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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)
from spack import *
class Repeatmodeler(Package):
"""RepeatModeler is a de-novo repeat family identification and modeling
package."""
homepage = "https://www.repeatmasker.org/RepeatModeler/"
url = "https://www.repeatmasker.org/RepeatModeler/RepeatModeler-open-1.0.11.tar.gz"
version('1.0.11', sha256='7ff0d588b40f9ad5ce78876f3ab8d2332a20f5128f6357413f741bb7fa172193')
depends_on('perl', type=('build', 'run'))
depends_on('perl-json', type=('build', 'run'))
depends_on('perl-uri', type=('build', 'run'))
depends_on('perl-libwww-perl', type=('build', 'run'))
depends_on('repeatmasker', type='run')
depends_on('recon+repeatmasker', type='run')
depends_on('repeatscout', type='run')
depends_on('trf', type='run')
depends_on('nseg', type='run')
depends_on('ncbi-rmblastn', type='run')
def install(self, spec, prefix):
# like repeatmasker, another interactive installer
# questions:
# 1. <enter to continue>
# 2. <perl path, default is OK>
# 3. <source path, default is OK>
# 4. RepeatMasker bin path
# 5. RECON bin path
# 6. RepeatScout bin path
# 7. Nseg bin path
# 8. trf bin path
# 9. Add a search engine:
# 1. RMBlast -> Path, Default? (Y/N)
# 2. WUBlast/ABBlast -> Path, Default? (Y/N)
# 3. Done
config_answers = [
'', '', '',
spec['repeatmasker'].prefix.bin,
spec['recon'].prefix.bin,
spec['repeatscout'].prefix.bin,
spec['nseg'].prefix.bin,
spec['trf'].prefix.bin,
'1', spec['ncbi-rmblastn'].prefix.bin, 'Y',
'3',
]
config_filename = 'spack-config.in'
with open(config_filename, 'w') as f:
f.write('\n'.join(config_answers))
with open(config_filename, 'r') as f:
perl = which('perl')
perl('configure', input=f)
install_tree('.', prefix.bin)
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