modified: b/BCFtools/BCFtools-1.6-intel-2017a.eb

new file: b/Boost/Boost-1.68.0-intel-2017a.eb new file: b/Boost/Boost-1.68.0-intel-2017c.eb new file: "b/bcl2fastq2/\\" new file: b/bcl2fastq2/bcl2fastq2-2.20.0-intel-2017a-Py-2.7.eb new file: b/bcl2fastq2/bcl2fastq2-2.20.0-intel-2017a-Py-3.6.eb modified: d/DIRAC/DIRAC-18.0-intel-2017c-Py-2.7-test.eb new file: f/FastQC/FastQC-0.11.3.eb new file: f/FastQC/FastQC-0.11.8.eb new file: f/fontconfig/fontconfig-2.13.0-libpng-1.6.34.eb new file: g/GATK/GATK-4.1.2.0-Java-1.8.0_202.eb new file: g/GDAL/GDAL-2.4.0-intel-2017a-Py-3.6.eb new file: g/GEOS/GEOS-3.7.2-Py-3.6.eb new file: g/gnuplot/gnuplot-5.2.7-GCC-6.3.0-2.27.eb modified: h/HTSlib/HTSlib-1.6-intel-2017a.eb new file: l/libMesh/libMesh-1.4.1-intel-2017a.eb new file: l/libMesh/libMesh-1.4.1-intel-2017c.eb new file: m/MUMPS/MUMPS-5.2.0-intel-2017c-parmetis.eb modified: p/Python/Python-3.6.8-GCC-6.3.0-2.27-base.eb new file: r/R/R-3.5.3-intel-2017a-Py-3.6.eb modified: s/SAMtools/SAMtools-1.6-intel-2017a.eb new file: s/SWIG/SWIG-3.0.12-Py-3.6.eb deleted: b/bcl2fastq2/bcl2fastq2-2.20.0-intel-2017a-Python-2.7.13.eb
2025-04-13 10:21:22 +01:00 · 2019-06-11 08:38:51 +02:00 · 2019-06-11 08:38:51 +02:00 · 506f8286d9
commit 506f8286d9
parent 647491a9c8
22 changed files with 2636 additions and 17 deletions
--- a/b/BCFtools/BCFtools-1.6-intel-2017a.eb
+++ b/b/BCFtools/BCFtools-1.6-intel-2017a.eb
@ -1,3 +1,5 @@
+# IT4Innovations 2019
+
 easyblock = 'ConfigureMake'

 name = 'BCFtools'
@ -19,8 +21,8 @@ source_urls = [
 dependencies = [
    ('zlib', '1.2.11', '', True),
    ('HTSlib', '1.6'),
-    ('GSL', '2.3'),
-    ('XZ', '5.2.3', '', True),
+    ('GSL', '2.5'),
+    ('XZ', '5.2.4', '', True),
 ]

 parallel = 1
--- a/b/Boost/Boost-1.68.0-intel-2017a.eb
+++ b/b/Boost/Boost-1.68.0-intel-2017a.eb
@ -0,0 +1,26 @@
+# IT4Innovations 201
+
+name = 'Boost'
+version = '1.68.0'
+
+homepage = 'http://www.boost.org/'
+description = """Boost provides free peer-reviewed portable C++ source libraries."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+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),
+]
+
+configopts = '--without-libraries=python'
+
+# also build boost_mpi
+boost_mpi = True
+
+moduleclass = 'devel'
--- a/b/Boost/Boost-1.68.0-intel-2017c.eb
+++ b/b/Boost/Boost-1.68.0-intel-2017c.eb
@ -0,0 +1,26 @@
+# IT4Innovations 2018
+
+name = 'Boost'
+version = '1.68.0'
+
+homepage = 'http://www.boost.org/'
+description = """Boost provides free peer-reviewed portable C++ source libraries."""
+
+toolchain = {'name': 'intel', 'version': '2017c'}
+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),
+]
+
+configopts = '--without-libraries=python'
+
+# also build boost_mpi
+boost_mpi = True
+
+moduleclass = 'devel'
--- a/b/bcl2fastq2/bcl2fastq2-2.20.0-intel-2017a-Python-2.7.13.eb
+++ b/b/bcl2fastq2/bcl2fastq2-2.20.0-intel-2017a-Python-2.7.13.eb
@ -1,8 +1,10 @@
+# IT4Innovations 2019
+
 easyblock = 'ConfigureMake'

 name = 'bcl2fastq2'
 version = '2.20.0'
-versionsuffix = '-Python-%(pyver)s'
+versionsuffix = '-Py-3.6'

 homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html'
 description = """bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by
@ -13,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2017a'}
 source_urls = [
    'ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/']
 sources = [{
-    'filename': '%(name)s-v%(version)s-tar.zip',
+    'filename': '%(name)s-v2-20-0-tar.zip',
    # source file is a .zip that contains a .tar.gz
    'extract_cmd': 'unzip -p %s | tar -xzvf -',
 }]
@ -22,11 +24,11 @@ start_dir = 'src'
 configopts = '--force-builddir --with-cmake=cmake '

 builddependencies = [
-    ('CMake', '3.9.1', '', True),
+    ('CMake', '3.8.1', '', True),
 ]

 dependencies = [
-    ('Python', '2.7.13', '', True),
+    ('Py', '3.6', '', True),
 ]

 sanity_check_paths = {
--- a/b/bcl2fastq2/bcl2fastq2-2.20.0-intel-2017a-Py-2.7.eb
+++ b/b/bcl2fastq2/bcl2fastq2-2.20.0-intel-2017a-Py-2.7.eb
@ -0,0 +1,39 @@
+# IT4Innovations 2019
+
+easyblock = 'ConfigureMake'
+
+name = 'bcl2fastq2'
+version = '2.20.0'
+versionsuffix = '-Py-2.7'
+
+homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html'
+description = """bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by
+ Illumina sequencing systems to standard FASTQ file formats for downstream analysis."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+
+source_urls = [
+    'ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/']
+sources = [{
+    'filename': '%(name)s-v2-20-0-tar.zip',
+    # source file is a .zip that contains a .tar.gz
+    'extract_cmd': 'unzip -p %s | tar -xzvf -',
+}]
+
+start_dir = 'src'
+configopts = '--force-builddir --with-cmake=cmake '
+
+builddependencies = [
+    ('CMake', '3.8.1', '', True),
+]
+
+dependencies = [
+    ('Py', '2.7', '', True),
+]
+
+sanity_check_paths = {
+    'files': ['bin/bcl2fastq'],
+    'dirs': ['lib']
+}
+
+moduleclass = 'bio'
--- a/b/bcl2fastq2/bcl2fastq2-2.20.0-intel-2017a-Py-3.6.eb
+++ b/b/bcl2fastq2/bcl2fastq2-2.20.0-intel-2017a-Py-3.6.eb
@ -0,0 +1,39 @@
+# IT4Innovations 2019
+
+easyblock = 'ConfigureMake'
+
+name = 'bcl2fastq2'
+version = '2.20.0'
+versionsuffix = '-Py-3.6'
+
+homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html'
+description = """bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by
+ Illumina sequencing systems to standard FASTQ file formats for downstream analysis."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+
+source_urls = [
+    'ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/software/bcl2fastq/']
+sources = [{
+    'filename': '%(name)s-v2-20-0-tar.zip',
+    # source file is a .zip that contains a .tar.gz
+    'extract_cmd': 'unzip -p %s | tar -xzvf -',
+}]
+
+start_dir = 'src'
+configopts = '--force-builddir --with-cmake=cmake '
+
+builddependencies = [
+    ('CMake', '3.8.1', '', True),
+]
+
+dependencies = [
+    ('Py', '3.6', '', True),
+]
+
+sanity_check_paths = {
+    'files': ['bin/bcl2fastq'],
+    'dirs': ['lib']
+}
+
+moduleclass = 'bio'
--- a/d/DIRAC/DIRAC-18.0-intel-2017c-Py-2.7-test.eb
+++ b/d/DIRAC/DIRAC-18.0-intel-2017c-Py-2.7-test.eb
@ -1,7 +1,5 @@
 # IT4Innovations 2019

-easyblock = 'ConfigureMake'
-
 name = 'DIRAC'
 version = '18.0'
 versionsuffix = '-Py-2.7-test'
@ -26,12 +24,12 @@ builddependencies = [
    ('CMake', '3.14.1', '', True)
 ]

-skipsteps = ['configure']
+#skipsteps = ['configure']

-prebuildopts = './setup --fc=mpiifort --mpi --cc=mpiicc --cxx=mpicxx --prefix=/apps/all/DIRAC/%(version)s-intel-2017c-Py-2.7 && '
-prebuildopts += 'cd build && '
-preinstallopts = 'cd build && '
-preinstallopts += 'make install && '
+#prebuildopts = './setup --fc=mpiifort --mpi --cc=mpiicc --cxx=mpicxx --prefix=/apps/all/DIRAC/%(version)s-intel-2017c-Py-2.7 && '
+#prebuildopts += 'cd build && '
+#preinstallopts = 'cd build && '
+#preinstallopts += 'make install && '

 sanity_check_paths = {
    'files': [],
--- a/f/FastQC/FastQC-0.11.3.eb
+++ b/f/FastQC/FastQC-0.11.3.eb
@ -0,0 +1,30 @@
+# IT4Innovations 2019
+
+easyblock = 'PackedBinary'
+
+name = 'FastQC'
+version = '0.11.3'
+
+homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'
+description = """FastQC is a quality control application for high throughput sequence data.
+ It reads in sequence data in a variety of formats and can either provide an interactive
+ application to review the results of several different QC checks, or create an HTML based
+ report which can be integrated into a pipeline."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s/']
+sources = ['%(namelower)s_v%(version)s.zip']
+
+dependencies = [('Java', '1.7.0_79')]
+
+install_cmd = "cp -a FastQC/* %(installdir)s && chmod +x %(installdir)s/fastqc"
+
+sanity_check_paths = {
+    'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt",
+                "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.103.jar"],
+    'dirs': ["Configuration", "Help", "Templates", "uk"],
+}
+# How to create working alias?
+
+moduleclass = 'bio'
--- a/f/FastQC/FastQC-0.11.8.eb
+++ b/f/FastQC/FastQC-0.11.8.eb
@ -0,0 +1,30 @@
+# IT4Innovations 2019
+
+easyblock = 'PackedBinary'
+
+name = 'FastQC'
+version = '0.11.8'
+
+homepage = 'http://www.bioinformatics.babraham.ac.uk/projects/fastqc/'
+description = """FastQC is a quality control application for high throughput sequence data.
+ It reads in sequence data in a variety of formats and can either provide an interactive
+ application to review the results of several different QC checks, or create an HTML based
+ report which can be integrated into a pipeline."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+source_urls = ['http://www.bioinformatics.babraham.ac.uk/projects/%(namelower)s/']
+sources = ['%(namelower)s_v%(version)s.zip']
+
+dependencies = [('Java', '1.8.0_202')]
+
+install_cmd = "cp -a FastQC/* %(installdir)s && chmod +x %(installdir)s/fastqc"
+
+sanity_check_paths = {
+    'files': ["fastqc", "fastqc_icon.ico", "INSTALL.txt", "jbzip2-0.9.jar", "LICENSE.txt",
+                "README.txt", "RELEASE_NOTES.txt", "run_fastqc.bat", "sam-1.103.jar"],
+    'dirs': ["Configuration", "Help", "Templates", "uk"],
+}
+# How to create working alias?
+
+moduleclass = 'bio'
--- a/f/fontconfig/fontconfig-2.13.0-libpng-1.6.34.eb
+++ b/f/fontconfig/fontconfig-2.13.0-libpng-1.6.34.eb
@ -0,0 +1,28 @@
+easyblock = 'ConfigureMake'
+
+name = 'fontconfig'
+version = '2.13.0'
+versionsuffix = '-libpng-1.6.34'
+
+homepage = 'http://www.freedesktop.org/software/fontconfig'
+description = """Fontconfig is a library designed to provide system-wide font configuration, customization and
+application access."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+source_urls = ['http://www.freedesktop.org/software/fontconfig/release/']
+sources = [SOURCE_TAR_GZ]
+
+dependencies = [
+    ('freetype', '2.9.1', versionsuffix),
+    ('util-linux', '2.32'),
+    ('expat', '2.2.0'),
+]
+
+builddependencies = [
+    ('gperf', '3.1'),
+]
+
+configopts = '--disable-docs '
+
+moduleclass = 'vis'
--- a/g/GATK/GATK-4.1.2.0-Java-1.8.0_202.eb
+++ b/g/GATK/GATK-4.1.2.0-Java-1.8.0_202.eb
@ -0,0 +1,43 @@
+# IT4Innovations 2019
+
+easyblock = 'Tarball'
+
+name = 'GATK'
+version = '4.1.2.0'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'http://www.broadinstitute.org/gatk/'
+description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute
+ to analyse next-generation resequencing data. The toolkit offers a wide variety of tools,
+ with a primary focus on variant discovery and genotyping as well as strong emphasis on
+ data quality assurance. Its robust architecture, powerful processing engine and
+ high-performance computing features make it capable of taking on projects of any size."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+# download manually from http://www.broadinstitute.org/gatk/download
+source_urls = [
+    ' https://github.com/broadinstitute/gatk/releases/download/%(version)s/']
+
+sources = ['gatk-%(version)s.zip']
+
+dependencies = [('Java', '1.8.0_202')]
+
+
+postinstallcmds = [
+    'mkdir %(installdir)s/bin',
+    'mv %(installdir)s/gatk %(installdir)s/bin',
+]
+
+modextravars = {
+    'export GATK_LOCAL_JAR': '%(installdir)s/gatk-package-%(version)s-local.jar'
+}
+
+sanity_check_paths = {
+    'files': [
+        'gatk-package-%(version)s-local.jar',
+        'gatk-package-%(version)s-spark.jar'],
+    'dirs': ['bin'],
+}
+
+moduleclass = 'bio'
--- a/g/GDAL/GDAL-2.4.0-intel-2017a-Py-3.6.eb
+++ b/g/GDAL/GDAL-2.4.0-intel-2017a-Py-3.6.eb
@ -0,0 +1,51 @@
+# ITInnovations 2018
+#
+# Error in SWIG build, finished by hand
+easyblock = 'ConfigureMake'
+
+name = 'GDAL'
+version = '2.4.0'
+versionsuffix = '-Py-3.6'
+
+homepage = 'http://www.gdal.org/'
+description = """GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style
+ Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model
+ to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for
+ data translation and processing."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+toolchainopts = {'usempi': True}
+
+source_urls = ['http://download.osgeo.org/gdal/%(version)s/']
+sources = [SOURCELOWER_TAR_XZ]
+
+dependencies = [
+    ('Py', '3.6', '', True),
+    ('netCDF', '4.6.3'),
+    ('expat', '2.2.6', '', True),
+    ('GEOS', '3.7.2', '', ('Py', '3.6')),
+    ('SQLite', '3.27.1', '', True),
+    ('libxml2', '2.9.9', '', True),
+    ('libpng', '1.6.34', '', True),
+    ('libjpeg-turbo', '1.5.3', '', True),
+    ('JasPer', '2.0.14', '', True),
+    ('LibTIFF', '4.0.7', '', True),
+    ('zlib', '1.2.11', '', True),
+    ('cURL', '7.56.1', '', True),
+    ('PCRE', '8.42','', True),
+    ('PROJ', '5.0.0'),
+]
+
+configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF'
+configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO'
+configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER'
+configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python'
+
+modextrapaths = {'PYTHONPATH': 'lib/python2.7/site-packages'}
+
+sanity_check_paths = {
+    'files': ['lib/libgdal.a', 'lib/libgdal.%s' % SHLIB_EXT],
+    'dirs': ['bin', 'include', 'lib/python3.6/site-packages']
+}
+
+moduleclass = 'data'
--- a/g/GEOS/GEOS-3.7.2-Py-3.6.eb
+++ b/g/GEOS/GEOS-3.7.2-Py-3.6.eb
@ -0,0 +1,35 @@
+# IT4Innovations 2019
+
+easyblock = 'ConfigureMake'
+
+name = 'GEOS'
+version = '3.7.2'
+
+homepage = 'http://trac.osgeo.org/geos'
+description = """GEOS (Geometry Engine - Open Source) is a C++ port of the  Java Topology Suite (JTS)"""
+
+toolchain = {'name': 'Py', 'version': '3.6'}
+
+source_urls = ['http://download.osgeo.org/geos/']
+sources = [SOURCELOWER_TAR_BZ2]
+
+patches = ['GEOS-%(version)s_fix-Python3.patch']
+
+builddependencies = [('SWIG', '3.0.12')]
+
+configopts = '--enable-python'
+
+modextrapaths = {'PYTHONPATH': 'lib/python3.6/site-packages'}
+
+sanity_check_paths = {
+    'files': [
+        'bin/geos-config',
+        'lib/libgeos.%s' %
+        SHLIB_EXT,
+        'lib/libgeos.a',
+        'include/geos.h'],
+    'dirs': [
+        'lib/python3.6/site-packages/geos']
+    }
+
+moduleclass = 'math'
--- a/g/gnuplot/gnuplot-5.2.7-GCC-6.3.0-2.27.eb
+++ b/g/gnuplot/gnuplot-5.2.7-GCC-6.3.0-2.27.eb
@ -0,0 +1,34 @@
+# IT4Innovations 2018
+
+easyblock = 'ConfigureMake'
+
+name = 'gnuplot'
+version = '5.2.7'
+
+homepage = 'http://gnuplot.sourceforge.net/'
+description = """Portable interactive, function plotting utility"""
+
+toolchain = {'name': 'GCC', 'version': '6.3.0-2.27'}
+
+sources = [SOURCE_TAR_GZ]
+source_urls = [('http://sourceforge.net/projects/gnuplot/files', 'download')]
+
+dependencies = [
+    ('cairo', '1.14.12', '', True),
+    ('libjpeg-turbo', '1.5.3', '', True),
+    ('libpng', '1.6.34', '', True),
+    ('libgd', '2.2.5', '', True),
+    ('Pango', '1.42.1'),
+    ('libcerf', '1.5', '', True),
+    ('Qt', '4.8.7', '', True),
+    ('LibTIFF', '4.0.7', '', True),
+]
+
+configopts = '--with-qt=qt4 '
+
+sanity_check_paths = {
+    'files': ['bin/gnuplot'],
+    'dirs': []
+}
+
+moduleclass = 'vis'
--- a/h/HTSlib/HTSlib-1.6-intel-2017a.eb
+++ b/h/HTSlib/HTSlib-1.6-intel-2017a.eb
@ -1,3 +1,5 @@
+# IT4Innovations 2019
+
 easyblock = 'ConfigureMake'

 name = 'HTSlib'
@ -15,7 +17,8 @@ sources = [SOURCELOWER_TAR_BZ2]

 dependencies = [
    ('zlib', '1.2.11', '', True),
-    ('XZ', '5.2.3', '', True),
+    ('XZ', '5.2.4', '', True),
+    ('bzip2', '1.0.6', '', True),
 ]

 sanity_check_paths = {
--- a/l/libMesh/libMesh-1.4.1-intel-2017a.eb
+++ b/l/libMesh/libMesh-1.4.1-intel-2017a.eb
@ -0,0 +1,35 @@
+# IT4Innovations 2019
+
+easyblock = 'ConfigureMake'
+
+name = 'libMesh'
+version = '1.4.1'
+
+homepage = 'http://libmesh.github.io/'
+description = """The libMesh library provides a framework for the numerical simulation of partial differential equations
+ using arbitrary unstructured discretizations on serial and parallel platforms. A major goal of the library is to
+ provide support for adaptive mesh refinement (AMR) computations in parallel while allowing a research scientist
+  to focus on the physics they are modeling."""
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = [
+    'https://github.com/libMesh/libmesh/releases/download/v%(version)s/',
+]
+
+sources = [SOURCELOWER_TAR_GZ]
+
+configopts = "--with-parmetis"
+
+dependencies = [
+        ('ParMETIS', '4.0.3'),
+        ('Boost', '1.68.0'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/meshtool-opt'],
+    'dirs': ['bin'],
+}
+
+moduleclass = 'lib'
--- a/l/libMesh/libMesh-1.4.1-intel-2017c.eb
+++ b/l/libMesh/libMesh-1.4.1-intel-2017c.eb
@ -0,0 +1,35 @@
+# IT4Innovations 2019
+
+easyblock = 'ConfigureMake'
+
+name = 'libMesh'
+version = '1.4.1'
+
+homepage = 'http://libmesh.github.io/'
+description = """The libMesh library provides a framework for the numerical simulation of partial differential equations
+ using arbitrary unstructured discretizations on serial and parallel platforms. A major goal of the library is to
+ provide support for adaptive mesh refinement (AMR) computations in parallel while allowing a research scientist
+  to focus on the physics they are modeling."""
+
+toolchain = {'name': 'intel', 'version': '2017c'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = [
+    'https://github.com/libMesh/libmesh/releases/download/v%(version)s/',
+]
+
+sources = [SOURCELOWER_TAR_GZ]
+
+configopts = "--with-parmetis"
+
+dependencies = [
+        ('ParMETIS', '4.0.3'),
+        ('Boost', '1.68.0'),
+]
+
+sanity_check_paths = {
+    'files': ['bin/meshtool-opt'],
+    'dirs': ['bin'],
+}
+
+moduleclass = 'lib'
--- a/m/MUMPS/MUMPS-5.2.0-intel-2017c-parmetis.eb
+++ b/m/MUMPS/MUMPS-5.2.0-intel-2017c-parmetis.eb
@ -0,0 +1,24 @@
+# IT4Innovations 2019
+
+name = 'MUMPS'
+version = '5.2.0'
+versionsuffix = '-parmetis'
+
+homepage = 'http://graal.ens-lyon.fr/MUMPS/'
+description = "A parallel sparse direct solver"
+
+toolchain = {'name': 'intel', 'version': '2017c'}
+toolchainopts = {'pic': True, 'usempi': True}
+
+source_urls = ['http://mumps.enseeiht.fr/']
+sources = ['%(name)s_%(version)s.tar.gz']
+
+dependencies = [
+    ('SCOTCH', '6.0.6'),
+    ('ParMETIS', '4.0.3'),
+]
+
+parallel = 1
+buildopts = 'all'
+
+moduleclass = 'math'
--- a/p/Python/Python-3.6.8-GCC-6.3.0-2.27-base.eb
+++ b/p/Python/Python-3.6.8-GCC-6.3.0-2.27-base.eb
@ -15,7 +15,7 @@ sources = [SOURCE_TGZ]

 prebuildopts = 'export CFLAGS="-I${EBROOTXZ}/include" && '
 prebuildopts += 'export LDFLAGS="-L${EBROOTXZ}/lib" && '
-configopts = "--enable-optimizations"
+configopts = "--enable-optimizations --enable-shared"

 # python needs bzip2 to build the bz2 package
 dependencies = [
@ -24,7 +24,7 @@ dependencies = [
    ('SQLite', '3.27.1', '', True),
    ('Tk', '8.6.9', '', True),
    ('GMP', '6.1.2', '', True),
-    ('XZ', '5.2.3', '', True),
+    ('XZ', '5.2.4', '', True),
    ('zlib', '1.2.11', '', True),
    ('ncurses', '6.0', '', True),
    #   ('OpenSSL', '1.0.1q'),  # OS dependency should be preferred if the os version is more recent then this version, it's
--- a/r/R/R-3.5.3-intel-2017a-Py-3.6.eb
+++ b/r/R/R-3.5.3-intel-2017a-Py-3.6.eb
--- a/s/SAMtools/SAMtools-1.6-intel-2017a.eb
+++ b/s/SAMtools/SAMtools-1.6-intel-2017a.eb
@ -18,7 +18,8 @@ sources = [SOURCELOWER_TAR_BZ2]
 dependencies = [
    ('ncurses', '6.0', '', True),
    ('zlib', '1.2.11', '', True),
-    ('XZ', '5.2.3', '', True),
+    ('XZ', '5.2.4', '', True),
+    ('bzip2', '1.0.6', '', True),
 ]

 moduleclass = 'bio'
--- a/s/SWIG/SWIG-3.0.12-Py-3.6.eb
+++ b/s/SWIG/SWIG-3.0.12-Py-3.6.eb
@ -0,0 +1,20 @@
+# IT4Innovations
+
+name = 'SWIG'
+version = '3.0.12'
+
+homepage = 'http://www.swig.org/'
+description = """SWIG is a software development tool that connects programs written in C and C++ with
+ a variety of high-level programming languages."""
+
+toolchain = {'name': 'Py', 'version': '3.6'}
+toolchainopts = {'pic': True, 'opt': True, 'optarch': True}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+
+dependencies = [
+    ('PCRE', '8.42', '', True),
+]
+
+moduleclass = 'devel'