Bio-SamTools and its dependencies. SAMTools wrong compiler corrected (wa...

easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.39-ictce-5.5.0-Perl-5.20.0.eb

@@ -0,0 +1,32 @@
+easyblock = 'PerlModule'
+
+name = 'Bio-SamTools'
+version = '1.39'
+
+homepage = 'http://www.bioperl.org/'
+description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology.
+ Examples include Sequence objects, Alignment objects and database searching objects."""
+
+toolchain = {'name': 'ictce', 'version': '5.5.0'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+source_urls = ['http://cpan.metacpan.org/authors/id/L/LD/LDS/']
+sources = [SOURCE_TAR_GZ]
+patches = ['Bio-SamTools-1.39.patch']
+
+perl = 'Perl'
+perlver = '5.20.0'
+versionsuffix = '-%s-%s' % (perl, perlver)
+
+dependencies = [
+    (perl, perlver),
+    ('SAMtools', '0.1.19'),
+    ('BioPerl', '1.6.924', versionsuffix)
+]
+
+preconfigopts = 'SAMTOOLS="$EBROOTSAMTOOLS" '
+
+options = {'modulename': 'Bio::DB::Sam'}
+
+moduleclass = 'bio'
+

easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.39-intel-2014b-Perl-5.20.0.eb

@@ -0,0 +1,32 @@
+easyblock = 'PerlModule'
+
+name = 'Bio-SamTools'
+version = '1.39'
+
+homepage = 'http://www.bioperl.org/'
+description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology.
+ Examples include Sequence objects, Alignment objects and database searching objects."""
+
+toolchain = {'name': 'intel', 'version': '2014b'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+source_urls = ['http://cpan.metacpan.org/authors/id/L/LD/LDS/']
+sources = [SOURCE_TAR_GZ]
+patches = ['Bio-SamTools-1.39.patch']
+
+perl = 'Perl'
+perlver = '5.20.0'
+versionsuffix = '-%s-%s' % (perl, perlver)
+
+dependencies = [
+    (perl, perlver),
+    ('SAMtools', '0.1.19'),
+    ('BioPerl', '1.6.924', versionsuffix)
+]
+
+preconfigopts = 'SAMTOOLS="$EBROOTSAMTOOLS" '
+
+options = {'modulename': 'Bio::DB::Sam'}
+
+moduleclass = 'bio'
+

easybuild/easyconfigs/b/Bio-SamTools/Bio-SamTools-1.39.patch

@@ -0,0 +1,23 @@
+# 1) Obey the CC and CFLAGS using make in the c_bin subdirectory
+# 2) Extend the header file search to the $samtools/include/bam directory
+# B. Hajgato August 6th 2014
+--- Bio-SamTools-1.39/Build.PL.orig	2013-08-29 18:59:35.000000000 +0200
++++ Bio-SamTools-1.39/Build.PL	2014-08-06 10:37:13.310401233 +0200
+@@ -15,7 +15,7 @@
+ 	chomp(my \$make  = `which make`);
+ 	chomp(my \$nmake = `which nmake`);
+ 	\$make ||= \$nmake;
+-	system "cd c_bin; \$make INCLUDES=-I$sam_include LIBPATH=-L$sam_lib";
++	system "cd c_bin; \$make CC=\\\$CC CFLAGS=\\\"\\\$CFLAGS\\\" INCLUDES=-I$sam_include LIBPATH=-L$sam_lib";
+ 	mkdir "blib/bin" unless -e "blib/bin";
+         my \@exec = grep {-x \$_} <c_bin/*>;
+ 	\$self->copy_if_modified(from   =>\$_,
+@@ -75,6 +75,8 @@
+ 	    if -e "$samtools/$HeaderFile";
+ 	$sam_include = "$samtools/include"
+ 	    if -e "$samtools/include/$HeaderFile";
++	$sam_include = "$samtools/include/bam"
++	    if -e "$samtools/include/bam/$HeaderFile";
+ 	$sam_lib     = $samtools
+ 	    if -e "$samtools/$LibFile";
+ 	$sam_lib     = "$samtools/lib"

easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-ictce-5.5.0-Perl-5.20.0.eb

@@ -0,0 +1,29 @@
+easyblock = 'PerlModule'
+
+name = 'BioPerl'
+version = '1.6.924'
+
+homepage = 'http://www.bioperl.org/'
+description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology.
+ Examples include Sequence objects, Alignment objects and database searching objects."""
+
+toolchain = {'name': 'ictce', 'version': '5.5.0'}
+
+source_urls = ['http://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/']
+sources = [SOURCE_TAR_GZ]
+
+perl = 'Perl'
+perlver = '5.20.0'
+versionsuffix = '-%s-%s' % (perl, perlver)
+
+dependencies = [
+    (perl, perlver),
+]
+
+builddependencies = [
+    ('XML-LibXML', '2.0116', versionsuffix),
+]
+
+options = {'modulename': 'Bio::Perl'}
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/BioPerl/BioPerl-1.6.924-intel-2014b-Perl-5.20.0.eb

@@ -0,0 +1,29 @@
+easyblock = 'PerlModule'
+
+name = 'BioPerl'
+version = '1.6.924'
+
+homepage = 'http://www.bioperl.org/'
+description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology.
+ Examples include Sequence objects, Alignment objects and database searching objects."""
+
+toolchain = {'name': 'intel', 'version': '2014b'}
+
+source_urls = ['http://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/']
+sources = [SOURCE_TAR_GZ]
+
+perl = 'Perl'
+perlver = '5.20.0'
+versionsuffix = '-%s-%s' % (perl, perlver)
+
+dependencies = [
+    (perl, perlver),
+]
+
+builddependencies = [
+    ('XML-LibXML', '2.0116', versionsuffix),
+]
+
+options = {'modulename': 'Bio::Perl'}
+
+moduleclass = 'bio'

easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.18-goalf-1.1.0-no-OFED.eb

@@ -30,4 +30,6 @@ dependencies = [
     ('zlib', '1.2.7'),
 ]
 
+buildopts = 'CC="$CC" CFLAGS="$CFLAGS" '
+
 moduleclass = 'bio'

easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.18-goolf-1.4.10.eb

@@ -30,4 +30,6 @@ dependencies = [
     ('zlib', '1.2.7'),
 ]
 
+buildopts = 'CC="$CC" CFLAGS="$CFLAGS" '
+
 moduleclass = 'bio'

easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.18-ictce-4.0.6.eb

@@ -30,4 +30,6 @@ dependencies = [
     ('zlib', '1.2.7'),
 ]
 
+buildopts = 'CC="$CC" CFLAGS="$CFLAGS" '
+
 moduleclass = 'bio'

easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.18-ictce-5.3.0.eb

@@ -30,4 +30,6 @@ dependencies = [
     ('zlib', '1.2.7'),
 ]
 
+buildopts = 'CC="$CC" CFLAGS="$CFLAGS" '
+
 moduleclass = 'bio'

easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-goolf-1.4.10.eb

@@ -30,4 +30,6 @@ dependencies = [
     ('zlib', '1.2.7'),
 ]
 
+buildopts = 'CC="$CC" CFLAGS="$CFLAGS" '
+
 moduleclass = 'bio'

easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-ictce-5.5.0.eb

@@ -30,4 +30,6 @@ dependencies = [
     ('zlib', '1.2.7'),
 ]
 
+buildopts = 'CC="$CC" CFLAGS="$CFLAGS" '
+
 moduleclass = 'bio'

easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.19-intel-2014b.eb

@@ -0,0 +1,35 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright 2012-2013 University of Luxembourg/Luxembourg Centre for Systems Biomedicine
+# Authors::   Cedric Laczny <[email protected]>, Fotis Georgatos <[email protected]>
+# 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 = 'SAMtools'
+version = '0.1.19'
+
+homepage = 'http://samtools.sourceforge.net/'
+description = """ SAM Tools provide various utilities for manipulating alignments in the SAM format, 
+ including sorting, merging, indexing and generating alignments in a per-position format."""
+
+toolchain = {'name': 'intel', 'version': '2014b'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+sources = [SOURCELOWER_TAR_BZ2]
+source_urls = [('http://sourceforge.net/projects/samtools/files/%(namelower)s/%(version)s', 'download')]
+
+patches = ['SAMtools-0.1.19_Makefile-ncurses.patch']
+
+dependencies = [
+    ('ncurses', '5.9'),
+    ('zlib', '1.2.8'),
+]
+
+buildopts = 'CC="$CC" CFLAGS="$CFLAGS" '
+
+moduleclass = 'bio'