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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 glob
from spack import *
class Guidance(MakefilePackage):
"""Guidance: Accurate detection of unreliable alignment regions accounting
for the uncertainty of multiple parameters."""
homepage = "http://guidance.tau.ac.il/ver2/"
url = "http://guidance.tau.ac.il/ver2/guidance.v2.02.tar.gz"
version('2.02', sha256='825e105dde526759fb5bda1cd539b24db0b90b8b586f26b1df74d9c5abaa7844')
depends_on('perl', type=('build', 'run'))
depends_on('perl-bioperl', type=('build', 'run'))
depends_on('ruby')
depends_on('prank')
depends_on('clustalw')
depends_on('mafft')
depends_on('muscle')
conflicts('%gcc@6.2.0:')
def edit(self, spec, prefix):
for dir in 'Guidance', 'Selecton', 'bioSequence_scripts_and_constants':
with working_dir(join_path('www', dir)):
files = glob.iglob('*.pl')
for file in files:
perl = FileFilter(file)
perl.filter('#!/usr/bin/perl -w', '#!/usr/bin/env perl')
def install(self, spac, prefix):
mkdir(prefix.bin)
install_tree('libs', prefix.bin.libs)
install_tree('programs', prefix.bin.programs)
install_tree('www', prefix.bin.www)
with working_dir(join_path('www', 'Guidance')): # copy without suffix
install('guidance.pl', join_path(prefix.bin.www.Guidance,
'guidance'))
def setup_run_environment(self, env):
env.prepend_path('PATH', prefix.bin.www.Guidance)
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