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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 PrinseqLite(Package):
"""PRINSEQ will help you to preprocess your genomic or metagenomic
sequence data in FASTA or FASTQ format."""
homepage = "http://prinseq.sourceforge.net"
url = "https://sourceforge.net/projects/prinseq/files/standalone/prinseq-lite-0.20.4.tar.gz"
version('0.20.4', '3be1a572073ebbbecfeba42a42853ff5')
variant('nopca', default=True, description="Graphs version without PCA")
depends_on('perl', type='run')
depends_on('perl-cairo', type='run')
depends_on('perl-digest-md5', type='run')
depends_on('perl-json', type='run')
def install(self, spec, prefix):
mkdirp(prefix.bin)
filter_file(r'#!/usr/bin/perl',
'#!/usr/bin/env perl',
'prinseq-graphs-noPCA.pl')
filter_file(r'#!/usr/bin/perl',
'#!/usr/bin/env perl',
'prinseq-lite.pl')
install('prinseq-graphs-noPCA.pl', prefix.bin)
install('prinseq-lite.pl', prefix.bin)
chmod = which('chmod')
chmod('+x', join_path(self.prefix.bin, 'prinseq-graphs-noPCA.pl'))
chmod('+x', join_path(self.prefix.bin, 'prinseq-lite.pl'))
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