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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 inspect
class Repeatmasker(Package):
"""RepeatMasker is a program that screens DNA sequences for interspersed
repeats and low complexity DNA sequences."""
homepage = "http://www.repeatmasker.org"
url = "http://www.repeatmasker.org/RepeatMasker-open-4-0-7.tar.gz"
version('4.0.7', '4dcbd7c88c5343e02d819f4b3e6527c6')
depends_on('perl', type=('build', 'run'))
depends_on('perl-text-soundex', type=('build', 'run'))
depends_on('hmmer')
depends_on('ncbi-rmblastn')
depends_on('trf')
def url_for_version(self, version):
url = 'http://www.repeatmasker.org/RepeatMasker-open-{0}.tar.gz'
return url.format(version.dashed)
def install(self, spec, prefix):
# Config questions consist of:
#
# <PRESS ENTER TO CONTINUE>
# Enter perl path
# Enter where repeatmasker is being configured from
# Enter trf path
# Add a Search Engine:
# 1. CrossMatch
# 2. RMBlast - NCBI Blast with RepeatMasker extensions
# 3. WUBlast/ABBlast (required by DupMasker)
# 4. HMMER3.1 & DFAM
# 5. Done
# Enter RMBlast path
# Do you want RMBlast to be your default search engine for
# Repeatmasker? (Y/N)
# Add a Search Engine: Done
config_answers = ['\n', '%s\n' % self.spec['perl'].command.path,
'%s\n' % self.stage.source_path,
'%s\n' % self.spec['trf'].prefix.bin.trf, '2\n',
'%s\n' % self.spec['ncbi-rmblastn'].prefix.bin,
'Y\n', '5\n']
config_answers_filename = 'spack-config.in'
with open(config_answers_filename, 'w') as f:
f.writelines(config_answers)
with open(config_answers_filename, 'r') as f:
inspect.getmodule(self).perl('configure', input=f)
install_tree('.', prefix.bin)
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