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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 FrHit(Package):
"""An efficient algorithm for fragment recruitment for next generation
sequences against microbial reference genomes."""
homepage = "http://weizhong-lab.ucsd.edu/frhit"
url = "http://weizhong-lab.ucsd.edu/frhit/fr-hit-v0.7.1-2013-02-20.tar.gz"
version(
"0.7.1-2013-02-20",
sha256="44dcfeb73106529fcefb02c017ec7b95b04b6523a2a57683b2bc905c142e62eb",
)
depends_on("perl")
depends_on("python@2.7:")
# The patch adds the python interpreter to the beginning of the script
# allowing it to be run directly without passing the entire path to the
# script to python.
patch("binning.patch")
def install(self, spec, prefix):
make()
filter_file(r"#!/bin/env perl", "#!/usr/bin/env perl", "frhit2pairend.pl")
filter_file(r"#!/bin/env perl", "#!/usr/bin/env perl", "psl2sam.pl")
mkdirp(prefix.bin)
install("fr-hit", prefix.bin)
install("frhit2pairend.pl", prefix.bin)
install("psl2sam.pl", prefix.bin)
install("binning-1.1.1/bacteria_gitax.pkl", prefix.bin)
install("binning-1.1.1/binning.py", prefix.bin)
install("binning-1.1.1/tax.pkl", prefix.bin)
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