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# Copyright 2013-2021 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)
import os
from spack import *
class Bracken(Package):
"""Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly
accurate statistical method that computes the abundance of species in DNA
sequences from a metagenomics sample."""
homepage = "https://ccb.jhu.edu/software/bracken"
url = "https://github.com/jenniferlu717/Bracken/archive/1.0.0.tar.gz"
version('1.0.0', sha256='8ee736535ad994588339d94d0db4c0b1ba554a619f5f96332ee09f2aabdfe176')
depends_on('perl', type=('build', 'link', 'run'))
depends_on('python@2.7:', type=('build', 'link', 'run'))
depends_on('perl-exporter-tiny')
depends_on('perl-list-moreutils')
depends_on('perl-parallel-forkmanager')
def install(self, spec, prefix):
mkdirp(prefix.bin)
install_tree('sample_data', prefix.sample_data)
filter_file(
r'#!/bin/env perl',
'#!/usr/bin/env perl',
'count-kmer-abundances.pl'
)
filter_file(
r'#!/usr/bin/python',
'#!/usr/bin/env {0}'.format(
os.path.basename(self.spec['python'].command.path)),
'est_abundance.py'
)
filter_file(
r'#!/usr/bin/python',
'#!/usr/bin/env {0}'.format(
os.path.basename(self.spec['python'].command.path)),
'generate_kmer_distribution.py'
)
files = (
'count-kmer-abundances.pl',
'est_abundance.py',
'generate_kmer_distribution.py',
)
chmod = which('chmod')
for name in files:
install(name, prefix.bin)
chmod('+x', join_path(self.prefix.bin, name))
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