2021-01-02 15:10:28 +08:00
|
|
|
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
|
2019-05-18 03:31:26 +08:00
|
|
|
# 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 = "http://www.repeatmasker.org/RepeatModeler/"
|
|
|
|
|
url = "http://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'))
|
2019-10-29 09:27:54 +08:00
|
|
|
depends_on('perl-libwww-perl', type=('build', 'run'))
|
2019-05-18 03:31:26 +08:00
|
|
|
|
|
|
|
|
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)
|
