new file: b/BCFtools/BCFtools-1.9-intel-2017a.eb

new file:   h/HTSlib/HTSlib-1.9-intel-2017a.eb
	modified:   o/OpenFOAM/OpenFOAM-6-foss-2018a.eb
	new file:   r/R/MCMCpack-1.4-4_icpc-wd308.patch
	modified:   r/R/R-3.5.3-intel-2017a.eb
	modified:   s/SAMtools/SAMtools-1.9-intel-2017a.eb

b/BCFtools/BCFtools-1.9-intel-2017a.eb

@@ -0,0 +1,47 @@
+# IT4Innovations 2019
+
+easyblock = 'ConfigureMake'
+
+name = 'BCFtools'
+version = '1.9'
+
+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': '2017a'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+sources = [SOURCELOWER_TAR_BZ2]
+source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s']
+
+dependencies = [
+    ('zlib', '1.2.11', '', True),
+    ('HTSlib', '1.9'),
+    ('GSL', '2.5'),
+    ('XZ', '5.2.4', '', True),
+]
+
+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'

h/HTSlib/HTSlib-1.9-intel-2017a.eb

@@ -0,0 +1,28 @@
+# IT4Innovations 2019
+
+easyblock = 'ConfigureMake'
+
+name = 'HTSlib'
+version = '1.9'
+
+homepage = "http://www.htslib.org/"
+description = """ A C library for reading/writing high-throughput sequencing data.
+ This package includes the utilities bgzip and tabix """
+
+toolchain = {'name': 'intel', 'version': '2017a'}
+
+source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/']
+sources = [SOURCELOWER_TAR_BZ2]
+
+dependencies = [
+    ('zlib', '1.2.11', '', True),
+    ('bzip2', '1.0.6', '', True),
+    ('XZ', '5.2.4', '', True),
+]
+
+sanity_check_paths = {
+    'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

o/OpenFOAM/OpenFOAM-6-foss-2018a.eb

@@ -38,4 +38,6 @@ builddependencies = [
     ('flex', '2.6.4', '', True),
 ]
 
+modextrapaths = {'PATH': 'OpenFOAM-%(version)s/bin'}
+
 moduleclass = 'cae'

r/R/MCMCpack-1.4-4_icpc-wd308.patch

@@ -0,0 +1,7 @@
+--- MCMCpack/src/Makevars.in.orig	2019-04-24 08:41:09.117144775 +0200
++++ MCMCpack/src/Makevars.in	2019-04-24 08:41:51.556233445 +0200
+@@ -1,2 +1,2 @@
+-PKG_CPPFLAGS = -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC @MV_HAVE_IEEEFP_H@ @MV_HAVE_TRUNC@ 
+-
++PKG_CPPFLAGS = -DSCYTHE_COMPILE_DIRECT -DSCYTHE_DEBUG=0 -DSCYTHE_RPACK -DHAVE_TRUNC @MV_HAVE_IEEEFP_H@ @MV_HAVE_TRUNC@
++PKG_CXXFLAGS = -wd308

r/R/R-3.5.3-intel-2017a.eb

@@ -65,6 +65,7 @@ exts_default_options = {
         'http://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
         'http://cran.r-project.org/src/contrib/',  # current version of packages
         'http://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
+        'https://bioconductor.org/packages/release/bioc/src/contrib/',
     ],
     'source_tmpl': '%(name)s_%(version)s.tar.gz',
 }
@@ -2059,6 +2060,7 @@ exts_list = [
     }),
     ('MCMCpack', '1.4-4', {
         'checksums': ['97e193d628f7161e59288ed594a313af3a520bf30d5a95f1ede0cb2a567cf9f7'],
+        'patches'  : [('MCMCpack-1.4-4_icpc-wd308.patch')],
     }),
     ('shinythemes', '1.1.2', {
         'checksums': ['2e13d4d5317fc61082e8f3128b15e0b10ed9736ce81e152dd7ae7f6109f9b18a'],
@@ -2070,6 +2072,7 @@ exts_list = [
         'checksums': ['dc7c1c8874d6cfa34d550d9af194389e13471dfbc55049a1ab66db112fbf1343'],
     }),
     # qualimap dependencies
+    ('BiocGenerics', '0.28.0'),
     ('Biobase', '2.42.0'),
     ('NOISeq', '2.26.1'),
 ]

s/SAMtools/SAMtools-1.9-intel-2017a.eb

@@ -17,7 +17,7 @@ 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),
 ]