Merge pull request #1343 from rjeschmi/cufflinks1

{bio}[goolf/1.4.10] Cufflinks 1.3.0  (REVIEW)

easybuild/easyconfigs/c/Cufflinks/Cufflinks-1.3.0-goolf-1.4.10.eb

@@ -0,0 +1,45 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Authors::   Cedric Laczny <cedric.laczny@uni.lu>, 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/HPCBIOS_2012-94.html
+##
+
+name = 'Cufflinks'
+version = "1.3.0" 
+
+homepage = 'http://cufflinks.cbcb.umd.edu/'
+description = """Transcript assembly, differential expression, and differential regulation for RNA-Seq"""
+
+toolchain = {'name': 'goolf', 'version': '1.4.10'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = ['http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/']
+
+dependencies = [
+    ('Boost', '1.51.0', '-Python-2.7.3'),
+    ('SAMtools', '0.1.18'),
+    ('Eigen', '3.1.1'),
+    ('zlib', '1.2.7'),
+]
+
+patches = [
+    'Cufflinks_GCC-4.7.patch', 
+    'cufflinks-1.x-ldflags.patch'
+]
+
+preconfigopts = 'CPPFLAGS="-I$EBROOTEIGEN/include $CPPFLAGS" LDFLAGS="-lboost_system $LDFLAGS" '
+configopts = '--with-boost=$EBROOTBOOST --with-bam-libdir=${EBROOTSAMTOOLS}/lib'
+
+sanity_check_paths = {
+    'files': ['bin/cufflinks'],
+    'dirs': []
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/Cufflinks/cufflinks-1.x-ldflags.patch

@@ -0,0 +1,45 @@
+diff -ru cufflinks-1.3.0/configure cufflinks-1.3.0_patched/configure
+--- cufflinks-1.3.0/configure	2012-01-02 13:36:44.000000000 +0000
++++ cufflinks-1.3.0_patched/configure	2015-01-27 18:32:24.810282390 +0000
+@@ -6386,7 +6386,8 @@
+ CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}"
+ CXXFLAGS="$CFLAGS"
+ CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS"
+-LDFLAGS="$ext_LDFLAGS"
++user_LDFLAGS="$LDFLAGS"
++LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}"
+
+ # Checks for structures/functions that can be used to determine system memory
+ echo "$as_me:$LINENO: checking for struct sysinfo.totalram" >&5
+diff -ru cufflinks-1.3.0/src/Makefile.in cufflinks-1.3.0_patched/src/Makefile.in
+--- cufflinks-1.3.0/src/Makefile.in	2012-01-02 13:36:43.000000000 +0000
++++ cufflinks-1.3.0_patched/src/Makefile.in	2015-01-27 18:20:02.944386541 +0000
+@@ -438,24 +438,24 @@
+ #	(echo '#!$(PYTHON)'; sed '/^#!/d' $<) > $@
+ cufflinks_SOURCES = cufflinks.cpp  
+ cufflinks_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB) 
+-cufflinks_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS) 
++cufflinks_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS) 
+ cuffcompare_SOURCES = cuffcompare.cpp
+ cuffcompare_LDADD = libgc.a
+ gffread_SOURCES = gffread.cpp
+ gffread_LDADD = libgc.a
+ cuffdiff_SOURCES = cuffdiff.cpp
+ cuffdiff_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB)
+-cuffdiff_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) 
++cuffdiff_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) 
+ gtf_to_sam_SOURCES = gtf_to_sam.cpp
+ gtf_to_sam_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB)
+-gtf_to_sam_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) 
++gtf_to_sam_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) 
+
+ #cuffcluster_SOURCES = cuffcluster.cpp
+ #cuffcluster_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB)
+ #cuffcluster_LDFLAGS =  $(BOOST_LDFLAGS) $(BAM_LDFLAGS) 
+ compress_gtf_SOURCES = compress_gtf.cpp
+ compress_gtf_LDADD = libcufflinks.a libgc.a $(BOOST_THREAD_LIB) $(BAM_LIB)
+-compress_gtf_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) 
++compress_gtf_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) 
+ all: all-am
+
+ .SUFFIXES: