new file: a/ABySS/ABySS-2.0.2-foss-2018a-Py-2.7.eb

new file:   a/ASE/ASE-3.15.0-Python-2.7.13-base-test.eb
	new file:   a/ASE/ASE-3.15.0-Python-3.6.4-base-test.eb
	new file:   b/Bash/Bash-4.4-GCC-6.3.0-2.27.eb
	new file:   b/Bash/Bash-4.4-intel-2017b.eb
	new file:   b/Boost/Boost-1.66.0-foss-2018a-Py-2.7.eb
	new file:   f/foss/foss-2018a.eb
	new file:   n/numpy/numpy-1.14.1-Py-3.6.eb
	new file:   n/numpy/numpy-1.14.1-mkl.patch
	new file:   o/OpenMPI/OpenMPI-3.0.0-GCC-6.3.0-2.27.eb
	new file:   s/SQLite/SQLite-3.21.0.eb

a/ABySS/ABySS-2.0.2-foss-2018a-Py-2.7.eb

@@ -0,0 +1,29 @@
+easyblock = 'ConfigureMake'
+
+name = 'ABySS'
+version = '2.0.2'
+
+homepage = 'http://www.bcgsc.ca/platform/bioinfo/software/abyss'
+description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler"""
+
+toolchain = {'name': 'foss', 'version': '2018a'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['d87b76edeac3a6fb48f24a1d63f243d8278a324c9a5eb29027b640f7089422df']
+
+dependencies = [
+    ('Boost', '1.66.0', '-Py-2.7'),
+    ('sparsehash', '2.0.3'),
+    ('SQLite', '3.21.0', '', True),
+]
+
+configopts = " --enable-maxk=256 "
+
+sanity_check_paths = {
+    'files': ["bin/ABYSS", "bin/ABYSS-P"],
+    'dirs': []
+}
+
+moduleclass = 'bio'

a/ASE/ASE-3.15.0-Python-2.7.13-base-test.eb

@@ -0,0 +1,31 @@
+# IT4Innovations 2017
+
+easyblock = 'PythonPackage'
+
+name = 'ASE'
+version = '3.15.0'
+versionsuffix = '-Python-%(pyver)s-base-test'
+
+homepage = 'https://wiki.fysik.dtu.dk/ase/'
+description = """ASE is a python package providing an open source Atomic Simulation Environment
+ in the Python scripting language."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+source_urls = [PYPI_LOWER_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['5e22d961b1311ef4ba2d83527f7cc7448abac8cf9bddd1593bee548459263fe8']
+
+dependencies = [
+    ('Python', '2.7.13'),
+#    ('numpy', '1.13.0', '-Python-2.7.13-base'),
+#    ('scipy', '0.19.1', '-Python-2.7.13-base'),
+#    ('matplotlib', '2.0.2', '-Python-2.7.13-base'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'chem'

a/ASE/ASE-3.15.0-Python-3.6.4-base-test.eb

@@ -0,0 +1,31 @@
+# IT4Innovations 2017
+
+easyblock = 'PythonPackage'
+
+name = 'ASE'
+version = '3.15.0'
+versionsuffix = '-Python-%(pyver)s-base-test'
+
+homepage = 'https://wiki.fysik.dtu.dk/ase/'
+description = """ASE is a python package providing an open source Atomic Simulation Environment
+ in the Python scripting language."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+source_urls = [PYPI_LOWER_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['5e22d961b1311ef4ba2d83527f7cc7448abac8cf9bddd1593bee548459263fe8']
+
+dependencies = [
+    ('Python', '3.6.1'),
+#    ('numpy', '1.13.0', '-Python-2.7.13-base'),
+#    ('scipy', '0.19.1', '-Python-2.7.13-base'),
+#    ('matplotlib', '2.0.2', '-Python-2.7.13-base'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/ase-build', 'bin/ase-db', 'bin/ase-gui', 'bin/ase-info', 'bin/ase-run'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+moduleclass = 'chem'

b/Bash/Bash-4.4-GCC-6.3.0-2.27.eb

@@ -0,0 +1,29 @@
+# IT4Innovations 2018
+
+easyblock = 'ConfigureMake'
+
+name = 'Bash'
+version = '4.4'
+
+homepage = 'http://www.gnu.org/software/bash'
+description = """Bash is an sh-compatible command language interpreter that executes commands
+ read from the standard input or from a file.  Bash also incorporates useful features from the
+ Korn and C shells (ksh and csh)."""
+
+toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = [GNU_SOURCE]
+
+dependencies = [
+    ('libreadline', '7.0', '', True),
+]
+
+configopts = " --enable-readline --enable-job-control --enable-history "
+
+sanity_check_paths = {
+    'files': ["bin/bash"],
+    'dirs': []
+}
+
+moduleclass = 'tools'

b/Bash/Bash-4.4-intel-2017b.eb

@@ -0,0 +1,29 @@
+# IT4Innovations 2018
+
+easyblock = 'ConfigureMake'
+
+name = 'Bash'
+version = '4.4'
+
+homepage = 'http://www.gnu.org/software/bash'
+description = """Bash is an sh-compatible command language interpreter that executes commands
+ read from the standard input or from a file.  Bash also incorporates useful features from the
+ Korn and C shells (ksh and csh)."""
+
+toolchain = {'name': 'intel', 'version': '2017b'}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = [GNU_SOURCE]
+
+dependencies = [
+    ('libreadline', '7.0', '', True),
+]
+
+configopts = " --enable-readline --enable-job-control --enable-history "
+
+sanity_check_paths = {
+    'files': ["bin/bash"],
+    'dirs': []
+}
+
+moduleclass = 'tools'

b/Boost/Boost-1.66.0-foss-2018a-Py-2.7.eb

@@ -0,0 +1,28 @@
+# IT4Innovations 2018
+
+name = 'Boost'
+version = '1.66.0'
+versionsuffix = '-Py-2.7'
+
+homepage = 'http://www.boost.org/'
+description = """Boost provides free peer-reviewed portable C++ source libraries."""
+
+toolchain = {'name': 'foss', 'version': '2018a'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))]
+
+
+dependencies = [
+    ('bzip2', '1.0.6', '', True),
+    ('zlib', '1.2.11', '', True),
+    ('Py', '2.7', '', True)
+]
+
+configopts = '--with-python=$EBROOTPYTHON/bin/python'
+
+# also build boost_mpi
+boost_mpi = True
+
+moduleclass = 'devel'

f/foss/foss-2018a.eb

@@ -0,0 +1,33 @@
+easyblock = 'Toolchain'
+
+name = 'foss'
+version = '2018a'
+
+homepage = '(none)'
+description = """GNU Compiler Collection (GCC) based compiler toolchain, including
+ OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+gccver = '6.3.0-2.27'
+
+blaslib = 'OpenBLAS'
+blasver = '0.2.20'
+blas = '%s-%s' % (blaslib, blasver)
+
+# toolchain used to build foss dependencies
+comp_mpi_tc_name = 'gompi'
+comp_mpi_tc = (comp_mpi_tc_name, version)
+
+# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain
+# because of toolchain preparation functions
+# For binutils, stick to http://wiki.osdev.org/Cross-Compiler_Successful_Builds
+dependencies = [
+    ('GCC', gccver),
+    ('OpenMPI', '3.0.0', '', ('GCC', gccver)),
+    (blaslib, blasver, '', ('GCC', gccver)),
+    ('FFTW', '3.3.7', '', comp_mpi_tc),
+    ('ScaLAPACK', '2.0.2', '-%s' % blas, comp_mpi_tc),
+]
+
+moduleclass = 'toolchain'

n/numpy/numpy-1.14.1-Py-3.6.eb

@@ -0,0 +1,35 @@
+# IT4Innovations 2018
+
+easyblock = 'PythonPackage'
+
+name = 'numpy'
+version = '1.14.1'
+
+homepage = 'http://www.numpy.org'
+description = """NumPy is the fundamental package needed for scientific computing with Python."""
+
+toolchain = {'name': 'Py', 'version': '3.6'}
+
+source_urls = ['https://github.com/numpy/numpy/releases/download/v%(version)s']
+sources = ['%(name)s-%(version)s.tar.gz']
+
+patches = [
+    'numpy-1.12.0-mkl.patch',
+#    'numpy-1.14.1-mkl.patch'
+]
+
+builddependencies = [
+#    ('mkl', '2017.4.239', '', True),
+    ('intel', '2017a', '', True),
+]
+
+#prebuildopts = 'mv site.cfg.example site.cfg && export MKL_THREADING_LAYER=GNU && ' # ' export CFLAGS="-fopenmp -m64 -mtune=native -O3 -Wl,--no-as-needed" && export CXXFLAGS="-fopenmp -m64 -mtune=native -O3 -Wl,--no-as-needed" && export LDFLAGS="-ldl -lm" && export FFLAGS="-fopenmp -m64 -mtune=native -O3" && '
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python3.6/site-packages/numpy-%(version)s-py3.6-linux-x86_64.egg/numpy'],
+}
+
+sanity_check_commands = [('python', '-c "import numpy; assert(numpy.__version__ == \'%(version)s\')"')]
+
+moduleclass = 'python'

n/numpy/numpy-1.14.1-mkl.patch

@@ -0,0 +1,19 @@
+--- site.cfg.example.old	2018-02-20 00:16:17.000000000 +0100
++++ site.cfg.example	2018-03-09 10:47:51.496213510 +0100
+@@ -159,11 +159,11 @@
+ # https://software.intel.com/en-us/articles/numpyscipy-with-intel-mkl
+ # Assuming you installed the mkl in /opt/intel/compilers_and_libraries_2018/linux/mkl, 
+ # for 64 bits code at Linux: 
+-# [mkl] 
+-# library_dirs = /opt/intel/compilers_and_libraries_2018/linux/mkl/lib/intel64
+-# include_dirs = /opt/intel/compilers_and_libraries_2018/linux/mkl/include 
+-# mkl_libs = mkl_rt 
+-# lapack_libs =  
++[mkl] 
++library_dirs = /apps/all/mkl/2017.4.239/mkl/lib/intel64
++include_dirs = /apps/all/mkl/2017.4.239/mkl/include 
++mkl_libs = mkl_def, mkl_intel_lp64, mkl_intel_thread, mkl_core
++lapack_libs = mkl_lapack95_lp64
+ # 
+ # For 32 bit code at Linux: 
+ # [mkl]

o/OpenMPI/OpenMPI-3.0.0-GCC-6.3.0-2.27.eb

@@ -0,0 +1,53 @@
+easyblock = 'ConfigureMake'
+
+name = 'OpenMPI'
+version = '3.0.0'
+
+homepage = 'http://www.open-mpi.org/'
+description = """The Open MPI Project is an open source MPI-2 implementation."""
+
+toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
+
+source_urls = ['http://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads']
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['0bbb279b88edc25bbded39520dab6d4b32020277a6088fb1456c9437a8231cf8']
+
+builddependencies = [
+     ('Java', '1.8.0_144', '', True)
+]
+
+dependencies = [
+     ('hwloc', '1.11.7'),
+     ('zlib', '1.2.11', '', True),
+]
+
+configopts = '--enable-shared --enable-mpi-thread-multiple --with-verbs '
+configopts += '--enable-mpirun-prefix-by-default '  # suppress failure modes in relation to mpirun path
+configopts += '--with-hwloc=$EBROOTHWLOC '  # hwloc support
+#configopts += '--disable-dlopen '  # dont disable dlopen! https://github.com/open-mpi/ompi/issues/3630
+configopts += '--with-tm=/opt/pbs/default '  # Enable PBS
+configopts += '--enable-mpi-java ' # Java support RT#4090
+configopts += '--enable-mpi-cxx ' # Enable building the C++ MPI bindings
+
+# for PBS Pro 13
+preconfigopts = 'export LIBS="-ldl" && '
+
+# to enable SLURM integration (site-specific)
+# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr'
+
+# needed for --with-verbs
+osdependencies = [('libibverbs-dev', 'libibverbs-devel')]
+
+libs = ["mpi_mpifh", "mpi", "ompitrace", "open-pal", "open-rte"]
+sanity_check_paths = {
+    'files': ["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] +
+             ["lib/lib%s.%s" % (libfile, SHLIB_EXT) for libfile in libs] +
+             ["include/%s.h" % x for x in ["mpi-ext", "mpif-config", "mpif", "mpi", "mpi_portable_platform"]],
+    'dirs': [],
+}
+
+modextravars = {'OMPI_MCA_btl_openib_if_include': 'mlx4_0',
+                'OMPI_MCA_oob_tcp_if_include': '10.0.0.0/8',
+}
+
+moduleclass = 'mpi'

s/SQLite/SQLite-3.21.0.eb

@@ -0,0 +1,33 @@
+# IT4Innovations 2018
+
+easyblock = 'ConfigureMake'
+
+name = 'SQLite'
+version = '3.21.0'
+
+homepage = 'http://www.sqlite.org/'
+description = 'SQLite: SQL Database Engine in a C Library'
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+source_urls = ['http://www.sqlite.org/2017/']
+version_minor_etc = version.split('.')[1:]
+version_minor_etc += '0' * (3 - len(version_minor_etc))
+version_str = '%(version_major)s' + ''.join('%02d' % int(x) for x in version_minor_etc)
+sources = [
+    'sqlite-autoconf-%s.tar.gz' % version_str,
+    'sqlite-amalgamation-%s.zip' % version_str,
+]
+
+dependencies = [
+    ('libreadline', '7.0'),
+    ('Tcl', '8.6.6'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', 'lib/libsqlite3.a',
+              'lib/libsqlite3.%s' % SHLIB_EXT],
+    'dirs': ['lib/pkgconfig'],
+}
+
+moduleclass = 'devel'