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Merged
JensTimmerman merged 7 commits into from
Aug 5, 2013
Merged

Stacks #367

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c03405c
added ictce TopHat + patch
May 8, 2013
f7c6f17
Merge branch 'develop' of github.com:hpcugent/easybuild-easyconfigs i…
May 15, 2013
1ce8e32
Merge branch 'develop' of github.com:hpcugent/easybuild-easyconfigs i…
May 29, 2013
9280e83
Merge branch 'develop' of github.com:hpcugent/easybuild-easyconfigs i…
Jul 2, 2013
52e1227
Merge branch 'develop' of github.com:hpcugent/easybuild-easyconfigs i…
Jul 10, 2013
f496c4a
added stacks easyconfig
Jul 15, 2013
ae91748
added Stacks ictce config
Jul 15, 2013
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29 changes: 29 additions & 0 deletions easybuild/easyconfigs/s/Stacks/Stacks-1.03-goolf-1.4.10.eb
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Original file line number Diff line number Diff line change
@@ -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
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@fgeorgatos fgeorgatos Jul 15, 2013

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I think 1-space indent is kind of the preferred standard, no?

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'
28 changes: 28 additions & 0 deletions easybuild/easyconfigs/s/Stacks/Stacks-1.03-ictce-4.1.13.eb
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Original file line number Diff line number Diff line change
@@ -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'})
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@fgeorgatos fgeorgatos Jul 15, 2013

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just do a cleanup here


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'
4 changes: 2 additions & 2 deletions easybuild/easyconfigs/t/TopHat/TopHat-2.0.8-ictce-4.0.6.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,8 @@
# 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 <cedric.laczny@uni.lu>, Fotis Georgatos <fotis.georgatos@uni.lu>, Jens Timmerman
# License:: GPL
# Authors:: Cedric Laczny <cedric.laczny@uni.lu>, Fotis Georgatos <fotis.georgatos@uni.lu>
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@fgeorgatos fgeorgatos Jul 15, 2013

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we're happy to have you as co-author, do as you fancy ;-)
(ah, I think I get it: it's the way to let license remain as upstream... yeah, whatever, we'll find some way)

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@JensTimmerman JensTimmerman Aug 5, 2013

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I don't know why this happened, I think I copied from an older goalf version where I was not in there

# License:: MIT/GPL
# $Id$
#
# This work implements a part of the HPCBIOS project and is a component of the policy:
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