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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 *
class Snphylo(Package):
"""A pipeline to generate a phylogenetic tree from huge SNP data"""
homepage = "http://chibba.pgml.uga.edu/snphylo/"
url = "http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz"
version('2016-02-04', sha256='d9e144021c83dbef97bebf743b92109ad0afcfe70f37c244059b43f11b8a50da')
depends_on('python', type=('build', 'run'))
depends_on('r', type=('build', 'run'))
depends_on('r-phangorn', type=('build', 'run'))
depends_on('r-gdsfmt', type=('build', 'run'))
depends_on('r-snprelate', type=('build', 'run'))
depends_on('r-getopt', type=('build', 'run'))
depends_on('muscle')
depends_on('phylip')
def install(self, spec, prefix):
install_answer = ['y', 'y', 'y', 'y']
install_answer_input = 'spack-config.in'
with open(install_answer_input, 'w') as f:
f.writelines(install_answer)
with open(install_answer_input, 'r') as f:
bash = which('bash')
bash('./setup.sh', input=f)
install_tree('.', prefix)
def setup_environment(self, spack_env, run_env):
run_env.prepend_path('PATH', self.spec.prefix)
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