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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 *
import glob
import os
class Hybpiper(Package):
"""HybPiper was designed for targeted sequence capture, in which DNA
sequencing libraries are enriched for gene regions of interest,
especially for phylogenetics. HybPiper is a suite of Python scripts
that wrap and connect bioinformatics tools in order to extract target
sequences from high-throughput DNA sequencing reads"""
homepage = "https://github.com/mossmatters/HybPiper"
url = "https://github.com/mossmatters/HybPiper/archive/v1.2.0.tar.gz"
git = "https://github.com/mossmatters/HybPiper/HybPiper.git"
version('1.3.1', sha256='7ca07a9390d1ca52c72721774fa220546f18d3fa3b58500f68f3b2d89dbc0ecf')
version('1.2.0', sha256='34c7b324e9bcacb6ccfe87dc50615d6f93866433b61a59291707efa858b6df57')
depends_on('python@2.7:', type=('build', 'run'))
depends_on('py-biopython', type=('build', 'run'))
depends_on('exonerate')
depends_on('blast-plus')
depends_on('spades')
depends_on('parallel')
depends_on('bwa')
depends_on('samtools')
def setup_envionment(self, spack_env, run_env):
run_env.set('HYBPIPER_HOME', prefix)
def install(self, spec, prefix):
mkdirp(prefix.bin)
files = glob.iglob("*.py")
for file in files:
if os.path.isfile(file):
install(file, prefix.bin)
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