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# Copyright 2013-2018 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 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', '3e8ea41ba09ab0c13e9973fe6f493f96')
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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