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# Copyright 2013-2023 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.package 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"
license("GPL-3.0-only")
version("0.4.3", sha256="fb4050418c26a5203220f6396263da554326657590cffd65053eb8adc465ac65")
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_run_environment(self, env):
env.prepend_path("PERL5LIB", self.prefix)
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