From c03405cbdd4195baccf6d0696c9052a9ff5249d2 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Wed, 8 May 2013 14:02:42 +0200 Subject: [PATCH 1/3] added ictce TopHat + patch --- .../t/TopHat/TopHat-2.0.8-ictce-4.0.6.eb | 42 +++++++++++++++++++ .../easyconfigs/t/TopHat/tophat_ictce.patch | 30 +++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/t/TopHat/TopHat-2.0.8-ictce-4.0.6.eb create mode 100644 easybuild/easyconfigs/t/TopHat/tophat_ictce.patch diff --git a/easybuild/easyconfigs/t/TopHat/TopHat-2.0.8-ictce-4.0.6.eb b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.8-ictce-4.0.6.eb new file mode 100644 index 000000000000..b8d871c5c87f --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/TopHat-2.0.8-ictce-4.0.6.eb @@ -0,0 +1,42 @@ +## +# 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 , Fotis Georgatos +# 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 = 'TopHat' +version = '2.0.8' + +homepage = 'http://tophat.cbcb.umd.edu/' +description = """TopHat is a fast splice junction mapper for RNA-Seq reads.""" + +toolchain = {'name': 'ictce', 'version': '4.0.6'} +toolchainopts = {'optarch': True, 'pic': True} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://tophat.cbcb.umd.edu/downloads/'] + +patches = ['tophat_ictce.patch'] + +dependencies = [ + ('Boost', '1.49.0', '-Python-2.7.3'), + ('SAMtools', '0.1.18'), + ('zlib', '1.2.5'), +] + +configopts = '--with-boost=$EBROOTBOOST --with-bam=$EBROOTSAMTOOLS' + +sanity_check_paths = { + 'files': ['bin/tophat'], + 'dirs': [], +} + +parallel = 1 # not sure for a parallel build + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TopHat/tophat_ictce.patch b/easybuild/easyconfigs/t/TopHat/tophat_ictce.patch new file mode 100644 index 000000000000..c2413ce9f9ff --- /dev/null +++ b/easybuild/easyconfigs/t/TopHat/tophat_ictce.patch @@ -0,0 +1,30 @@ +--- src/SeqAn-1.3/seqan/platform/platform_gcc.h 2013-05-08 13:40:52.556526907 +0200 ++++ src/SeqAn-1.3/seqan/platform/platform_gcc.h 2013-05-08 13:42:46.521473828 +0200 +@@ -61,22 +61,22 @@ + #define finline __inline__ + + // default 64bit type +-typedef int64_t __int64; ++typedef __int64 int64_t; + typedef uint64_t __uint64; + + // default 32bit type +-typedef int32_t __int32; ++typedef __int32 int32_t; + typedef uint32_t __uint32; + + // default 16bit type +-typedef int16_t __int16; ++typedef __int16 int16_t; + typedef uint16_t __uint16; + + // default 8bit type +-typedef int8_t __int8; ++ + typedef uint8_t __uint8; + +-//define SEQAN_SWITCH_USE_FORWARDS to use generated forwards ++//define SEQAN_SWITCH_USE_FORWARDS to use generated forwards + #define SEQAN_SWITCH_USE_FORWARDS + + #include "platform_generated_forwards.h" From f496c4a72eb4fb80ffb043e43506e4552ab7e5d3 Mon Sep 17 00:00:00 2001 From: Jens Timmerman Date: Mon, 15 Jul 2013 16:59:54 +0200 Subject: [PATCH 2/3] added stacks easyconfig --- .../s/stacks/stacks-1.03-goolf-1.4.10.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/stacks/stacks-1.03-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/s/stacks/stacks-1.03-goolf-1.4.10.eb b/easybuild/easyconfigs/s/stacks/stacks-1.03-goolf-1.4.10.eb new file mode 100644 index 000000000000..21ec2a110b3b --- /dev/null +++ b/easybuild/easyconfigs/s/stacks/stacks-1.03-goolf-1.4.10.eb @@ -0,0 +1,29 @@ +name = 'Stacks' +version = '1.03' + +homepage = 'http://creskolab.uoregon.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on +the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose +of building genetic maps and conducting population genomics and phylogeography. +""" + +toolchain = {'name': 'goolf', 'version': '1.4.10'} + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://creskolab.uoregon.edu/stacks/source/'] + +runtest = "check" + +sanity_check_paths = { + 'files': [ + 'bin/%s' % binfile for binfile in [ + 'clone_filter', 'denovo_map.pl', 'exec_velvet.pl', 'genotypes', 'index_radtags.pl', 'load_radtags.pl', + 'populations', 'process_shortreads', 'ref_map.pl', 'sstacks', 'ustacks', 'cstacks', 'estacks', + 'export_sql.pl', 'hstacks', 'kmer_filter', 'load_sequences.pl', 'process_radtags', 'pstacks', + 'sort_read_pairs.pl', 'stacks_export_notify.pl', + ] + ], + 'dirs': [], +} + +moduleclass = 'bio' From ae91748ce4139e1840d60e32490513490cd31d8f Mon Sep 17 00:00:00 2001 From: admin6 Date: Mon, 15 Jul 2013 17:08:55 +0200 Subject: [PATCH 3/3] added Stacks ictce config --- .../Stacks-1.03-goolf-1.4.10.eb} | 0 .../s/Stacks/Stacks-1.03-ictce-4.1.13.eb | 28 +++++++++++++++++++ 2 files changed, 28 insertions(+) rename easybuild/easyconfigs/s/{stacks/stacks-1.03-goolf-1.4.10.eb => Stacks/Stacks-1.03-goolf-1.4.10.eb} (100%) create mode 100644 easybuild/easyconfigs/s/Stacks/Stacks-1.03-ictce-4.1.13.eb diff --git a/easybuild/easyconfigs/s/stacks/stacks-1.03-goolf-1.4.10.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.03-goolf-1.4.10.eb similarity index 100% rename from easybuild/easyconfigs/s/stacks/stacks-1.03-goolf-1.4.10.eb rename to easybuild/easyconfigs/s/Stacks/Stacks-1.03-goolf-1.4.10.eb diff --git a/easybuild/easyconfigs/s/Stacks/Stacks-1.03-ictce-4.1.13.eb b/easybuild/easyconfigs/s/Stacks/Stacks-1.03-ictce-4.1.13.eb new file mode 100644 index 000000000000..d87059e97846 --- /dev/null +++ b/easybuild/easyconfigs/s/Stacks/Stacks-1.03-ictce-4.1.13.eb @@ -0,0 +1,28 @@ +name = 'Stacks' +version = '1.03' + +homepage = 'http://creskolab.uoregon.edu/stacks/' +description = """Stacks is a software pipeline for building loci from short-read sequences, such as those generated on +the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose +of building genetic maps and conducting population genomics and phylogeography. +""" +toolchain = {'name': 'ictce', 'version': '4.1.13'} # tweaked by EasyBuild (was: {'name': 'goolf', 'version': '1.4.10'}) + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['http://creskolab.uoregon.edu/stacks/source/'] + +runtest = "check" + +sanity_check_paths = { + 'files': [ + 'bin/%s' % binfile for binfile in [ + 'clone_filter', 'denovo_map.pl', 'exec_velvet.pl', 'genotypes', 'index_radtags.pl', 'load_radtags.pl', + 'populations', 'process_shortreads', 'ref_map.pl', 'sstacks', 'ustacks', 'cstacks', 'estacks', + 'export_sql.pl', 'hstacks', 'kmer_filter', 'load_sequences.pl', 'process_radtags', 'pstacks', + 'sort_read_pairs.pl', 'stacks_export_notify.pl', + ] + ], + 'dirs': [], +} + +moduleclass = 'bio'