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new package: deconseq-standalone (#7290)

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Eric 2018-03-09 12:13:41 -06:00 committed by scheibelp
parent f27f20e5b3
commit 2f97aea4e4
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var/spack/repos/builtin/packages/deconseq-standalone/package.py Normal file
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##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
class DeconseqStandalone(Package):
"""The DeconSeq tool can be used to automatically detect and efficiently
remove sequence contaminations from genomic and metagenomic datasets."""
homepage = "http://deconseq.sourceforge.net"
url = "https://sourceforge.net/projects/deconseq/files/standalone/deconseq-standalone-0.4.3.tar.gz"
version('0.4.3', 'cb3fddb90e584d89fd9c2b6b8f2e20a2')
depends_on('perl@5:')
def install(self, spec, prefix):
filter_file(r'#!/usr/bin/perl',
'#!/usr/bin/env perl', 'deconseq.pl')
filter_file(r'#!/usr/bin/perl',
'#!/usr/bin/env perl', 'splitFasta.pl')
mkdirp(prefix.bin)
install('bwa64', prefix.bin)
install('bwaMAC', prefix.bin)
install('deconseq.pl', prefix.bin)
install('splitFasta.pl', prefix.bin)
install('DeconSeqConfig.pm', prefix)
chmod = which('chmod')
chmod('+x', join_path(prefix.bin, 'bwa64'))
chmod('+x', join_path(prefix.bin, 'bwaMAC'))
chmod('+x', join_path(prefix.bin, 'deconseq.pl'))
chmod('+x', join_path(prefix.bin, 'splitFasta.pl'))
def setup_environment(self, spack_env, run_env):
run_env.prepend_path('PERL5LIB', prefix)