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# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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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