add easyconfigs for QIIME and dependencies

easybuild/easyconfigs/a/AmpliconNoise/AmpliconNoise-1.27-ictce-5.5.0.eb

@@ -0,0 +1,35 @@
+easyblock = 'MakeCp'
+
+name = 'AmpliconNoise'
+version = '1.27'
+
+homepage = 'https://code.google.com/p/ampliconnoise/'
+description = """AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons.
+ It involves two steps the removal of noise from the sequencing itself and the removal of PCR point errors. This
+ project also includes the Perseus algorithm for chimera removal."""
+
+toolchain = {'name': 'ictce', 'version': '5.5.0'}
+toolchainopts = {'usempi': True}
+
+source_urls = [GOOGLECODE_SOURCE]
+sources = ['%(name)sV%(version)s.tar.gz']
+
+dependencies = [
+    ('GSL', '1.16'),
+    ('MAFFT', '7.164', '-with-extensions'),
+]
+
+buildopts = 'clean && make all CC="$CC" && make install'
+
+files_to_copy = ['bin', 'Data', 'Scripts']
+
+modextrapaths = {'PATH': ['Scripts']}
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['FastaUnique', 'FCluster', 'NDist', 'Perseus', 'PerseusD', 'PyroDist',
+                                     'PyroNoise', 'PyroNoiseM', 'SeqDist', 'SeqNoise',
+                                     'SplitClusterClust', 'SplitClusterEven']],
+    'dirs': ['Data', 'Scripts'],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/BLAST/BLAST-2.2.22-Linux_x86_64.eb

@@ -0,0 +1,27 @@
+# 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
+
+easyblock = "Tarball"
+
+name = 'BLAST'
+version = '2.2.22'
+versionsuffix = "-Linux_x86_64"
+
+homepage = 'http://blast.ncbi.nlm.nih.gov/'
+description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm
+ for comparing primary biological sequence information, such as the amino-acid
+ sequences of different proteins or the nucleotides of DNA sequences."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+source_urls = ['http://ftp.ncbi.nlm.nih.gov/blast/executables/release/%(version)s/']
+sources = ['%(namelower)s-%(version)s-x64-linux.tar.gz']
+
+sanity_check_paths = {
+    'files': ["bin/blastall", "bin/impala", "bin/blastpgp" ],
+    'dirs': []
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/BWA/BWA-0.7.10-ictce-5.5.0.eb

@@ -0,0 +1,26 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB
+# Authors::   George Tsouloupas <g.tsouloupas@cyi.ac.cy>, Fotis Georgatos <fotis.georgatos@uni.lu>
+# 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 = 'BWA'
+version = '0.7.10'
+
+homepage = 'http://bio-bwa.sourceforge.net/'
+description = """Burrows-Wheeler Aligner (BWA) is an efficient program that aligns
+ relatively short nucleotide sequences against a long reference sequence such as the human genome."""
+
+toolchain = {'name': 'ictce', 'version': '5.5.0'}
+toolchainopts = {'optarch': True, 'pic': True}
+
+sources = [SOURCELOWER_TAR_BZ2]
+source_urls = [('http://sourceforge.net/projects/bio-bwa/files/', 'download')]
+
+moduleclass = 'bio'

easybuild/easyconfigs/b/biom-format/biom-format-1.3.1-ictce-5.5.0-Python-2.7.3.eb

@@ -0,0 +1,33 @@
+easyblock = "PythonPackage"
+
+name = 'biom-format'
+version = '1.3.1'
+
+homepage = 'http://biom-format.org/'
+description = """The BIOM file format (canonically pronounced biome) is designed to be a general-use format for
+ representing biological sample by observation contingency tables."""
+
+toolchain = {'name': 'ictce', 'version': '5.5.0'}
+
+source_urls = [PYPI_SOURCE]
+sources = [SOURCE_TAR_GZ]
+
+python = "Python"
+pythonversion = '2.7.3'
+pythonshortversion = ".".join(pythonversion.split(".")[:-1])
+
+versionsuffix = "-%s-%s" % (python, pythonversion)
+
+dependencies = [
+    (python, pythonversion),
+    ('pyqi', '0.3.2', versionsuffix),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%s/site-packages/biom' % pythonshortversion],
+}
+
+options = {'modulename': 'biom'}
+
+moduleclass = 'math'

easybuild/easyconfigs/c/CD-HIT/CD-HIT-3.1.1-ictce-5.5.0-2007-02-01.eb

@@ -0,0 +1,48 @@
+##
+# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
+#
+# Copyright:: Copyright 2012-2013 The Cyprus Institute
+# Authors::   Andreas Panteli <a.panteli@cyi.ac.cy>, George Tsouloupas <g.tsouloupas@cyi.ac.cy>
+# License::   MIT/GPL
+#
+##
+
+easyblock = "MakeCp"
+
+name = 'CD-HIT'
+version = '3.1.1'
+versionsuffix='-2007-02-01'
+
+homepage = 'http://www.bioinformatics.org/cd-hit/'
+description = """CD-HIT stands for Cluster Database at High Identity with Tolerance. The program 
+takes a fasta format sequence database as input and produces a set of 'non-redundant' (nr) 
+representative sequences as output. In addition cd-hit outputs a cluster file, documenting the 
+sequence 'groupies' for each nr sequence representative. """
+
+toolchain = {'name': 'ictce', 'version': '5.5.0'}
+toolchainopts = {'openmp': True}
+
+source_urls = ['http://www.bioinformatics.org/downloads/index.php/cd-hit/']
+sources = ['%(namelower)s-2007-0131.tar.gz']
+
+# make sure compilation flags are passed down (e.g. to enable OpenMP)
+buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"'
+
+binfiles = [
+    "cd-hit", "cd-hit-est", "cd-hit-2d", "cd-hit-est-2d", "cd-hit-div",
+    "cd-hit-2d-para.pl", "cd-hit-div.pl", "cd-hit-para.pl", "clstr2tree.pl", "clstr_merge_noorder.pl",
+    "clstr_merge.pl", "clstr_reduce.pl", "clstr_renumber.pl", "clstr_rev.pl", "clstr_sort_by.pl",
+    "clstr_sort_prot_by.pl", "make_multi_seq.pl", "plot_2d.pl", "plot_len1.pl",
+    "psi-cd-hit-2d.pl", "psi-cd-hit-local.pl", "psi-cd-hit.pl",
+]
+files_to_copy = [
+    (binfiles, 'bin'),
+    "cd-hit-user-guide.pdf",
+]
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in binfiles] + ["cd-hit-user-guide.pdf"],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/Cytoscape/Cytoscape-2.7.0-Java-1.7.0_60.eb

@@ -0,0 +1,31 @@
+easyblock = 'Tarball'
+
+name = 'Cytoscape'
+version = '2.7.0'
+
+homepage = 'http://cytoscape.org/'
+description = """Cytoscape is an open source software platform for visualizing molecular interaction networks and
+ biological pathways and integrating these networks with annotations, gene expression profiles and other state data."""
+
+toolchain = {'name': 'dummy', 'version': 'dummy'}
+
+cytover = '_'.join(version.split('.'))
+source_urls = ['http://chianti.ucsd.edu/Cyto-%s' % cytover]
+sources = ['%(namelower)s-v%(version)s.tar.gz']
+
+java = 'Java'
+javaver = '1.7.0_60'
+versionsuffix = '-%s-%s' % (java, javaver)
+dependencies = [(java, javaver)]
+
+modextrapaths = {
+    'PATH': [''],
+    'CLASSPATH': ['cytoscape.jar'],
+}
+
+sanity_check_paths = {
+    'files': ['cytoscape.jar', 'cytoscape.sh'],
+    'dirs': ['lib'],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/cdbfasta/cdbfasta-20100722-ictce-5.5.0.eb

@@ -0,0 +1,26 @@
+easyblock = 'MakeCp'
+
+name = 'cdbfasta'
+version = '20100722'
+
+homepage = 'http://sourceforge.net/projects/cdbfasta/'
+description = """fast indexing and retrieval of fasta records from flat file databases."""
+
+toolchain = {'name': 'ictce', 'version': '5.5.0'}
+
+source_urls = [SOURCEFORGE_SOURCE]
+sources = ['%(name)s.tar.gz']
+checksums = ['ed07e474d67e0e79e7e89f9f43ee96df']
+
+dependencies = [('zlib', '1.2.7')]
+
+buildopts = 'ZDIR=$EBROOTZLIB CC="$CXX" CFLAGS="$CFLAGS -DNDEBUG -DENABLE_COMPRESSION=1 -Igclib" LINKER="$CXX" LIBS='
+
+files_to_copy = [(['cdbfasta', 'cdbyank'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/cdbfasta', 'bin/cdbyank'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/c/clearcut/clearcut-1.0.9-ictce-5.5.0.eb

@@ -0,0 +1,24 @@
+easyblock = 'MakeCp'
+
+name = 'clearcut'
+version = '1.0.9'
+
+homepage = 'http://bioinformatics.hungry.com/clearcut/'
+description = """Clearcut is the reference implementation for Relaxed Neighbor Joining (RNJ). Neighbor joining (NJ)
+ is a popular distance-based phylogenetic tree reconstruction method."""
+
+toolchain = {'name': 'ictce', 'version': '5.5.0'}
+
+source_urls = ['http://bioinformatics.hungry.com/clearcut/']
+sources = [SOURCE_TAR_GZ]
+
+buildopts = 'CC="$CC" CFLAGS="$CFLAGS"'
+
+files_to_copy = [(['clearcut'], 'bin')]
+
+sanity_check_paths = {
+    'files': ['bin/clearcut'],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/e/Emperor/Emperor-0.9.3-ictce-5.5.0-Python-2.7.3.eb

@@ -0,0 +1,27 @@
+easyblock = "PythonPackage"
+
+name = 'Emperor'
+version = '0.9.3'
+
+homepage = 'https://pypi.python.org/pypi/emperor'
+description = """Emperor: a tool for visualizing high-throughput microbial community data."""
+
+toolchain = {'name': 'ictce', 'version': '5.5.0'}
+
+source_urls = [PYPI_LOWER_SOURCE]
+sources = [SOURCELOWER_TAR_GZ]
+
+python = "Python"
+pythonversion = '2.7.3'
+pythonshortversion = ".".join(pythonversion.split(".")[:-1])
+
+versionsuffix = "-%s-%s" % (python, pythonversion)
+
+dependencies = [(python, pythonversion)]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%s/site-packages/emperor' % pythonshortversion],
+}
+
+moduleclass = 'devel'

easybuild/easyconfigs/e/ea-utils/ea-utils-1.1.2-686-ictce-5.5.0.eb

@@ -0,0 +1,36 @@
+easyblock = 'ConfigureMake'
+
+name = 'ea-utils'
+version = '1.1.2-686'
+
+homepage = 'https://code.google.com/p/ea-utils'
+description = """Command-line tools for processing biological sequencing data. Barcode demultiplexing,
+ adapter trimming, etc."""
+
+toolchain = {'name': 'ictce', 'version': '5.5.0'}
+
+# download from https://drive.google.com/folderview?id=0B7KhouP0YeRAOTFWWGVFYkFSQjg&usp=sharing
+sources = ['%(name)s.%(version)s.tar.gz']
+
+dependencies = [
+    ('zlib', '1.2.7'),
+    ('ncurses', '5.9'),
+    ('GSL', '1.16'),
+]
+
+patches = ['ea-utils-%(version)s_Makefile-fix.patch']
+
+skipsteps = ['configure', 'build']
+
+# $CXX, $CXXFLAGS, $CPPFLAGS, $PREFIX used in top dir ($CXX/$CXXFLAGS thanks to patch)
+installopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS -I." CPPFLAGS="$CXXFLAGS -I." PREFIX=%(installdir)s '
+# $CC, $CFLAGS used by samtools part
+installopts += 'CC="$CC" CFLAGS="$CFLAGS"'
+
+sanity_check_paths = {
+    'files': ['bin/%s' % x for x in ['alc', 'determine-phred', 'fastq-clipper', 'fastq-join', 'fastq-mcf',
+                                     'fastq-multx', 'fastq-stats', 'fastx-graph', 'randomFQ', 'sam-stats', 'varcall']],
+    'dirs': [],
+}
+
+moduleclass = 'bio'

easybuild/easyconfigs/e/ea-utils/ea-utils-1.1.2-686_Makefile-fix.patch

@@ -0,0 +1,70 @@
+fix hardcoding of compiler commands/flags, use $CXX rather than $CC
+author: Kenneth Hoste (HPC-UGent)
+--- ea-utils.1.1.2-686/Makefile.orig	2014-04-07 19:26:35.000000000 +0200
++++ ea-utils.1.1.2-686/Makefile	2014-08-06 15:20:47.803786753 +0200
+@@ -1,13 +1,13 @@
+ #
+ # $Id: Makefile 670 2013-12-13 16:47:07Z earonesty $
+
+-CC=g++
++CXX=g++
+ PREFIX?=/usr
+ BINDIR?=$(PREFIX)/bin
+-CFLAGS?=-O3 -I. 
++CXXFLAGS?=-O3 -I. 
+ CPPFLAGS?=-O3 -I.
+ # for debugging:
+-# CFLAGS?=-g -I. 
++# CXXFLAGS?=-g -I. 
+ # CPPFLAGS?=-g -I.
+
+ PKG=ea-utils
+@@ -64,24 +64,24 @@
+ 	cp $< $@
+
+ %: %.c fastq-lib.cpp fastq-lib.h 
+-	$(CC) $(CFLAGS) fastq-lib.cpp -o $@ $<
++	$(CXX) $(CXXFLAGS) fastq-lib.cpp -o $@ $<
+
+ %: %.cpp fastq-lib.cpp fastq-lib.h
+-	$(CC) $(CFLAGS) fastq-lib.cpp -o $@ $<
++	$(CXX) $(CXXFLAGS) fastq-lib.cpp -o $@ $<
+
+
+ %: %.c gcModel.c gcModel.h
+-	$(CC) $(CFLAGS) gcModel.c -o $@ $<
++	$(CXX) $(CXXFLAGS) gcModel.c -o $@ $<
+
+ %: %.cpp gcModel.c gcModel.h
+-	$(CC) $(CFLAGS) gcModel.c -o $@ $<
++	$(CXX) $(CXXFLAGS) gcModel.c -o $@ $<
+
+ # why the libbam.a doesn't work?  not sure... *.o works
+ sam-stats: sam-stats.cpp samtools/libbam.a samtools/bam.h fastq-lib.h
+ ifeq ($(OS),Windows_NT)
+-	$(CC) $(CFLAGS) samtools/*.o -lz -lpthread -lws2_32 fastq-lib.cpp $< -o $@
++	$(CXX) $(CXXFLAGS) samtools/*.o -lz -lpthread -lws2_32 fastq-lib.cpp $< -o $@
+ else
+-	$(CC) $(CFLAGS) samtools/*.o -lz -lpthread fastq-lib.cpp $< -o $@
++	$(CXX) $(CXXFLAGS) samtools/*.o -lz -lpthread fastq-lib.cpp $< -o $@
+ endif
+
+ samtools/libbam.a: samtools/*.c samtools/*.h
+@@ -91,14 +91,14 @@
+ ifeq ($(OS),Windows_NT)
+ 	echo varcall: not supported yet
+ else
+-	$(CC) $(CFLAGS) fastq-lib.cpp tidx/tidx-lib.cpp -o $@ $< -lgsl -lgslcblas
++	$(CXX) $(CXXFLAGS) fastq-lib.cpp tidx/tidx-lib.cpp -o $@ $< -lgsl -lgslcblas
+ endif
+
+ fastq-stats: fastq-stats.cpp fastq-lib.cpp gcModel.c
+-	$(CC) $(CFLAGS) fastq-lib.cpp gcModel.c -o $@ $<
++	$(CXX) $(CXXFLAGS) fastq-lib.cpp gcModel.c -o $@ $<
+
+ bam-filter:  bam-filter.cpp 
+-	$(CC) $(CFLAGS) fastq-lib.cpp -o $@  $< -lbamtools 
++	$(CXX) $(CXXFLAGS) fastq-lib.cpp -o $@  $< -lbamtools 
+
+ clean:
+ 	rm -f *.o $(BIN)