tarball'
+
+name = 'ADF'
+version = '2014.02'
+
+homepage = 'http://www.scm.com/ADF/'
+description = """ADF is an accurate, parallelized, powerful computational chemistry program to understand and
+ predict chemical structure and reactivity with density functional theory (DFT)."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+sources = ['%(namelower)s%(version)s.pc64_linux.IntelMPI+CUDA.tgz']
+
+keepsymlinks = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['atomicdata', 'bin', 'examples'],
+}
+
+modextravars = {
+    'ADFHOME': '%(installdir)s',
+    'ADFBIN': '%(installdir)s/bin',
+    'ADFRESOURCES': '%(installdir)s/atomicdata',
+}
+
+modloadmsg = "These environment variables need to be defined before using ADF:\n"
+modloadmsg += "  * $SCMLICENSE: path to ADF license file\n"
+modloadmsg += "  * $SCM_TMPDIR: path to user scratch directory"
+
+moduleclass = 'chem'

a/ADF/ADF-2014.11.r48287-intel-2016a.eb

@@ -0,0 +1,22 @@
+name = 'ADF'
+version = '2014.11.r48287'
+
+homepage = 'http://www.scm.com/ADF/'
+description = """ADF is an accurate, parallelized, powerful computational chemistry program to understand and
+ predict chemical structure and reactivity with density functional theory (DFT)."""
+
+toolchain = {'name': 'intel', 'version': '2016a'}
+
+sources = [
+    '%(namelower)s%(version)s.src.tgz',
+    # no exact match on revision ID available, but not strictly needed
+    'fix2014.pc64_linux.intelmpi.r48660.2.555.bin.tgz',
+]
+
+license_file = HOME + "/licenses/ADF/license.txt"
+
+modloadmsg = "These environment variables need to be defined before using ADF:\n"
+modloadmsg += "  * $SCMLICENSE: path to ADF license file\n"
+modloadmsg += "  * $SCM_TMPDIR: path to user scratch directory"
+
+moduleclass = 'chem'

a/ADF/ADF-2016.101.eb

@@ -0,0 +1,31 @@
+easyblock = 'Tarball'
+
+name = 'ADF'
+version = '2016.101'
+
+homepage = 'http://www.scm.com/ADF/'
+description = """ADF is an accurate, parallelized, powerful computational chemistry program to understand and
+ predict chemical structure and reactivity with density functional theory (DFT)."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+sources = ['adf%(version)s.pc64_linux.intelmpi.tgz']
+
+keepsymlinks = True
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['atomicdata', 'bin', 'examples'],
+}
+
+modextravars = {
+    'ADFHOME': '%(installdir)s',
+    'ADFBIN': '%(installdir)s/bin',
+    'ADFRESOURCES': '%(installdir)s/atomicdata',
+}
+
+modloadmsg = "These environment variables need to be defined before using ADF:\n"
+modloadmsg += "  * $SCMLICENSE: path to ADF license file\n"
+modloadmsg += "  * $SCM_TMPDIR: path to user scratch directory"
+
+moduleclass = 'chem'

a/ALLPATHS-LG/ALLPATHS-LG-46968-goolf-1.4.10.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 <a.panteli@cyi.ac.cy>, Thekla Loizou <t.loizou@cyi.ac.cy>, George Tsouloupas <g.tsouloupas@cyi.ac.cy>
+# License::   MIT/GPL
+#
+##
+
+easyblock = 'ConfigureMake'
+
+name = 'ALLPATHS-LG'
+version = '46968'
+
+homepage = 'http://www.broadinstitute.org/software/allpaths-lg/blog/'
+description = """ALLPATHS-LG, the new short read genome assembler."""
+
+toolchain = {'name': 'goolf', 'version': '1.4.10'}
+
+# source is moved over time, hence multiple URLs below
+source_urls = [
+    'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code',
+    'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013-06',
+    'ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/2013/2013-06',
+]
+sources = ['allpathslg-%(version)s.tar.gz']
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['bin'],
+}
+
+moduleclass = 'bio'

a/ALPS/ALPS-2.3.0-foss-2016b-Python-2.7.12.eb

@@ -0,0 +1,40 @@
+easyblock = 'CMakeMake'
+
+name = 'ALPS'
+version = '2.3.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = "http://alps.comp-phys.org/"
+description = """The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort
+ aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as 
+ C++ libraries for simplifying the development of such code.
+"""
+
+toolchain = {'name': 'foss', 'version': '2016b'}
+toolchainopts = {'cstd': 'c++03'}
+
+sources = ['%(namelower)s-%(version)s-src.tar.gz']
+source_urls = ['http://alps.comp-phys.org/static/software/releases/']
+
+dependencies = [
+    ('CMake', '3.6.2'),
+    ('Python', '2.7.12'),
+    ('Boost', '1.63.0', versionsuffix),
+    ('HDF5', '1.8.17')
+]
+
+separate_build_dir = True
+
+modextravars = {
+    'ALPS_ROOT': '$root',
+}
+modextrapaths = {
+    'PYTHONPATH': ['lib/']
+}
+
+sanity_check_paths={
+    'files': ['lib/libalps.%s' % SHLIB_EXT],
+    'dirs': ['include/alps', 'bin/', 'share/'],
+}
+
+moduleclass = 'phys'

a/ALPS/ALPS-2.3.0-foss-2016b-Python-3.5.2.eb

@@ -0,0 +1,40 @@
+easyblock = 'CMakeMake'
+
+name = 'ALPS'
+version = '2.3.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = "http://alps.comp-phys.org/"
+description = """The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort
+ aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as 
+ C++ libraries for simplifying the development of such code.
+"""
+
+toolchain = {'name': 'foss', 'version': '2016b'}
+toolchainopts = {'cstd': 'c++03'}
+
+sources = ['%(namelower)s-%(version)s-src.tar.gz']
+source_urls = ['http://alps.comp-phys.org/static/software/releases/']
+
+dependencies = [
+    ('CMake', '3.6.2'),
+    ('Python', '3.5.2'),
+    ('Boost', '1.63.0', versionsuffix),
+    ('HDF5', '1.8.17')
+]
+
+separate_build_dir = True
+
+modextravars = {
+    'ALPS_ROOT': '$root',
+}
+modextrapaths = {
+    'PYTHONPATH': ['lib/']
+}
+
+sanity_check_paths={
+    'files': ['lib/libalps.%s' % SHLIB_EXT],
+    'dirs': ['include/alps', 'bin/', 'share/'],
+}
+
+moduleclass = 'phys'

a/ANSYS/ANSYS-18.0.eb

@@ -0,0 +1,19 @@
+name = 'ANSYS'
+version = '18.0'
+
+homepage = 'http://www.ansys.com'
+description = """ANSYS simulation software enables organizations to confidently predict 
+    how their products will operate in the real world. We believe that every product is 
+    a promise of something greater. """
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+# create a zip file from the 3 install iso files.
+# make sure all files of the iso's are in the same directory.
+sources = ['ANSYS-18.0.zip']
+
+import os
+license_server = os.getenv('EB_ANSYS_LICENSE_SERVER', 'license.it4i.cz')
+license_server_port = os.getenv('EB_ANSYS_LICENSE_SERVER_PORT', '2325:1055')
+
+moduleclass = 'tools'

a/ASHS/ASHS-rev103_20140612.eb

@@ -0,0 +1,29 @@
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+# Author: Ravi Tripathi
+# Email: ravi89@uab.edu
+
+easyblock = "Tarball"
+
+name = 'ASHS'
+version = 'rev103_20140612'
+
+homepage = 'https://sites.google.com/site/hipposubfields/home'
+description = """ Automatic Segmentation of Hippocampal Subfields (ASHS) """
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+#You need to create an account to download the source
+#from https://www.nitrc.org/frs/?group_id=370
+sources = ['ashs_Linux64_%(version)s.tgz']
+
+checksums= ["07fea2883b856af8797b200212b72e71"]
+
+modextravars = {'ASHS_ROOT': '%(installdir)s'}
+
+sanity_check_paths = {
+    'files': ["bin/ashs_main.sh", "bin/ashs_template_qsub.sh", "bin/ashs_train.sh", 
+             "bin/ashs_util_makepdf.sh"],
+    'dirs': ["ext"]
+}
+
+moduleclass = 'bio'

a/Advisor/Advisor-2016_update2.eb

@@ -0,0 +1,21 @@
+name = 'Advisor'
+version = '2016_update2'
+
+homepage = 'https://software.intel.com/intel-advisor-xe'
+description = """Vectorization Optimization and Thread Prototyping
+ - Vectorize & thread code or performance “dies”
+ - Easy workflow + data + tips = faster code faster
+ - Prioritize, Prototype & Predict performance gain
+ """
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+sources = ['advisor_xe_%(version)s.tar.gz']
+
+dontcreateinstalldir = 'True'
+
+# license file
+import os
+license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic")
+
+moduleclass = 'perf'

a/Advisor/Advisor-2017_update1.eb

@@ -0,0 +1,23 @@
+name = 'Advisor'
+version = '2017_update1'
+
+homepage = 'https://software.intel.com/intel-advisor-xe'
+description = """Vectorization Optimization and Thread Prototyping
+ - Vectorize & thread code or performance “dies”
+ - Easy workflow + data + tips = faster code faster
+ - Prioritize, Prototype & Predict performance gain
+ """
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+sources = ['advisor_%(version)s.tar.gz']
+
+checksums = ['af87b381394be3100507827a3461b3bc']
+
+dontcreateinstalldir = 'True'
+
+# license file
+import os
+license_file = os.path.join(os.getenv('HOME'), "licenses", "intel", "license.lic")
+
+moduleclass = 'perf'

a/Allinea/Allinea-4.1-32834-Redhat-5.7-x86_64.eb

@@ -0,0 +1,17 @@
+name = 'Allinea'
+version = '4.1-32834-Redhat-5.7-x86_64'
+
+homepage = 'http://www.allinea.com'
+description = """The Allinea environment is an essential toolkit for developers and computational scientists
+looking to get results faster."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+source_urls = ['http://content.allinea.com/downloads/']
+sources = ['%(namelower)s-tools-%(version)s.tar']
+
+# license file
+import os
+license_file = os.path.join(os.getenv('HOME'), "licenses", "allinea", "license.lic")
+
+moduleclass = 'tools'

a/Allinea/Allinea-4.1-32834-Redhat-6.0-x86_64.eb

@@ -0,0 +1,17 @@
+name = 'Allinea'
+version = '4.1-32834-Redhat-6.0-x86_64'
+
+homepage = 'http://www.allinea.com'
+description = """The Allinea environment is an essential toolkit for developers and computational scientists
+looking to get results faster."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+source_urls = ['http://content.allinea.com/downloads/']
+sources = ['%(namelower)s-tools-%(version)s.tar']
+
+# license file
+import os
+license_file = os.path.join(os.getenv('HOME'), "licenses", "allinea", "license.lic")
+
+moduleclass = 'tools'

a/Allinea/Allinea-6.1.1-Ubuntu-14.04-x86_64.eb

@@ -0,0 +1,25 @@
+name = 'Allinea'
+version = '6.1.1-Ubuntu-14.04-x86_64'
+
+homepage = 'http://www.allinea.com'
+description = """The Allinea environment is an essential toolkit for developers and computational scientists
+looking to get results faster."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+source_urls = ['http://content.allinea.com/downloads/']
+sources = ['%(namelower)s-forge-%(version)s.tar']
+
+# Example of templates usage
+#templates = [
+#    'kebnekaise.qtf',
+#    'kebnekaise-gpu.qtf',
+#]
+
+# Example of sysconfig usage
+#sysconfig = 'system.config.hpc2n'
+
+# license file
+license_file = HOME + '/licenses/allinea/license.lic'
+
+moduleclass = 'tools'

a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14-serial.eb

@@ -0,0 +1,29 @@
+name = 'Amber'
+version = '16'
+ambertools_ver = '16'
+# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html
+patchlevels = (5, 14)  # (AmberTools, Amber)
+versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-serial' %(ambertools_ver, patchlevels[0], patchlevels[1])
+
+homepage = 'http://ambermd.org/amber.html'
+description = """Amber (originally Assisted Model Building with Energy
+ Refinement) is software for performing molecular dynamics and structure
+ prediction."""
+
+toolchain = {'name': 'iomkl', 'version': '2016.07'}
+toolchainopts = {'usempi': False}
+
+sources = [
+    'Amber%(version)s.tar.bz2',
+    'AmberTools%s.tar.bz2' % ambertools_ver,
+]
+
+patches = ['Amber-%(version)s_fix-hardcoding.patch']
+
+dependencies = [
+    ('netCDF', '4.4.0'),
+    ('netCDF-Fortran', '4.4.4'),
+    ('Python', '2.7.11'),
+]
+
+moduleclass = 'chem'

a/Amber/Amber-16-iomkl-2016.07-AmberTools-16-patchlevel-5-14.eb

@@ -0,0 +1,29 @@
+name = 'Amber'
+version = '16'
+ambertools_ver = '16'
+# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html
+patchlevels = (5, 14)  # (AmberTools, Amber)
+versionsuffix = '-AmberTools-%s-patchlevel-%s-%s' %(ambertools_ver, patchlevels[0], patchlevels[1])
+
+homepage = 'http://ambermd.org/amber.html'
+description = """Amber (originally Assisted Model Building with Energy
+ Refinement) is software for performing molecular dynamics and structure
+ prediction."""
+
+toolchain = {'name': 'iomkl', 'version': '2016.07'}
+toolchainopts = {'usempi': True}
+
+sources = [
+    'Amber%(version)s.tar.bz2',
+    'AmberTools%s.tar.bz2' % ambertools_ver,
+]
+
+patches = ['Amber-%(version)s_fix-hardcoding.patch']
+
+dependencies = [
+    ('netCDF', '4.4.0'),
+    ('netCDF-Fortran', '4.4.4'),
+    ('Python', '2.7.11'),
+]
+
+moduleclass = 'chem'

a/Amber/Amber-16-iomkl-2016.09-GCC-4.9.3-2.25-AmberTools-16-patchlevel-5-14-CUDA.eb

@@ -0,0 +1,32 @@
+name = 'Amber'
+version = '16'
+ambertools_ver = '16'
+# Patch levels from http://ambermd.org/bugfixes16.html and http://ambermd.org/bugfixesat.html
+patchlevels = (5, 14)  # (AmberTools, Amber)
+versionsuffix = '-AmberTools-%s-patchlevel-%s-%s-CUDA' %(ambertools_ver, patchlevels[0], patchlevels[1])
+
+homepage = 'http://ambermd.org/amber.html'
+description = """Amber (originally Assisted Model Building with Energy
+ Refinement) is software for performing molecular dynamics and structure
+ prediction."""
+
+toolchain = {'name': 'iomkl', 'version': '2016.09-GCC-4.9.3-2.25'}
+toolchainopts = {'usempi': True}
+
+sources = [
+    'Amber%(version)s.tar.bz2',
+    'AmberTools%s.tar.bz2' % ambertools_ver,
+]
+
+patches = ['Amber-%(version)s_fix-hardcoding.patch',
+           'Amber-%(version)s_test_cuda.patch']
+
+
+dependencies = [
+    ('CUDA', '7.5.18', '', True),
+    ('netCDF', '4.4.0'),
+    ('netCDF-Fortran', '4.4.4'),
+    ('Python', '2.7.11'),
+]
+
+moduleclass = 'chem'

a/AmberTools/AmberTools-15-intel-2015b-Python-2.7.11.eb

@@ -0,0 +1,46 @@
+#
+# modified by Stephane Thiell (Stanford University) for Amber v14
+#
+# author: Benjamin P. Roberts (University of Auckland)
+#
+# based on work by Marios Constantinou (University of Cyprus)
+#
+easyblock = 'ConfigureMake'
+
+name = 'AmberTools'
+version = '14'
+
+homepage = 'http://ambermd.org/amber.html'
+description = """Amber (originally Assisted Model Building with Energy
+ Refinement) is software for performing molecular dynamics and structure
+ prediction."""
+
+toolchain = {'name': 'intel', 'version': '2016a'}
+toolchainopts = {'openmp': False, 'usempi': True}
+
+ambertools_ver = '15'
+sources = [
+#    'Amber%(version)s.tar.bz2',
+    'AmberTools%s.tar.bz2' % ambertools_ver,
+]
+
+configopts = '--no-updates'
+
+#patches = [
+#    'Amber-%(version)s_fix-hardcoding.patch',
+#    'AmberTools-%s_fix-mdgx-print-bug.patch' % ambertools_ver,
+#]
+
+dependencies = [
+#    ('CUDA', '7.5.18', '', True),
+#    ('netCDF', '4.4.0'),
+#    ('netCDF-Fortran', '4.4.4'),
+    ('Python', '2.7.11'),
+]
+
+patchlevels = (13, 13)
+patchruns = 1
+
+versionsuffix = '-Python-2.7.11)'
+
+moduleclass = 'chem'

a/AmberTools/AmberTools-16-intel-2015b-Python-2.7.11.eb

@@ -0,0 +1,36 @@
+easyblock = 'ConfigureMake'
+
+name = 'AmberTools'
+version = '16'
+
+homepage = 'http://ambermd.org/amber.html'
+description = """Amber (originally Assisted Model Building with Energy
+ Refinement) is software for performing molecular dynamics and structure
+ prediction."""
+
+toolchain = {'name': 'intel', 'version': '2015b'}
+toolchainopts = {'openmp': False, 'usempi': True}
+
+ambertools_ver = '16'
+sources = [
+#    'Amber%(version)s.tar.bz2',
+    'AmberTools%s.tar.bz2' % ambertools_ver,
+]
+patches = [
+#    'Amber-%(version)s_fix-hardcoding.patch',
+    'AmberTools-%s_fix-mdgx-print-bug.patch' % ambertools_ver,
+]
+
+dependencies = [
+ #   ('CUDA', '7.5.18', '', True),
+ #   ('netCDF', '4.4.0'),
+ #   ('netCDF-Fortran', '4.4.4'),
+    ('Python', '2.7.11'),
+]
+
+patchlevels = (13, 13)
+patchruns = 1
+
+versionsuffix = '-AmberTools-%s-patchlevel-%d-%d' % (ambertools_ver, patchlevels[0], patchlevels[1])
+
+moduleclass = 'chem'

a/Armadillo/Armadillo-7.500.0-foss-2016a-Python-3.5.2.eb

@@ -0,0 +1,24 @@
+name = 'Armadillo'
+version = '7.500.0'
+versionsuffix = '-Python-3.5.2'
+
+homepage = 'http://arma.sourceforge.net/'
+description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards
+ a good balance between speed and ease of use. Integer, floating point and complex numbers are supported,
+ as well as a subset of trigonometric and statistics functions."""
+
+toolchain = {'name': 'foss', 'version': '2016a'}
+
+sources = [SOURCELOWER_TAR_XZ]
+source_urls = ['http://sourceforge.net/projects/arma/files']
+
+dependencies = [
+    ('Boost', '1.61.0', '-serial'),
+    ('arpack-ng', '3.3.0'),
+    ('CMake', '3.5.2'),
+    ('HDF5', '1.8.16'),
+    ('libxml2', '2.9.3'),
+    ('XZ', '5.2.2'),
+]
+
+moduleclass = 'numlib'

a/Autoconf/Autoconf-2.69-GCC-4.7.2.eb

@@ -0,0 +1,22 @@
+easyblock = 'ConfigureMake'
+
+name = 'Autoconf'
+version = '2.69'
+
+homepage = 'http://www.gnu.org/software/autoconf/'
+description = """Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls."""
+
+toolchain = {'name': 'GCC', 'version': '4.7.2'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+
+dependencies = [('M4', '1.4.16')]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf",
+                                     "autoscan", "autoupdate", "ifnames"]],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

a/Autoconf/Autoconf-2.69-GCC-6.3.0-2.27.eb

@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'Autoconf'
+version = '2.69'
+
+homepage = 'http://www.gnu.org/software/autoconf/'
+description = """Autoconf is an extensible package of M4 macros that produce shell scripts
+ to automatically configure software source code packages. These scripts can adapt the
+ packages to many kinds of UNIX-like systems without manual user intervention. Autoconf
+ creates a configuration script for a package from a template file that lists the
+ operating system features that the package can use, in the form of M4 macro calls."""
+
+toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+
+dependencies = [('M4', '1.4.18')]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan",
+                                     "autoupdate", "ifnames"]],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

a/Autoconf/Autoconf-2.69-goolf-1.4.10.eb

@@ -0,0 +1,22 @@
+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': 'goolf', 'version': '1.4.10'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+
+dependencies = [('M4', '1.4.16')]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf",
+                                     "autoscan", "autoupdate", "ifnames"]],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

a/Autoconf/Autoconf-2.69-intel-2017.00.eb

@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'Autoconf'
+version = '2.69'
+
+homepage = 'http://www.gnu.org/software/autoconf/'
+description = """Autoconf is an extensible package of M4 macros that produce shell scripts
+ to automatically configure software source code packages. These scripts can adapt the
+ packages to many kinds of UNIX-like systems without manual user intervention. Autoconf
+ creates a configuration script for a package from a template file that lists the
+ operating system features that the package can use, in the form of M4 macro calls."""
+
+toolchain = {'name': 'intel', 'version': '2017.00'}
+
+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'

a/Autoconf/Autoconf-2.69-intel-2017a.eb

@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'Autoconf'
+version = '2.69'
+
+homepage = 'http://www.gnu.org/software/autoconf/'
+description = """Autoconf is an extensible package of M4 macros that produce shell scripts
+ to automatically configure software source code packages. These scripts can adapt the
+ packages to many kinds of UNIX-like systems without manual user intervention. Autoconf
+ creates a configuration script for a package from a template file that lists the
+ operating system features that the package can use, in the form of M4 macro calls."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+
+dependencies = [('M4', '1.4.18')]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan",
+                                     "autoupdate", "ifnames"]],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

a/Autoconf/Autoconf-2.69.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': 'dummy', 'version': ''}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+
+dependencies = [('M4', '1.4.18')]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in ["autoconf", "autoheader", "autom4te", "autoreconf", "autoscan",
+                                     "autoupdate", "ifnames"]],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

a/Automake/Automake-1.15-GCC-6.3.0-2.27.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 <fotis@cern.ch>
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/
+##
+
+easyblock = 'ConfigureMake'
+
+name = 'Automake'
+version = "1.15"
+
+homepage = 'http://www.gnu.org/software/automake/automake.html'
+description = "Automake: GNU Standards-compliant Makefile generator"
+
+toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+
+dependencies = [('Autoconf', '2.69')]
+
+sanity_check_paths = {
+    'files': ['bin/automake', 'bin/aclocal'],
+    'dirs': []
+}
+
+moduleclass = 'devel'

a/Automake/Automake-1.15-intel-2017.00.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 <fotis@cern.ch>
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/
+##
+
+easyblock = 'ConfigureMake'
+
+name = 'Automake'
+version = "1.15"
+
+homepage = 'http://www.gnu.org/software/automake/automake.html'
+description = "Automake: GNU Standards-compliant Makefile generator"
+
+toolchain = {'name': 'intel', 'version': '2017.00'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+
+dependencies = [('Autoconf', '2.69')]
+
+sanity_check_paths = {
+    'files': ['bin/automake', 'bin/aclocal'],
+    'dirs': []
+}
+
+moduleclass = 'devel'

a/Automake/Automake-1.15-intel-2017a.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 <fotis@cern.ch>
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a component of the policy:
+# http://hpcbios.readthedocs.org/en/latest/
+##
+
+easyblock = 'ConfigureMake'
+
+name = 'Automake'
+version = "1.15"
+
+homepage = 'http://www.gnu.org/software/automake/automake.html'
+description = "Automake: GNU Standards-compliant Makefile generator"
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+
+source_urls = [GNU_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+
+dependencies = [('Autoconf', '2.69')]
+
+sanity_check_paths = {
+    'files': ['bin/automake', 'bin/aclocal'],
+    'dirs': []
+}
+
+moduleclass = 'devel'

a/Autotools/Autotools-20150215-GCC-6.3.0-2.27.eb

@@ -0,0 +1,17 @@
+easyblock = 'Bundle'
+
+name = 'Autotools'
+version = '20150215'  # date of the most recent change
+
+homepage = 'http://autotools.io'
+description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool"""
+
+toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
+
+dependencies = [
+    ('Autoconf', '2.69'),  # 20120424
+    ('Automake', '1.15'),  # 20150105
+    ('libtool', '2.4.6'),  # 20150215
+]
+
+moduleclass = 'devel'

a/Autotools/Autotools-20150215-foss-2017a.eb

@@ -0,0 +1,17 @@
+easyblock = 'Bundle'
+
+name = 'Autotools'
+version = '20150215'  # date of the most recent change
+
+homepage = 'http://autotools.io'
+description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool"""
+
+toolchain = {'name': 'foss', 'version': '2017a'}
+
+dependencies = [
+    ('Autoconf', '2.69'),  # 20120424
+    ('Automake', '1.15'),  # 20150105
+    ('libtool', '2.4.6'),  # 20150215
+]
+
+moduleclass = 'devel'

a/Autotools/Autotools-20150215-intel-2017.00.eb

@@ -0,0 +1,17 @@
+easyblock = 'Bundle'
+
+name = 'Autotools'
+version = '20150215'  # date of the most recent change
+
+homepage = 'http://autotools.io'
+description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool"""
+
+toolchain = {'name': 'intel', 'version': '2017.00'}
+
+dependencies = [
+    ('Autoconf', '2.69'),  # 20120424
+    ('Automake', '1.15'),  # 20150105
+    ('libtool', '2.4.6'),  # 20150215
+]
+
+moduleclass = 'devel'

a/Autotools/Autotools-20150215-intel-2017a.eb

@@ -0,0 +1,17 @@
+easyblock = 'Bundle'
+
+name = 'Autotools'
+version = '20150215'  # date of the most recent change
+
+homepage = 'http://autotools.io'
+description = """This bundle collect the standard GNU build tools: Autoconf, Automake and libtool"""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+
+dependencies = [
+    ('Autoconf', '2.69'),  # 20120424
+    ('Automake', '1.15'),  # 20150105
+    ('libtool', '2.4.6'),  # 20150215
+]
+
+moduleclass = 'devel'

a/almost/almost-2.1.0-foss-2015b.eb

@@ -0,0 +1,31 @@
+easyblock = 'ConfigureMake'
+
+name = 'almost'
+version = '2.1.0'
+
+homepage = 'http://www-almost.ch.cam.ac.uk/site'
+description = """all atom molecular simulation toolkit
+ - is a fast and flexible molecular modeling environment 
+ that provides powerful and efficient algorithms for molecular
+ simulation, homology modeling, de novo design and ab-initio 
+ calculations.
+ """
+
+toolchain = {'name': 'foss', 'version': '2015b'}
+
+source_urls = ['http://www-almost.ch.cam.ac.uk/site/downloads']
+sources = [SOURCELOWER_TAR_GZ]
+
+builddependencies = [
+     ('ScaLAPACK', '2.0.2', '-OpenBLAS-0.2.14-LAPACK-3.5.0', ('gompi', '2015b')),
+     ('OpenBLAS', '0.2.14', '-LAPACK-3.5.0', ('GNU', '5.1.0-2.25')),
+     ('SQLite', '3.8.8.1', '', ('intel', '2015b')),
+     ('gzip', '1.6', '', ('intel','2015b'))
+]
+
+sanity_check_paths = {
+    'files': ['bin/almost'],
+    'dirs': []
+}
+
+moduleclass = 'bio'

a/almost/almost-2.1.0-foss-2015g.eb

@@ -0,0 +1,44 @@
+easyblock = 'ConfigureMake'
+
+name = 'almost'
+version = '2.1.0'
+
+homepage = 'http://www-almost.ch.cam.ac.uk/site'
+description = """all atom molecular simulation toolkit
+ - is a fast and flexible molecular modeling environment
+ that provides powerful and efficient algorithms for molecular
+ simulation, homology modeling, de novo design and ab-initio
+ calculations.
+ """
+
+toolchain = {'name': 'foss', 'version': '2015g'}
+
+# Sources checked out using svn
+# svn checkout svn://svn.code.sf.net/p/almost/code/ almost-code).
+# ALMOST 2.1 can be found in branches/almost-2.1
+# tar.gz file created from almost-2.1 directory and put to the
+# /easybuild/sources
+source_urls = ['http://www-almost.ch.cam.ac.uk/site/downloads']
+sources = [SOURCELOWER_TAR_GZ]
+
+builddependencies = [
+     ('ScaLAPACK', '2.0.2', '-OpenBLAS-0.2.14-LAPACK-3.5.0', ('gompi', '2015g')),
+     ('OpenBLAS', '0.2.14', '-LAPACK-3.5.0', ('GNU', '4.9.3-2.25')),
+     ('SQLite', '3.8.8.1'),
+     ('gzip', '1.6'),
+     ('Autotools', '20150215', '', ('GNU', '4.9.3-2.25')),
+]
+
+configopts = 'CPPFLAGS="-I$EBROOTOPENMPI/include" '
+configopts += 'LDFLAGS="-L$EBROOTOPENMPI/lib -lmpi" '
+configopts += 'CXXFLAGS="-O3 -fPIC" CFLAGS="-O3 -fPIC" '
+configopts += '--enable-mpi '
+
+preconfigopts = 'autoreconf -fi && automake && '
+
+sanity_check_paths = {
+    'files': ['bin/almost'],
+    'dirs': []
+}
+
+moduleclass = 'bio'

a/almost/almost-2.1.0-foss-2016a.eb

@@ -0,0 +1,44 @@
+easyblock = 'ConfigureMake'
+
+name = 'almost'
+version = '2.1.0'
+
+homepage = 'http://www-almost.ch.cam.ac.uk/site'
+description = """all atom molecular simulation toolkit
+ - is a fast and flexible molecular modeling environment
+ that provides powerful and efficient algorithms for molecular
+ simulation, homology modeling, de novo design and ab-initio
+ calculations.
+ """
+
+toolchain = {'name': 'foss', 'version': '2016a'}
+
+# Sources checked out using svn
+# svn checkout svn://svn.code.sf.net/p/almost/code/ almost-code).
+# ALMOST 2.1 can be found in branches/almost-2.1
+# tar.gz file created from almost-2.1 directory and put to the
+# /easybuild/sources
+source_urls = ['http://www-almost.ch.cam.ac.uk/site/downloads']
+sources = [SOURCELOWER_TAR_GZ]
+
+builddependencies = [
+     ('ScaLAPACK', '2.0.2', '-OpenBLAS-0.2.15-LAPACK-3.6.0', ('gompi', '2016a')),
+     ('OpenBLAS', '0.2.15', '-LAPACK-3.6.0', ('GCC', '4.9.3-2.25')),
+     ('SQLite', '3.8.8.1'),
+     ('gzip', '1.6'),
+     ('Autotools', '20150215'),
+]
+
+configopts = 'CPPFLAGS="-I$EBROOTOPENMPI/include" '
+configopts += 'LDFLAGS="-L$EBROOTOPENMPI/lib -lmpi" '
+configopts += 'CXXFLAGS="-O3 -fPIC" CFLAGS="-O3 -fPIC" '
+configopts += '--enable-mpi '
+
+preconfigopts = 'autoreconf -fi && automake && '
+
+sanity_check_paths = {
+    'files': ['bin/almost'],
+    'dirs': []
+}
+
+moduleclass = 'bio'

a/almost/almost-2.1.0-intel-2015b.eb

@@ -0,0 +1,31 @@
+easyblock = 'ConfigureMake'
+
+name = 'almost'
+version = '2.1.0'
+
+homepage = 'http://www-almost.ch.cam.ac.uk/site'
+description = """all atom molecular simulation toolkit
+ - is a fast and flexible molecular modeling environment 
+ that provides powerful and efficient algorithms for molecular
+ simulation, homology modeling, de novo design and ab-initio 
+ calculations.
+ """
+
+toolchain = {'name': 'intel', 'version': '2015b'}
+
+source_urls = ['http://www-almost.ch.cam.ac.uk/site/downloads']
+sources = [SOURCELOWER_TAR_GZ]
+
+builddependencies = [
+     ('ScaLAPACK', '2.0.2', '-OpenBLAS-0.2.14-LAPACK-3.5.0', ('gompi', '2015b')),
+     ('OpenBLAS', '0.2.14', '-LAPACK-3.5.0', ('GNU', '5.1.0-2.25')),
+     ('SQLite', '3.8.8.1'),
+     ('gzip', '1.6')
+]
+
+sanity_check_paths = {
+    'files': ['bin/almost'],
+    'dirs': []
+}
+
+moduleclass = 'bio'

a/almost/almost-2.1.0.eb

@@ -0,0 +1,44 @@
+easyblock = 'ConfigureMake'
+
+name = 'almost'
+version = '2.1.0'
+
+homepage = 'http://www-almost.ch.cam.ac.uk/site'
+description = """all atom molecular simulation toolkit
+ - is a fast and flexible molecular modeling environment
+ that provides powerful and efficient algorithms for molecular
+ simulation, homology modeling, de novo design and ab-initio
+ calculations.
+ """
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+# Sources checked out using svn
+# svn checkout svn://svn.code.sf.net/p/almost/code/ almost-code).
+# ALMOST 2.1 can be found in branches/almost-2.1
+# tar.gz file created from almost-2.1 directory and put to the
+# /easybuild/sources
+source_urls = ['http://www-almost.ch.cam.ac.uk/site/downloads']
+sources = [SOURCELOWER_TAR_GZ]
+
+builddependencies = [
+     ('ScaLAPACK', '2.0.2', '-OpenBLAS-0.2.15-LAPACK-3.6.0', ('gompi', '2016a')),
+     ('OpenBLAS', '0.2.15', '-LAPACK-3.6.0', ('GCC', '4.9.3-2.25')),
+     ('SQLite', '3.8.8.1'),
+     ('gzip', '1.6'),
+     ('Autotools', '20150215'),
+]
+
+configopts = 'CPPFLAGS="-I$EBROOTOPENMPI/include" '
+configopts += 'LDFLAGS="-L$EBROOTOPENMPI/lib -lmpi" '
+configopts += 'CXXFLAGS="-O3 -fPIC" CFLAGS="-O3 -fPIC" '
+configopts += '--enable-mpi '
+
+preconfigopts = 'autoreconf -fi && automake && '
+
+sanity_check_paths = {
+    'files': ['bin/almost'],
+    'dirs': []
+}
+
+moduleclass = 'bio'

a/angsd/angsd-0.910-foss-2016a.eb

@@ -0,0 +1,26 @@
+easyblock = 'MakeCp'
+
+name = 'angsd'
+version = '0.910'
+
+homepage = 'http://www.popgen.dk/angsd'
+description = """Program for analysing NGS data."""
+ 
+toolchain = {'name': 'foss', 'version': '2016a'}
+
+source_urls = ['https://github.com/ANGSD/angsd/archive/']
+sources = ['%(version)s.tar.gz']
+
+dependencies = [('HTSlib', '1.3.1')]
+
+files_to_copy = [
+    (['angsd'], 'bin'),
+    'doc',
+]
+
+sanity_check_paths = {
+    'files': ['bin/angsd'],
+    'dirs': ['doc'],
+}
+
+moduleclass = 'bio'

a/ant/ant-1.10.0-Java-1.8.0_112.eb

@@ -0,0 +1,25 @@
+name = 'ant'
+version = '1.10.0'
+versionsuffix = '-Java-%(javaver)s' 
+
+homepage = 'http://ant.apache.org/'
+description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
+ as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+sources = ['apache-%(name)s-%(version)s-src.tar.gz']
+source_urls = ['http://archive.apache.org/dist/%(name)s/source/']
+
+dependencies = [('Java', '1.8.0_112')]
+
+builddependencies = [('JUnit', '4.12', versionsuffix)]
+
+sanity_check_paths = {
+    'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
+    'dirs': [],
+}
+
+modextravars = {'ANT_HOME': '%(installdir)s'}
+
+moduleclass = 'devel'

a/ant/ant-1.8.4-Java-1.7.0_10.eb

@@ -0,0 +1,26 @@
+name = 'ant'
+version = '1.8.4'
+
+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-%s-%s-src.tar.gz' % (name, version)]
+source_urls = ['http://archive.apache.org/dist/%s/source/' % name]
+
+java = 'Java'
+javaver = '1.7.0_10'
+versionsuffix = '-%s-%s' % (java, javaver)
+
+dependencies = [(java, javaver)]
+
+builddependencies = [('JUnit', '4.10', versionsuffix)]
+
+sanity_check_paths = {
+    'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

a/ant/ant-1.8.4-Java-1.7.0_21.eb

@@ -0,0 +1,26 @@
+name = 'ant'
+version = '1.8.4'
+
+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-%s-%s-src.tar.gz' % (name, version)]
+source_urls = ['http://archive.apache.org/dist/%s/source/' % name]
+
+java = 'Java'
+javaver = '1.7.0_21'
+versionsuffix = '-%s-%s' % (java, javaver)
+
+dependencies = [(java, javaver)]
+
+builddependencies = [('JUnit', '4.10', versionsuffix)]
+
+sanity_check_paths = {
+    'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

a/ant/ant-1.9.0-Java-1.7.0_15.eb

@@ -0,0 +1,26 @@
+name = 'ant'
+version = '1.9.0'
+
+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-%s-%s-src.tar.gz' % (name, version)]
+source_urls = ['http://archive.apache.org/dist/%s/source/' % name]
+
+java = 'Java'
+javaver = '1.7.0_15'
+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'

a/ant/ant-1.9.0-Java-1.7.0_21.eb

@@ -0,0 +1,26 @@
+name = 'ant'
+version = '1.9.0'
+
+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-%s-%s-src.tar.gz' % (name, version)]
+source_urls = ['http://archive.apache.org/dist/%s/source/' % name]
+
+java = 'Java'
+javaver = '1.7.0_21'
+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'

a/ant/ant-1.9.3-Java-1.7.0_60.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_60'
+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'

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'

a/ant/ant-1.9.6-Java-1.7.0_75.eb

@@ -0,0 +1,26 @@
+name = 'ant'
+version = '1.9.6'
+
+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_75'
+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'

a/ant/ant-1.9.6-Java-1.7.0_79.eb

@@ -0,0 +1,23 @@
+name = 'ant'
+version = '1.9.6'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'http://ant.apache.org/'
+description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
+ as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+sources = ['apache-%(name)s-%(version)s-src.tar.gz']
+source_urls = ['http://archive.apache.org/dist/%(name)s/source/']
+
+dependencies = [('Java', '1.7.0_79')]
+
+builddependencies = [('JUnit', '4.11', versionsuffix)]
+
+sanity_check_paths = {
+    'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

a/ant/ant-1.9.6-Java-1.7.0_80.eb

@@ -0,0 +1,23 @@
+name = 'ant'
+version = '1.9.6'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'http://ant.apache.org/'
+description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
+ as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+sources = ['apache-%(name)s-%(version)s-src.tar.gz']
+source_urls = ['http://archive.apache.org/dist/%(name)s/source/']
+
+dependencies = [('Java', '1.7.0_80')]
+
+builddependencies = [('JUnit', '4.12', versionsuffix)]
+
+sanity_check_paths = {
+    'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

a/ant/ant-1.9.6-Java-1.8.0_51.eb

@@ -0,0 +1,26 @@
+name = 'ant'
+version = '1.9.6'
+
+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 = '1.8.0_51'
+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'

a/ant/ant-1.9.6-Java-1.8.0_66.eb

@@ -0,0 +1,26 @@
+name = 'ant'
+version = '1.9.6'
+
+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 = '1.8.0_66'
+versionsuffix = '-%s-%s' % (java, javaver)
+
+dependencies = [(java, javaver)]
+
+builddependencies = [('JUnit', '4.12', versionsuffix)]
+
+sanity_check_paths = {
+    'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

a/ant/ant-1.9.6-Java-1.8.0_72.eb

@@ -0,0 +1,25 @@
+name = 'ant'
+version = '1.9.6'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'http://ant.apache.org/'
+description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
+ as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+sources = ['apache-%(name)s-%(version)s-src.tar.gz']
+source_urls = ['http://archive.apache.org/dist/%(name)s/source/']
+
+dependencies = [('Java', '1.8.0_72')]
+
+builddependencies = [('JUnit', '4.12', versionsuffix)]
+
+sanity_check_paths = {
+    'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
+    'dirs': [],
+}
+
+modextravars = {'ANT_HOME': '%(installdir)s'}
+
+moduleclass = 'devel'

a/ant/ant-1.9.6-Java-1.8.0_77.eb

@@ -0,0 +1,25 @@
+name = 'ant'
+version = '1.9.6'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'http://ant.apache.org/'
+description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
+ as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+sources = ['apache-%(name)s-%(version)s-src.tar.gz']
+source_urls = ['http://archive.apache.org/dist/%(name)s/source/']
+
+dependencies = [('Java', '1.8.0_77')]
+
+builddependencies = [('JUnit', '4.12', versionsuffix)]
+
+sanity_check_paths = {
+    'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
+    'dirs': [],
+}
+
+modextravars = {'ANT_HOME': '%(installdir)s'}
+
+moduleclass = 'devel'

a/ant/ant-1.9.7-Java-1.8.0_92.eb

@@ -0,0 +1,25 @@
+name = 'ant'
+version = '1.9.7'
+versionsuffix = '-Java-%(javaver)s' 
+
+homepage = 'http://ant.apache.org/'
+description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
+ as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+sources = ['apache-%(name)s-%(version)s-src.tar.gz']
+source_urls = ['http://archive.apache.org/dist/%(name)s/source/']
+
+dependencies = [('Java', '1.8.0_92')]
+
+builddependencies = [('JUnit', '4.12', versionsuffix)]
+
+sanity_check_paths = {
+    'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
+    'dirs': [],
+}
+
+modextravars = {'ANT_HOME': '%(installdir)s'}
+
+moduleclass = 'devel'

a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0-mt.eb

@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'arpack-ng'
+version = '3.1.3'
+versionsuffix = '-mt'
+
+homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
+description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
+
+toolchain = {'name': 'ictce', 'version': '5.3.0'}
+toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': False}
+
+source_urls = ['http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/']
+sources = [SOURCELOWER_TAR_GZ]
+
+# do not change the order of the patches or things will break
+patches = [
+    'arpack-ng-3.1.3-update-to-head.patch',
+    'arpack-ng-3.1.3-pkgconfig.patch',
+]
+
+configopts = '--with-pic --with-blas="$LIBBLAS_MT" --with-lapack="$LIBLAPACK_MT"'
+
+sanity_check_paths = {
+    'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT],
+    'dirs': []
+}
+
+moduleclass = 'numlib'

a/arpack-ng/arpack-ng-3.1.3-ictce-5.3.0.eb

@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'arpack-ng'
+version = '3.1.3'
+
+homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
+description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
+
+toolchain = {'name': 'ictce', 'version': '5.3.0'}
+toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': True}
+
+source_urls = ['http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/']
+sources = [SOURCELOWER_TAR_GZ]
+
+# do not change the order of the patches or things will break
+patches = [
+    'arpack-ng-3.1.3-update-to-head.patch',
+    'arpack-ng-3.1.3-pkgconfig.patch',
+    'arpack-ng-3.1.3-configure-mpi.patch',
+]
+
+configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
+
+sanity_check_paths = {
+    'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT, "lib/libparpack.a", "lib/libparpack.%s" % SHLIB_EXT],
+    'dirs': []
+}
+
+moduleclass = 'numlib'

a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0-mt.eb

@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'arpack-ng'
+version = '3.1.3'
+versionsuffix = '-mt'
+
+homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
+description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
+
+toolchain = {'name': 'ictce', 'version': '5.5.0'}
+toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': False}
+
+source_urls = ['http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/']
+sources = [SOURCELOWER_TAR_GZ]
+
+# do not change the order of the patches or things will break
+patches = [
+    'arpack-ng-3.1.3-update-to-head.patch',
+    'arpack-ng-3.1.3-pkgconfig.patch',
+]
+
+configopts = '--with-pic --with-blas="$LIBBLAS_MT" --with-lapack="$LIBLAPACK_MT"'
+
+sanity_check_paths = {
+    'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT],
+    'dirs': []
+}
+
+moduleclass = 'numlib'

a/arpack-ng/arpack-ng-3.1.3-ictce-5.5.0.eb

@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'arpack-ng'
+version = '3.1.3'
+
+homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
+description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
+
+toolchain = {'name': 'ictce', 'version': '5.5.0'}
+toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': True}
+
+source_urls = ['http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/']
+sources = [SOURCELOWER_TAR_GZ]
+
+# do not change the order of the patches or things will break
+patches = [
+    'arpack-ng-3.1.3-update-to-head.patch',
+    'arpack-ng-3.1.3-pkgconfig.patch',
+    'arpack-ng-3.1.3-configure-mpi.patch',
+]
+
+configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
+
+sanity_check_paths = {
+    'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT, "lib/libparpack.a", "lib/libparpack.%s" % SHLIB_EXT],
+    'dirs': []
+}
+
+moduleclass = 'numlib'

a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2-mt.eb

@@ -0,0 +1,23 @@
+easyblock = 'ConfigureMake'
+
+name = 'arpack-ng'
+version = '3.1.5'
+versionsuffix = '-mt'
+
+homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
+description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
+
+toolchain = {'name': 'ictce', 'version': '7.1.2'}
+toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': False}
+
+source_urls = ['http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/']
+sources = ['%(name)s_%(version)s.tar.gz']
+
+configopts = '--with-pic --with-blas="$LIBBLAS_MT" --with-lapack="$LIBLAPACK_MT"'
+
+sanity_check_paths = {
+    'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT],
+    'dirs': []
+}
+
+moduleclass = 'numlib'

a/arpack-ng/arpack-ng-3.1.5-ictce-7.1.2.eb

@@ -0,0 +1,22 @@
+easyblock = 'ConfigureMake'
+
+name = 'arpack-ng'
+version = '3.1.5'
+
+homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
+description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
+
+toolchain = {'name': 'ictce', 'version': '7.1.2'}
+toolchainopts = {'opt': True, 'optarch': True, 'pic': True, 'usempi': True}
+
+source_urls = ['http://forge.scilab.org/index.php/p/arpack-ng/downloads/get/']
+sources = ['%(name)s_%(version)s.tar.gz']
+
+configopts = '--with-pic --with-blas="$LIBBLAS_MT" --with-lapack="$LIBLAPACK_MT"'
+
+sanity_check_paths = {
+    'files': ["lib/libarpack.a", "lib/libarpack.%s" % SHLIB_EXT],
+    'dirs': []
+}
+
+moduleclass = 'numlib'

a/arpack-ng/arpack-ng-3.3.0-GCC-4.9.3.eb

@@ -0,0 +1,25 @@
+easyblock = 'ConfigureMake'
+
+name = 'arpack-ng'
+version = '3.3.0'
+
+homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
+description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
+
+toolchain = {'name': 'GCC', 'version': '4.9.3'}
+#toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
+
+source_urls = ['https://github.com/opencollab/arpack-ng/archive/']
+sources = ['%(version)s.tar.gz']
+
+builddependencies = [('Autotools', '20150215', '', ('GCC', '4.9.3-2.25'))]
+
+preconfigopts = "sh bootstrap && "
+configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
+
+sanity_check_paths = {
+    'files': ["lib/libarpack.a", "lib/libarpack.so"],
+    'dirs': []
+}
+
+moduleclass = 'numlib'

a/arpack-ng/arpack-ng-3.3.0-foss-2016a.eb

@@ -0,0 +1,25 @@
+easyblock = 'ConfigureMake'
+
+name = 'arpack-ng'
+version = '3.3.0'
+
+homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
+description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
+
+toolchain = {'name': 'foss', 'version': '2016a'}
+toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
+
+source_urls = ['https://github.com/opencollab/arpack-ng/archive/']
+sources = ['%(version)s.tar.gz']
+
+builddependencies = [('Autotools', '20150215', '', ('foss', '2016a'))]
+
+preconfigopts = "sh bootstrap && "
+configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
+
+sanity_check_paths = {
+    'files': ["lib/libarpack.a", "lib/libarpack.so"],
+    'dirs': []
+}
+
+moduleclass = 'numlib'

a/arpack-ng/arpack-ng-3.3.0-intel-2015b.eb

@@ -0,0 +1,26 @@
+easyblock = 'ConfigureMake'
+
+name = 'arpack-ng'
+version = '3.3.0'
+
+homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
+description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
+
+toolchain = {'name': 'intel', 'version': '2015b'}
+toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
+
+source_urls = ['https://github.com/opencollab/arpack-ng/archive/']
+sources = ['%(version)s.tar.gz']
+
+# IT4I modification: because we have GCC 5.1.0 in intel/2015b toolchain...
+builddependencies = [('Autotools', '20150215', '', ('GNU', '5.1.0-2.25'))]
+
+preconfigopts = "sh bootstrap && "
+configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
+
+sanity_check_paths = {
+    'files': ["lib/libarpack.a", "lib/libarpack.so"],
+    'dirs': []
+}
+
+moduleclass = 'numlib'

a/arpack-ng/arpack-ng-3.3.0-intel-2017.00.eb

@@ -0,0 +1,25 @@
+easyblock = 'ConfigureMake'
+
+name = 'arpack-ng'
+version = '3.3.0'
+
+homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
+description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
+
+toolchain = {'name': 'intel', 'version': '2017.00'}
+toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
+
+source_urls = ['https://github.com/opencollab/arpack-ng/archive/']
+sources = ['%(version)s.tar.gz']
+
+builddependencies = [('Autotools', '20150215', '', ('intel', '2017.00'))]
+
+preconfigopts = "sh bootstrap && "
+configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
+
+sanity_check_paths = {
+    'files': ["lib/libarpack.a", "lib/libarpack.so"],
+    'dirs': []
+}
+
+moduleclass = 'numlib'

a/arpack-ng/arpack-ng-3.4.0-intel-2017.00.eb

@@ -0,0 +1,25 @@
+easyblock = 'ConfigureMake'
+
+name = 'arpack-ng'
+version = '3.4.0'
+
+homepage = 'http://forge.scilab.org/index.php/p/arpack-ng/'
+description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems."""
+
+toolchain = {'name': 'intel', 'version': '2017.00'}
+toolchainopts = {'opt': True, 'pic': True, 'usempi': True}
+
+source_urls = ['https://github.com/opencollab/arpack-ng/archive/']
+sources = ['%(version)s.tar.gz']
+
+builddependencies = [('Autotools', '20150215', '', ('intel', '2017.00'))]
+
+preconfigopts = "sh bootstrap && "
+configopts = '--with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"'
+
+sanity_check_paths = {
+    'files': ["lib/libarpack.a", "lib/libarpack.so"],
+    'dirs': []
+}
+
+moduleclass = 'numlib'

b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_66.eb

@@ -0,0 +1,36 @@
+easyblock = 'MakeCp'
+
+name = 'BBMap'
+version = '35.82'
+
+homepage = 'https://sourceforge.net/projects/bbmap/'
+description = """BBMap short read aligner, and other bioinformatic tools."""
+
+toolchain = {'name': 'foss', 'version': '2015b'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%(name)s_%(version)s.tar.gz' ]
+
+java = 'Java'
+javaver = '1.8.0_66'
+versionsuffix = '-%s-%s' % (java, javaver)
+dependencies = [(java, javaver, '', True)]
+
+prebuildopts = 'cd jni && '
+
+suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE]
+buildopts = "-f makefile.%s" % suff
+
+files_to_copy = ['*']
+
+sanity_check_paths = {
+    'files': ['bbmap.sh'],
+    'dirs': []
+}
+
+modextrapaths = {'PATH': ''}
+
+modloadmsg = """For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the
+  compiled jni C code."""
+
+moduleclass = 'bio'

b/BBMap/BBMap-35.82-foss-2015b-Java-1.8.0_74.eb

@@ -0,0 +1,36 @@
+easyblock = 'MakeCp'
+
+name = 'BBMap'
+version = '35.82'
+
+homepage = 'https://sourceforge.net/projects/bbmap/'
+description = """BBMap short read aligner, and other bioinformatic tools."""
+
+toolchain = {'name': 'foss', 'version': '2015b'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%(name)s_%(version)s.tar.gz' ]
+
+java = 'Java'
+javaver = '1.8.0_74'
+versionsuffix = '-%s-%s' % (java, javaver)
+dependencies = [(java, javaver, '', True)]
+
+prebuildopts = 'cd jni && '
+
+suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE]
+buildopts = "-f makefile.%s" % suff
+
+files_to_copy = ['*']
+
+sanity_check_paths = {
+    'files': ['bbmap.sh'],
+    'dirs': []
+}
+
+modextrapaths = {'PATH': ''}
+
+modloadmsg = """For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the
+  compiled jni C code."""
+
+moduleclass = 'bio'

b/BBMap/BBMap-36.62-intel-2016b-Java-1.8.0_112.eb

@@ -0,0 +1,34 @@
+easyblock = 'MakeCp'
+
+name = 'BBMap'
+version = '36.62'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'https://sourceforge.net/projects/bbmap/'
+description = """BBMap short read aligner, and other bioinformatic tools."""
+
+toolchain = {'name': 'intel', 'version': '2016b'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%(name)s_%(version)s.tar.gz' ]
+
+dependencies = [('Java', '1.8.0_112', '', True)]
+
+prebuildopts = 'cd jni && '
+
+suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE]
+buildopts = "-f makefile.%s" % suff
+
+files_to_copy = ['*']
+
+sanity_check_paths = {
+    'files': ['bbmap.sh'],
+    'dirs': []
+}
+
+modextrapaths = {'PATH': ''}
+
+modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the"
+modloadmsg += " compiled jni C code.\n"
+
+moduleclass = 'bio'

b/BCFtools/BCFtools-1.2-foss-2015a.eb

@@ -0,0 +1,39 @@
+easyblock = 'ConfigureMake'
+
+name = 'BCFtools'
+version = '1.2'
+
+homepage = 'http://www.htslib.org/'
+description = """Samtools is a suite of programs for interacting with high-throughput sequencing data.
+ BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants"""
+
+toolchain = {'name': 'foss', 'version': '2015a'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+sources = [SOURCELOWER_TAR_BZ2]
+source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
+
+patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch']
+
+dependencies = [
+    ('HTSlib', '1.2.1'),
+    ('zlib', '1.2.8'),
+]
+
+parallel = 1
+
+skipsteps = ['configure']
+
+installopts = ' prefix=%(installdir)s'
+
+postinstallcmds = [
+    'mkdir -p %(installdir)s/lib/plugins',
+    'cp -a plugins/*.so %(installdir)s/lib/plugins/.',
+]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']],
+    'dirs': ['lib/plugins'],
+}
+
+moduleclass = 'bio'

b/BCFtools/BCFtools-1.2-intel-2015a.eb

@@ -0,0 +1,39 @@
+easyblock = 'ConfigureMake'
+
+name = 'BCFtools'
+version = '1.2'
+
+homepage = 'http://www.htslib.org/'
+description = """Samtools is a suite of programs for interacting with high-throughput sequencing data.
+ BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants"""
+
+toolchain = {'name': 'intel', 'version': '2015a'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+sources = [SOURCELOWER_TAR_BZ2]
+source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
+
+patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch']
+
+dependencies = [
+    ('HTSlib', '1.2.1'),
+    ('zlib', '1.2.8'),
+]
+
+parallel = 1
+
+skipsteps = ['configure']
+
+installopts = ' prefix=%(installdir)s'
+
+postinstallcmds = [
+    'mkdir -p %(installdir)s/lib/plugins',
+    'cp -a plugins/*.so %(installdir)s/lib/plugins/.',
+]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']],
+    'dirs': ['lib/plugins'],
+}
+
+moduleclass = 'bio'

b/BCFtools/BCFtools-1.3-foss-2015g.eb

@@ -0,0 +1,37 @@
+easyblock = 'ConfigureMake'
+
+name = 'BCFtools'
+version = '1.3'
+
+homepage = 'http://www.htslib.org/'
+description = """Samtools is a suite of programs for interacting with high-throughput sequencing data.
+ BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants"""
+
+toolchain = {'name': 'foss', 'version': '2015g'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+sources = [SOURCELOWER_TAR_BZ2]
+source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
+
+dependencies = [
+    ('HTSlib', '1.3'),
+    ('zlib', '1.2.8'),
+]
+
+parallel = 1
+
+skipsteps = ['configure']
+
+installopts = ' prefix=%(installdir)s'
+
+postinstallcmds = [
+    'mkdir -p %(installdir)s/lib/plugins',
+    'cp plugins/*.so %(installdir)s/lib/plugins/.',
+]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']],
+    'dirs': ['lib/plugins'],
+}
+
+moduleclass = 'bio'

b/BCFtools/BCFtools-1.3-foss-2016a.eb

@@ -0,0 +1,41 @@
+easyblock = 'ConfigureMake'
+
+name = 'BCFtools'
+version = '1.3'
+
+homepage = 'http://www.htslib.org/'
+description = """Samtools is a suite of programs for interacting with high-throughput sequencing data.
+ BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants"""
+
+toolchain = {'name': 'foss', 'version': '2016a'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+sources = [SOURCELOWER_TAR_BZ2]
+source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
+
+patches = ['%(name)s-%(version)s_extHTSlib_Makefile.patch']
+
+dependencies = [
+    ('HTSlib', '1.3'),
+    ('zlib', '1.2.8'),
+    ('GSL', '2.1'),
+]
+
+parallel = 1
+
+skipsteps = ['configure']
+
+buildopts = 'CC="$CC" CFLAGS="$CFLAGS" USE_GSL=1'
+installopts = ' prefix=%(installdir)s'
+
+postinstallcmds = [
+    'mkdir -p %(installdir)s/lib/plugins',
+    'cp -a plugins/*.so %(installdir)s/lib/plugins/.',
+]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']],
+    'dirs': ['lib/plugins'],
+}
+
+moduleclass = 'bio'

b/BCFtools/BCFtools-1.3-intel-2016a.eb

@@ -0,0 +1,41 @@
+easyblock = 'ConfigureMake'
+
+name = 'BCFtools'
+version = '1.3'
+
+homepage = 'http://www.htslib.org/'
+description = """Samtools is a suite of programs for interacting with high-throughput sequencing data.
+ BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants"""
+
+toolchain = {'name': 'intel', 'version': '2016a'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+sources = [SOURCELOWER_TAR_BZ2]
+source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
+
+patches = ['BCFtools-%(version)s_extHTSlib_Makefile.patch']
+
+dependencies = [
+    ('zlib', '1.2.8'),
+    ('HTSlib', '1.3'),
+    ('GSL', '2.1'),
+]
+
+parallel = 1
+
+skipsteps = ['configure']
+
+buildopts = 'CC="$CC" CFLAGS="$CFLAGS" USE_GSL=1'
+installopts = ' prefix=%(installdir)s'
+
+postinstallcmds = [
+    'mkdir -p %(installdir)s/lib/plugins',
+    'cp -a plugins/*.so %(installdir)s/lib/plugins/.',
+]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']],
+    'dirs': ['lib/plugins'],
+}
+
+moduleclass = 'bio'

b/BCFtools/BCFtools-1.3.1-goolf-1.7.20.eb

@@ -0,0 +1,37 @@
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics 
+
+easyblock = 'MakeCp'
+
+name = 'BCFtools'
+version = '1.3.1'
+
+homepage = 'http://www.htslib.org/'
+description = """BCFtools is a set of utilities that manipulate variant calls in the 
+ Variant Call Format (VCF) and its binary counterpart BCF"""
+
+toolchain = {'name': 'goolf', 'version': '1.7.20'}
+
+source_urls = ['https://github.com/samtools/bcftools/releases/download/%(version)s/']
+sources = [SOURCELOWER_TAR_BZ2]
+
+dependencies = [
+	('zlib', '1.2.8'),
+	('GSL', '1.16'),
+]
+
+buildopts = " USE_GPL=1 GSL_LIBS='-lgsl -lgslcblas'"
+
+runtest = 'test'
+
+files_to_copy = [(["bcftools", "plot-vcfstats", "vcfutils.pl"], "bin"), 
+		   "doc", "plugins", "test", "LICENSE", "README", "AUTHORS"]
+
+sanity_check_paths = {
+    'files': ["bin/bcftools"],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

b/BEDOPS/BEDOPS-2.4.1-GCC-4.8.4.eb

@@ -0,0 +1,36 @@
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+# Author: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics
+# Biozentrum - University of Basel
+
+easyblock = 'MakeCp'
+
+name = "BEDOPS"
+version = "2.4.1"
+
+homepage = 'https://github.com/bedops/bedops'
+description = """ BEDOPS is an open-source command-line toolkit that performs highly 
+ efficient and scalable Boolean and other set operations, statistical calculations, 
+ archiving, conversion and other management of genomic data of arbitrary scale.""" 
+
+# this application requires GCC-4.8.x or higher
+# be aware if you switch to a different toolchain
+toolchain = {'name': 'GCC', 'version': '4.8.4'}
+
+source_urls = ['https://github.com/bedops/bedops/archive/']
+sources = ['v%(version)s.tar.gz']
+
+buildopts = ' static && make install'
+
+parallel = 1
+
+files_to_copy = ["bin"]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in ["bedmap", "bam2bed" , "sort-bed",
+                                    "starchcat", "vcf2bed", "wig2bed",
+                                    "gtf2bed", "bedops", "wig2bed"]],
+    'dirs': []
+}
+
+moduleclass = 'bio'

b/BLAST/BLAST-2.2.26-Linux_x86_64.eb

@@ -0,0 +1,27 @@
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+# Author: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics
+# Biozentrum - University of Basel
+
+easyblock = "Tarball"
+
+name = 'BLAST'
+version = '2.2.26'
+versionsuffix = "-Linux_x86_64"
+
+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': 'dummy', 'version': 'dummy'}
+
+source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/release/%(version)s/']
+sources = ['%(namelower)s-%(version)s-x64-linux.tar.gz']
+
+sanity_check_paths = {
+    'files': ["bin/blastall", "bin/impala", "bin/blastpgp"],
+    'dirs': []
+}
+
+moduleclass = 'bio'

b/BLAT/BLAT-3.5-goolf-1.4.10.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 <a.panteli@cyi.ac.cy>, Thekla Loizou <t.loizou@cyi.ac.cy>
+# License::   MIT/GPL
+#
+##
+
+name = 'BLAT'
+version = '3.5'
+
+homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html'
+description = "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more."
+
+toolchain = {'name': 'goolf', 'version': '1.4.10'}
+
+sources = ['%%(namelower)sSrc%s.zip' % ''.join(version.split('.'))]
+source_urls = ['http://users.soe.ucsc.edu/~kent/src']
+
+dependencies = [('libpng', '1.6.2')]
+
+buildopts = 'CC="$CC" COPT= L="$LIBS"'
+
+files_to_copy = ["bin", "blat", "gfClient", "gfServer", "hg", "inc", "jkOwnLib", "lib", "utils", "webBlat"]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag',
+                                     'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']],
+    'dirs': files_to_copy,
+}
+
+moduleclass = 'bio'

b/BLAT/BLAT-3.5-ictce-5.5.0-libpng-1.6.9.eb

@@ -0,0 +1,37 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright 2012-2013 The Cyprus Institute
+# Authors::   Andreas Panteli <a.panteli@cyi.ac.cy>, Thekla Loizou <t.loizou@cyi.ac.cy>
+# License::   MIT/GPL
+#
+##
+
+name = 'BLAT'
+version = '3.5'
+
+homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html'
+description = "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more."
+
+toolchain = {'name': 'ictce', 'version': '5.5.0'}
+
+sources = ['%%(namelower)sSrc%s.zip' % ''.join(version.split('.'))]
+source_urls = ['http://users.soe.ucsc.edu/~kent/src']
+
+libpng = 'libpng'
+libpng_ver = '1.6.9'
+versionsuffix = '-%s-%s' % (libpng, libpng_ver)
+
+dependencies = [(libpng, libpng_ver)]
+
+buildopts = 'CC="$CC" COPT= L="$LIBS"'
+
+files_to_copy = ["bin", "blat", "gfClient", "gfServer", "hg", "inc", "jkOwnLib", "lib", "utils", "webBlat"]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag',
+                                     'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']],
+    'dirs': files_to_copy,
+}
+
+moduleclass = 'bio'

b/BLAT/BLAT-3.5-ictce-5.5.0.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 <a.panteli@cyi.ac.cy>, Thekla Loizou <t.loizou@cyi.ac.cy>
+# License::   MIT/GPL
+#
+##
+
+name = 'BLAT'
+version = '3.5'
+
+homepage = 'http://genome.ucsc.edu/FAQ/FAQblat.html'
+description = "BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more."
+
+toolchain = {'name': 'ictce', 'version': '5.5.0'}
+
+sources = ['%%(namelower)sSrc%s.zip' % ''.join(version.split('.'))]
+source_urls = ['http://users.soe.ucsc.edu/~kent/src']
+
+dependencies = [('libpng', '1.6.6')]
+
+buildopts = 'CC="$CC" COPT= L="$LIBS"'
+
+files_to_copy = ["bin", "blat", "gfClient", "gfServer", "hg", "inc", "jkOwnLib", "lib", "utils", "webBlat"]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag',
+                                     'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']],
+    'dirs': files_to_copy,
+}
+
+moduleclass = 'bio'

b/BLCR/BLCR-0.8.5-GNU-5.1.0-2.25.eb

@@ -0,0 +1,23 @@
+easyblock = 'ConfigureMake'
+
+name = 'BLCR'
+version = '0.8.5'
+
+homepage = 'http://crd.lbl.gov/departments/computer-science/CLaSS/research/BLCR/'
+description = """Berkeley Lab Checkpoint/Restart (BLCR) for LINUX. Future Technologies Group researchers 
+are developing a hybrid kernel/user implementation of checkpoint/restart. Their goal is to provide 
+a robust, production quality implementation that checkpoints a wide range of applications, 
+without requiring changes to be made to application code. """
+
+toolchain = {'name': 'GNU', 'version': '5.1.0-2.25'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = [('http://crd.lbl.gov/assets/Uploads/FTG/Projects/CheckpointRestart/downloads')]
+
+sanity_check_paths = {
+    'files': ['include/libcr.h'],
+    'dirs': [],
+}
+
+moduleclass = 'lib'

b/BWA/BWA-0.7.13-goolf-1.4.10.eb

@@ -0,0 +1,28 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA
+# Authors::   George Tsouloupas <g.tsouloupas@cyi.ac.cy>, Fotis Georgatos <fotis@cern.ch>, Daniel Navarro <daniel_navarro@meei.harvard.edu>
+# 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 = 'BWA'
+version = '0.7.13'
+
+homepage = 'http://bio-bwa.sourceforge.net/'
+description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns
+ relatively short nucleotide sequences against a long reference sequence such as the human genome."""
+
+toolchain = {'name': 'goolf', 'version': '1.4.10'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+sources = [SOURCELOWER_TAR_BZ2]
+source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')]
+
+dependencies = [('zlib', '1.2.8')]
+
+moduleclass = 'bio'

b/BXH_XCEDE_TOOLS/BXH_XCEDE_TOOLS-1.11.1.eb

@@ -0,0 +1,28 @@
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+# Author: Ravi Tripathi
+# Email: ravi89@uab.edu
+
+easyblock = "Tarball"
+
+name = 'BXH_XCEDE_TOOLS'
+version = '1.11.1'
+
+homepage = 'http://www.nitrc.org/projects/bxh_xcede_tools/'
+description = """A collection of data processing and image analysis 
+tools for data in BXH or XCEDE format. This includes data format 
+encapsulation/conversion, event-related analysis, QA tools, and more. 
+These tools form the basis of the fBIRN QA procedures and are also 
+distributed as part of the fBIRN Data Upload Scripts."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+source_urls = ['http://www.nitrc.org/frs/download.php/7384/']
+sources = ['bxh_xcede_tools-%(version)s-lsb30.x86_64.tgz']
+
+sanity_check_paths = {
+    'files': ["bin/dicom2bxh", "bin/dicom2xcede"],
+    'dirs': []
+}
+
+moduleclass = 'bio'
+

b/BamUtil/BamUtil-1.0.13-foss-2015b.eb

@@ -0,0 +1,31 @@
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+#
+# Author: Adam Huffman
+# adam.huffman@crick.ac.uk
+# The Francis Crick Institute
+#
+# This is the version with the bundled libStatGen library
+
+name = 'BamUtil'
+version = '1.0.13'
+
+easyblock = 'MakeCp'
+
+homepage = 'http://genome.sph.umich.edu/wiki/BamUtil'
+description = """BamUtil is a repository that contains several programs
+  that perform operations on SAM/BAM files. All of these programs
+  are built into a single executable, bam."""
+
+toolchain = {'name': 'foss', 'version': '2015b'}
+
+sources = ['%(name)sLibStatGen.%(version)s.tgz']
+source_urls = ['http://genome.sph.umich.edu/w/images/7/70/']
+
+files_to_copy = ["bamUtil/bin", "libStatGen"]
+
+sanity_check_paths = {
+    'files': ["bin/bam"],
+    'dirs': ["libStatGen"],
+}
+
+moduleclass = 'bio'

b/Bash/Bash-4.2-intel-2015b.eb

@@ -0,0 +1,59 @@
+# Built with EasyBuild version 2.1.1 on 2015-06-30_09-17-37
+##
+# 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 <valentin.plugaru@gmail.com>
+# 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 = 'Bash'
+version = '4.2'
+
+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': '2015b'}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = [GNU_SOURCE]
+
+sanity_check_paths = {
+    'files': ["bin/bash"],
+    'dirs': []
+}
+
+moduleclass = 'tools'
+
+# Build statistics
+buildstats = [{
+    "easybuild-framework_version": "2.1.1",
+    "easybuild-easyblocks_version": "2.1.1",
+    "timestamp": 1435648657,
+    "build_time": 125.54,
+    "install_size": 4996169,
+    "command_line": ['--buildpath=/easybuild/build', '--installpath=/apps', '--installpath-modules=/apps/modules', '--installpath-software=/apps', '--module-naming-scheme=IT4IModuleNamingScheme', '--modules-footer=/easybuild/templates/modules/jas02_footer.txt', '--repositorypath=/easybuild/file-repository', '--robot=/easybuild/easyconfigs-salomon/easybuild/easyconfigs', '--robot-paths=/easybuild/easyconfigs-salomon/easybuild/easyconfigs', '--sourcepath=/easybuild/sources', '--try-toolchain="[\'intel\', \'2015b\']"', 'Bash-4.2-ictce-5.3.0.eb'],
+    "modules_tool": ('EnvironmentModulesC', '/usr/bin/modulecmd', '3.2.10'),
+    "core_count": 28,
+    "cpu_model": "Intel(R) Xeon(R) CPU E5-2695 v3 @ 2.30GHz",
+    "cpu_speed": 2300.041,
+    "cpu_vendor": "Intel",
+    "gcc_version": "Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/apps/all/GCC/5.1.0-binutils-2.25/libexec/gcc/x86_64-unknown-linux-gnu/5.1.0/lto-wrapper; Target: x86_64-unknown-linux-gnu; Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/apps/all/GCC/5.1.0-binutils-2.25 --with-local-prefix=/apps/all/GCC/5.1.0-binutils-2.25 --enable-bootstrap --with-isl=/easybuild/build/GCC/5.1.0/dummy--binutils-2.25/gcc-5.1.0/stage2_stuff; Thread model: posix; gcc version 5.1.0 (GCC) ; ",
+    "glibc_version": "2.12",
+    "hostname": "login1",
+    "os_name": "centos",
+    "os_type": "Linux",
+    "os_version": "6.6",
+    "platform_name": "x86_64-unknown-linux",
+    "python_version": "2.6.6 (r266:84292, Jan 22 2014, 09:42:36) ; [GCC 4.4.7 20120313 (Red Hat 4.4.7-4)]",
+    "system_gcc_path": "/apps/all/GCC/5.1.0-binutils-2.25/bin/gcc",
+    "system_python_path": "/usr/bin/python",
+}]

b/BayPass/BayPass-2.1-goolf-1.7.20.eb

@@ -0,0 +1,40 @@
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics 
+
+easyblock = 'MakeCp'
+
+name = 'BayPass'
+version = '2.1'
+
+homepage = 'http://www1.montpellier.inra.fr/CBGP/software/baypass/index.html'
+description = """BayPass is a population genomics software which is primarily aimed at identifying 
+ genetic markers subjected to selection and/or associated to population-specific covariates 
+ (e.g., environmental variables, quantitative or categorical phenotypic characteristics). 
+ The underlying models explicitly account for (and may estimate) the covariance structure among the
+ population allele frequencies that originates from the shared history of the populations under study"""
+
+toolchain = {'name': 'goolf', 'version': '1.7.20'}
+toolchainopts = {'openmp': True}
+
+source_urls = ['http://www1.montpellier.inra.fr/CBGP/software/baypass/files/']
+sources = ['%(namelower)s_%(version)s.tar.gz']
+
+start_dir = 'sources'
+
+parallel = 1
+
+files_to_copy = [(['sources/g_baypass'], 'bin/'), 
+		  'BayPass_manual_2.1.pdf', 
+ 		  'examples', 
+		  'Licence_CeCILL-B_V1-en.txt', 
+		  'utils'
+]
+
+sanity_check_paths = {
+    'files': ['bin/g_baypass'],
+    'dirs': []
+}
+
+moduleclass = 'bio'

b/BayeScEnv/BayeScEnv-1.1-foss-2016a.eb

@@ -0,0 +1,32 @@
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics 
+
+easyblock = 'MakeCp'
+
+name = 'BayeScEnv'
+version = '1.1'
+
+homepage = 'https://github.com/devillemereuil/bayescenv'
+description = """BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detect
+local adaptation."""
+
+toolchain = {'name': 'foss', 'version': '2016a'}
+toolchainopts = {'openmp': True}
+
+source_urls = ['https://github.com/devillemereuil/bayescenv/archive/']
+sources = ['v%(version)s.tar.gz']
+
+start_dir = 'source'
+
+files_to_copy = [(['source/bayescenv'], 'bin'), 'test', 'COPYING', 'README.md', 'ChangeLog']
+
+parallel = 1
+                
+sanity_check_paths = {
+    'files': ['bin/bayescenv'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

b/BayeScEnv/BayeScEnv-1.1-goolf-1.4.10.eb

@@ -0,0 +1,31 @@
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics 
+
+easyblock = 'MakeCp'
+
+name = 'BayeScEnv'
+version = '1.1'
+
+homepage = 'https://github.com/devillemereuil/bayescenv'
+description = """BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detect local adaptation."""
+
+toolchain = {'name': 'goolf', 'version': '1.4.10'}
+toolchainopts = {'openmp': True}
+
+source_urls = ['https://github.com/devillemereuil/bayescenv/archive/']
+sources = ['v%(version)s.tar.gz']
+
+start_dir = 'source'
+
+files_to_copy = [(['source/bayescenv'], 'bin'), 'test', 'COPYING', 'README.md', 'ChangeLog']
+
+parallel = 1
+                
+sanity_check_paths = {
+    'files': ['bin/bayescenv'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

b/BayeScan/BayeScan-2.1-foss-2016a.eb

@@ -0,0 +1,39 @@
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics 
+
+easyblock = 'MakeCp'
+
+name = 'BayeScan'
+version = '2.1'
+
+homepage = 'http://cmpg.unibe.ch/software/BayeScan/'
+description = """BayeScan aims at identifying candidate loci under natural selection from genetic data, 
+ using differences in allele frequencies between populations."""
+
+toolchain = {'name': 'foss', 'version': '2016a'}
+toolchainopts = {'openmp': True}
+
+source_urls = ['http://cmpg.unibe.ch/software/BayeScan/files/']
+sources = ['%(name)s%(version)s.zip']
+
+prebuildopts = "sed -i.bk 's/g++/${CXX} ${CXXFLAGS}/g' Makefile && "
+
+start_dir = 'source'
+
+files_to_copy = [
+    (['source/bayescan_%(version)s'], 'bin'),
+    'BayeScan%(version)s_manual.pdf',
+    'input_examples',
+    'R functions'
+]
+
+parallel = 1
+                
+sanity_check_paths = {
+    'files': ['bin/bayescan_%(version)s'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

b/BayeScan/BayeScan-2.1-goolf-1.4.10.eb

@@ -0,0 +1,40 @@
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+# Author: Pablo Escobar Lopez
+# sciCORE - University of Basel
+# SIB Swiss Institute of Bioinformatics 
+
+easyblock = 'MakeCp'
+
+name = 'BayeScan'
+version = '2.1'
+
+homepage = 'http://cmpg.unibe.ch/software/BayeScan/'
+description = """BayeScan aims at identifying candidate loci under natural selection from genetic data, 
+ using differences in allele frequencies between populations."""
+
+# BayeScan makefile is hardcoded to use g++. In case you want to use a non-gcc toolchain you will need to patch the makefile 
+toolchain = {'name': 'goolf', 'version': '1.4.10'}
+toolchainopts = {'openmp': True}
+
+source_urls = ['http://cmpg.unibe.ch/software/BayeScan/files/']
+sources = ['%(name)s%(version)s.zip']
+
+start_dir = 'source'
+
+# fix the makefile which hardcodes g++ compiler
+prebuildopts = "sed -i -e 's/g++/${CXX} ${CFLAGS}/g' Makefile && "
+
+files_to_copy = [
+    (['source/bayescan_%(version)s'], 'bin'),
+    'BayeScan%(version)s_manual.pdf',
+    'input_examples',
+    'R functions']
+
+parallel = 1
+                
+sanity_check_paths = {
+    'files': ['bin/bayescan_%(version)s'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

b/BayesAss/BayesAss-3.0.4-foss-2016a.eb

@@ -0,0 +1,27 @@
+easyblock = 'ConfigureMake'
+
+name = 'BayesAss'
+version = '3.0.4'
+
+homepage = 'http://www.rannala.org/?page_id=245'
+description = """ 
+BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes 
+"""
+
+toolchain = {'name': 'foss','version': '2016a'}
+sources = ['BA3-%(version)s.tar.gz']
+
+source_urls = ['http://downloads.sourceforge.net/project/bayesass/BA3/%(version)s/src/']
+
+dependencies = [
+    ('GSL','2.1')
+]
+
+runtest = 'check'
+
+sanity_check_paths = {
+    'files': ['bin/BA3'],
+    'dirs' : ['bin', 'include']
+}
+
+moduleclass = 'bio'

b/Bazel/Bazel-0.3.0-CrayGNU-2016.03.eb

@@ -0,0 +1,30 @@
+# @author: Guilherme Peretti-Pezzi (CSCS) 
+
+easyblock = "CmdCp"
+
+name = 'Bazel'
+version = '0.3.0'
+
+homepage = 'http://bazel.io/'
+description = """Bazel is a build tool that builds code quickly and reliably. 
+It is used to build the majority of Google's software."""
+
+toolchain = {'name': 'CrayGNU', 'version': '2016.03'}
+
+dependencies = [
+    ('java/jdk1.8.0_51', EXTERNAL_MODULE),
+]
+
+sources = ['%(version)s.tar.gz']
+source_urls = ['https://github.com/bazelbuild/bazel/archive/']
+
+cmds_map = [('.*', "JAVA_VERSION=1.8 CC=gcc CXX=g++ ./compile.sh")]
+
+files_to_copy = [(['output/bazel'], 'bin')]
+
+sanity_check_paths={
+    'files': ['bin/bazel'],
+    'dirs': ['bin'],
+}
+
+moduleclass = 'devel'

b/Bazel/Bazel-0.4.4.eb

@@ -0,0 +1,31 @@
+# @author: Robert Schmidt (OHRI)
+# @author: Guilherme Peretti-Pezzi (CSCS) 
+
+easyblock = "CmdCp"
+
+name = 'Bazel'
+version = '0.4.4'
+
+homepage = 'http://bazel.io/'
+description = """Bazel is a build tool that builds code quickly and reliably. 
+It is used to build the majority of Google's software."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+sources = ['%(namelower)s-%(version)s-dist.zip']
+source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s']
+
+dependencies = [
+    ('Java', '1.8.0_121'),
+]
+
+cmds_map = [('.*', "./compile.sh")]
+
+files_to_copy = [(['output/bazel'], 'bin')]
+
+sanity_check_paths={
+    'files': ['bin/bazel'],
+    'dirs':  [],
+}
+
+moduleclass = 'devel'

b/Beast/Beast-1.8.4.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 = "Tarball"
+
+name = 'Beast'
+version = '1.8.4'
+
+homepage = 'http://beast.bio.ed.ac.uk/'
+description = """ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular 
+ sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using 
+ strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies 
+ but is also a framework for testing evolutionary hypotheses without conditioning on a single 
+ tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted 
+ proportional to its posterior probability. """
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+source_urls= ['https://github.com/beast-dev/beast-mcmc/releases/download/v%(version)s/']
+sources = ['BEASTv%(version)s.tgz']
+
+dependencies = [
+    ('Java', '1.8.0_74', '', True),
+]
+
+sanity_check_paths = {
+    'files': ["bin/beast"],
+    'dirs': []
+}
+
+moduleclass = 'bio'

b/BerkeleyGW/BerkeleyGW-1.0.6-intel-2016.02-GCC-4.9.eb

@@ -0,0 +1,37 @@
+easyblock = 'ConfigureMake'
+
+name = 'BerkeleyGW'
+version = "1.0.6"
+
+homepage = 'http://www.berkeleygw.org'
+description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle
+ properties and the optical responses of a large variety of materials from bulk periodic crystals to
+ nanostructures such as slabs, wires and molecules."""
+
+toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['http://www.berkeleygw.org/releases/']
+sources = ['BGW-%(version)s.tar.gz']
+checksums = ['8740562da41e87a62eb8d457675e4bfd']
+
+skipsteps = ['configure']
+
+prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && '
+
+buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" '
+buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" '
+buildopts += 'C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" LAPACKLIB="$LIBLAPACK" '
+buildopts += 'BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" '
+buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" '
+
+installopts = 'INSTDIR=%(installdir)s'
+
+sanity_check_paths = {
+    'files': ['bin/'+prog+'.'+flavor+'.x'
+              for prog in ['epsilon', 'sigma', 'kernel', 'absorption']
+              for flavor in ['real', 'cplx']],
+    'dirs': []
+}
+
+moduleclass = 'phys'

b/BerkeleyGW/BerkeleyGW-1.1-beta2-intel-2016.02-GCC-4.9.eb

@@ -0,0 +1,37 @@
+easyblock = 'ConfigureMake'
+
+name = 'BerkeleyGW'
+version = "1.1-beta2"
+
+homepage = 'http://www.berkeleygw.org'
+description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle
+ properties and the optical responses of a large variety of materials from bulk periodic crystals to
+ nanostructures such as slabs, wires and molecules."""
+
+toolchain = {'name': 'intel', 'version': '2016.02-GCC-4.9'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['http://www.berkeleygw.org/releases/']
+sources = ['BGW-%(version)s.tar.gz']
+checksums = ['75a258c9a5d255da9e0b15bd3e7f08b2']
+
+skipsteps = ['configure']
+
+prebuildopts = 'cp config/generic.mpi.linux.mk arch.mk && '
+
+buildopts = 'all-flavors COMPFLAG=-DINTEL PARAFLAG="-DMPI -DOMP" DEBUGFLAG="" F90free="$MPIF90 -free" LINK="$MPIF90" '
+buildopts += 'FOPTS="$FFLAGS -qopenmp" MOD_OPT="-module " C_PARAFLAG="$PARAFLAG" CC_COMP="$MPICXX" C_COMP="$MPICC" '
+buildopts += 'C_LINK="$MPICXX" C_OPTS="$CFLAGS -qopenmp" MKLPATH="$MKLROOT" LAPACKLIB="$LIBLAPACK" '
+buildopts += 'BLACSDIR="$BLACS_LIB_DIR" BLACS="$LIBBLACS" SCALAPACKLIB="$LIBSCALAPACK" '
+buildopts += 'FFTWINCLUDE="$FFTW_INC_DIR" FFTWLIB="$MKLROOT/lib/intel64/libfftw2xf_double_intel.a" '
+
+installopts = 'INSTDIR=%(installdir)s'
+
+sanity_check_paths = {
+    'files': ['bin/'+prog+'.'+flavor+'.x'
+              for prog in ['epsilon', 'sigma', 'kernel', 'absorption']
+              for flavor in ['real', 'cplx']],
+    'dirs': []
+}
+
+moduleclass = 'phys'