Merge pull request #4 from boegel/20160325162402_new_pr_MDSplus7067

sync with develop & resolve conflict

easybuild/easyconfigs/a/ABySS/ABySS-1.3.7-intel-2015a-Python-2.7.9.eb

@@ -31,7 +31,7 @@ dependencies = [
     ('Boost', '1.58.0', versionsuffix),
 ]
 
-preconfigopts = 'CPPFLAGS=-I$EBROOTSPARSEHASH/include'
+preconfigopts = 'env CPPFLAGS=-I$EBROOTSPARSEHASH/include'
 
 sanity_check_paths = {
     'files': ["bin/ABYSS", "bin/ABYSS-P"],

easybuild/easyconfigs/a/ABySS/ABySS-1.9.0-foss-2016a.eb

@@ -0,0 +1,36 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Authors::   Maxime Schmitt <[email protected]>, Fotis Georgatos <[email protected]>
+# License::   MIT/GPL
+# $Id$
+#
+##
+
+easyblock = 'ConfigureMake'
+
+name = 'ABySS'
+version = '1.9.0'
+
+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': '2016a'}
+toolchainopts = {'usempi': True}
+
+sources = [SOURCELOWER_TAR_GZ]
+source_urls = ['https://github.com/bcgsc/abyss/releases/download/%(version)s/']
+
+dependencies = [
+    ('Boost', '1.60.0'),
+    ('sparsehash', '2.0.2'),
+    ('SQLite', '3.9.2'),
+]
+
+sanity_check_paths = {
+    'files': ["bin/ABYSS", "bin/ABYSS-P"],
+    'dirs': []
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/a/a2ps/a2ps-4.14-goalf-1.1.0-no-OFED.eb

@@ -25,7 +25,7 @@ dependencies = [
     ('gperf', '3.0.4'),
 ]
 
-preconfigopts = 'EMACS=no'
+preconfigopts = 'env EMACS=no'
 configopts = '--with-gnu-gettext'
 
 sanity_check_paths = {

easybuild/easyconfigs/a/a2ps/a2ps-4.14-goolf-1.4.10.eb

@@ -25,7 +25,7 @@ dependencies = [
     ('gperf', '3.0.4'),
 ]
 
-preconfigopts = 'EMACS=no'
+preconfigopts = 'env EMACS=no'
 configopts = '--with-gnu-gettext'
 
 sanity_check_paths = {

easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-4.0.6.eb

@@ -25,7 +25,7 @@ dependencies = [
     ('gperf', '3.0.4'),
 ]
 
-preconfigopts = 'EMACS=no'
+preconfigopts = 'env EMACS=no'
 configopts = '--with-gnu-gettext'
 
 sanity_check_paths = {

easybuild/easyconfigs/a/a2ps/a2ps-4.14-ictce-5.3.0.eb

@@ -26,7 +26,7 @@ dependencies = [
     ('gperf', '3.0.4'),
 ]
 
-preconfigopts = 'EMACS=no'
+preconfigopts = 'env EMACS=no'
 configopts = '--with-gnu-gettext'
 
 sanity_check_paths = {

easybuild/easyconfigs/a/ant/ant-1.9.6-Java-1.7.0_79.eb

@@ -0,0 +1,23 @@
+name = 'ant'
+version = '1.9.6'
+versionsuffix = '-Java-%(javaver)s'
+
+homepage = 'http://ant.apache.org/'
+description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files
+ as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications."""
+
+toolchain = {'name': 'dummy', 'version': ''}
+
+sources = ['apache-%(name)s-%(version)s-src.tar.gz']
+source_urls = ['http://archive.apache.org/dist/%(name)s/source/']
+
+dependencies = [('Java', '1.7.0_79')]
+
+builddependencies = [('JUnit', '4.11', versionsuffix)]
+
+sanity_check_paths = {
+    'files': ['bin/ant', 'lib/ant.jar', 'lib/ant.jar'],
+    'dirs': [],
+}
+
+moduleclass = 'devel'

easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2015b.eb

@@ -0,0 +1,33 @@
+# Author: Maxime Schmitt, University of Luxembourg
+# Author: Adam Huffman, The Francis Crick Institute
+#
+# Based on the work of: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics (SIB)
+# Biozentrum - University of Basel
+
+easyblock = 'MakeCp'
+
+name = 'BEDTools'
+version = '2.25.0'
+
+homepage = "https://github.com/arq5x/bedtools2"
+description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps
+ and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF,
+ and SAM/BAM."""
+
+toolchain = {'name': 'foss', 'version': '2015b'}
+
+# https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz
+source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/']
+sources = ['bedtools-%(version)s.tar.gz']
+
+buildopts = 'CXX="$CXX"'
+
+files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']],
+    'dirs': files_to_copy,
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/BEDTools/BEDTools-2.25.0-foss-2016a.eb

@@ -0,0 +1,33 @@
+# Author: Maxime Schmitt, University of Luxembourg
+# Author: Adam Huffman, The Francis Crick Institute
+#
+# Based on the work of: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics (SIB)
+# Biozentrum - University of Basel
+
+easyblock = 'MakeCp'
+
+name = 'BEDTools'
+version = '2.25.0'
+
+homepage = "https://github.com/arq5x/bedtools2"
+description = """The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps
+ and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF,
+ and SAM/BAM."""
+
+toolchain = {'name': 'foss', 'version': '2016a'}
+
+# https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz
+source_urls = ['https://github.com/arq5x/bedtools2/releases/download/v%(version)s/']
+sources = ['bedtools-%(version)s.tar.gz']
+
+buildopts = 'CXX="$CXX"'
+
+files_to_copy = ["bin", "docs", "data", "genomes", "scripts", "test"]
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['bedtools', 'pairToBed', 'mergeBed', 'bedToBam', 'fastaFromBed']],
+    'dirs': files_to_copy,
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2015b.eb

@@ -0,0 +1,40 @@
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+# Author: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics
+# Biozentrum - University of Basel
+# Modified by: Robert Schmidt <[email protected]>
+# Ottawa Hospital Research Institute - Bioinformatics Team
+# Modified by: Adam Huffman <[email protected]>
+# The Francis Crick Institute
+
+easyblock = 'MakeCp'
+
+name = 'Bowtie2'
+version = '2.2.8'
+
+homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
+description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads 
+ to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s 
+ of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. 
+ Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, 
+ its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
+
+toolchain = {'name': 'foss', 'version': '2015b'}
+
+sources = ['%(namelower)s-%(version)s-source.zip']
+source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')]
+
+files_to_copy = [
+    (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s",
+      "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'),
+    "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"]
+
+sanity_check_paths = {
+    'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"],
+    'dirs': [],
+}
+
+# to add script folder to path just uncomment this line
+#modextrapaths = {'PATH': 'scripts'}
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.2.8-foss-2016a.eb

@@ -0,0 +1,40 @@
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+# Author: Pablo Escobar Lopez
+# Swiss Institute of Bioinformatics
+# Biozentrum - University of Basel
+# Modified by: Robert Schmidt <[email protected]>
+# Ottawa Hospital Research Institute - Bioinformatics Team
+# Modified by: Adam Huffman <[email protected]>
+# The Francis Crick Institute
+
+easyblock = 'MakeCp'
+
+name = 'Bowtie2'
+version = '2.2.8'
+
+homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml'
+description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads 
+ to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s 
+ of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. 
+ Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, 
+ its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes."""
+
+toolchain = {'name': 'foss', 'version': '2016a'}
+
+sources = ['%(namelower)s-%(version)s-source.zip']
+source_urls = [('http://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')]
+
+files_to_copy = [
+    (["bowtie2", "bowtie2-align-l", "bowtie2-align-s", "bowtie2-build", "bowtie2-build-l", "bowtie2-build-s",
+      "bowtie2-inspect", "bowtie2-inspect-l", "bowtie2-inspect-s"], 'bin'),
+    "doc", "example", "scripts", "MANUAL", "MANUAL.markdown", "NEWS"]
+
+sanity_check_paths = {
+    'files': ["bin/bowtie2-align-l", "bin/bowtie2-build", "bin/bowtie2-inspect"],
+    'dirs': [],
+}
+
+# to add script folder to path just uncomment this line
+#modextrapaths = {'PATH': 'scripts'}
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-cmake_install_prefix.patch

@@ -0,0 +1,16 @@
+# patch to remove hard-coded installation prefix
+# Adam Huffman
+# The Francis Crick Institute
+
+diff -u bam-readcount-0.7.4/CMakeLists.txt bam-readcount-0.7.4.new/CMakeLists.txt
+--- bam-readcount-0.7.4/CMakeLists.txt	2014-12-07 19:45:03.000000000 +0000
++++ bam-readcount-0.7.4.new/CMakeLists.txt	2016-04-06 22:06:12.336807391 +0100
+@@ -2,7 +2,7 @@
+
+ project(bam-readcount)
+
+-set(CMAKE_INSTALL_PREFIX "/usr")
++#set(CMAKE_INSTALL_PREFIX "/usr")
+ set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake;${CMAKE_SOURCE_DIR}/build-common/cmake")
+ include(TestHelper)
+ include(VersionHelper)

easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.7.4-foss-2015b.eb

@@ -0,0 +1,37 @@
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+# Author: Adam Huffman
+# The Francis Crick Institute
+easyblock = 'CMakeMake'
+
+name = 'bam-readcount'
+version = '0.7.4'
+
+homepage = 'https://github.com/genome/bam-readcount'
+description = """Count DNA sequence reads in BAM files"""
+
+toolchain = {'name': 'foss', 'version': '2015b'}
+
+sources = ['v%(version)s.tar.gz']
+source_urls = ['https://github.com/genome/%(name)s/archive']
+
+patches = ['%(name)s-%(version)s-cmake_install_prefix.patch']
+
+builddependencies = [
+    ('CMake', '3.4.1'),
+]
+
+dependencies = [
+    ('SAMtools', '1.3'),
+    ('zlib', '1.2.8'),
+]
+
+prebuildopts = "export SAMTOOLS_ROOT=${EBROOTSAMTOOLS}/include/bam && make deps &&"
+
+separate_build_dir = True
+
+sanity_check_paths = {
+    'files': ["bin/bam-readcount"],
+    'dirs': []
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/beagle-lib/beagle-lib-2.1.2-foss-2016a.eb

@@ -0,0 +1,35 @@
+easyblock = 'ConfigureMake'
+
+name = 'beagle-lib'
+version = '2.1.2'
+homepage=  'https://github.com/beagle-dev/beagle-lib'
+description = """
+beagle-lib is a high-performance library that can perform the core
+calculations at the heart of most Bayesian and Maximum Likelihood
+phylogenetics packages.
+"""
+
+toolchain = {'name': 'foss', 'version': '2016a'}
+
+# https://github.com/beagle-dev/beagle-lib/archive/beagle_release_2_1_2.tar.gz
+source_urls = ['https://github.com/beagle-dev/beagle-lib/archive/']
+sources = ['beagle_release_%s.tar.gz' % version.replace('.', '_')]
+
+dependencies = [('Java', '1.8.0_74', '', True)]
+
+builddependencies = [('Autotools', '20150215')]
+
+# parallel build does not work (to test)
+parallel = 1
+
+preconfigopts = "./autogen.sh && "
+
+sanity_check_paths = {
+    'files': ["include/libhmsbeagle-1/libhmsbeagle/%s" % includefile
+              for includefile in ["beagle.h", "platform.h"]] +
+             ["lib/libhmsbeagle%s.so" % libfile
+              for libfile in ["-cpu", "-cpu-sse", "-jni", ""]],
+    'dirs': []
+}
+
+moduleclass = 'numlib'

easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2-binutils-2.25.eb

@@ -21,8 +21,8 @@ builddependencies = [
 ]
 
 # statically link with zlib, to avoid runtime dependency on zlib
-preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"'
-prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"'
+preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"'
+prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"'
 
 # make sure that system libraries are also considered by ld and ld.gold is also built
 # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html

easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.2.eb

@@ -20,8 +20,8 @@ builddependencies = [
 ]
 
 # statically link with zlib, to avoid runtime dependency on zlib
-preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"'
-prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"'
+preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"'
+prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"'
 
 # make sure that system libraries are also considered by ld and ld.gold is also built
 # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html

easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3-binutils-2.25.eb

@@ -21,8 +21,8 @@ builddependencies = [
 ]
 
 # statically link with zlib, to avoid runtime dependency on zlib
-preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"'
-prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"'
+preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"'
+prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"'
 
 # make sure that system libraries are also considered by ld and ld.gold is also built
 # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html

easybuild/easyconfigs/b/binutils/binutils-2.25-GCC-4.9.3.eb

@@ -20,8 +20,8 @@ builddependencies = [
 ]
 
 # statically link with zlib, to avoid runtime dependency on zlib
-preconfigopts = 'LIBS="$EBROOTZLIB/lib/libz.a"'
-prebuildopts = 'LIBS="$EBROOTZLIB/lib/libz.a"'
+preconfigopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"'
+prebuildopts = 'env LIBS="$EBROOTZLIB/lib/libz.a"'
 
 # make sure that system libraries are also considered by ld and ld.gold is also built
 # --enable-plugins should be used whenever --enable-gold is used, see http://llvm.org/docs/GoldPlugin.html