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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 *
import glob
class Repeatmasker(Package):
"""RepeatMasker is a program that screens DNA sequences for interspersed
repeats and low complexity DNA sequences."""
homepage = "http://www.repeatmasker.org"
version('4.1.2-p1', sha256='4be54bf6c050422b211e24a797feb06fd7954c8b4ee6f3ece94cb6faaf6b0e96')
version('4.0.9', sha256='8d67415d89ed301670b7632ea411f794c6e30d8ed0f007a726c4b0a39c8638e5')
version('4.0.7', sha256='16faf40e5e2f521146f6692f09561ebef5f6a022feb17031f2ddb3e3aabcf166')
variant('crossmatch', description='Enable CrossMatch search engine',
default=False)
depends_on('perl', type=('build', 'run'))
depends_on('perl-text-soundex', type=('build', 'run'))
depends_on('hmmer')
depends_on('ncbi-rmblastn')
depends_on('trf')
depends_on('python', when='@4.1:', type=('build', 'run'))
depends_on('py-h5py', when='@4.1:', type=('build', 'run'))
depends_on('phrap-crossmatch-swat', type=('build', 'run'),
when='+crossmatch')
patch('utf8.patch', when='@:4.0')
def url_for_version(self, version):
if version >= Version('4.1.0'):
url = 'http://www.repeatmasker.org/RepeatMasker/RepeatMasker-{0}.tar.gz'
return url.format(version)
else:
url = 'http://www.repeatmasker.org/RepeatMasker/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 = []
if spec.satisfies('@:4.0.7'):
# 4.0.9 removes a bunch of the interactive options
config_answers.extend(['',
self.spec['perl'].command.path,
self.stage.source_path])
# set path to trf
config_answers.append(self.spec['trf'].prefix.bin.trf)
# add crossmatch search
if '+crossmatch' in spec:
crossmatch = self.spec['phrap-crossmatch-swat'].prefix.bin
config_answers.extend(['1', crossmatch, 'N'])
# set default BLAST search
config_answers.extend(['2',
self.spec['ncbi-rmblastn'].prefix.bin,
'Y'])
# set non-default HMMER search
if spec.satisfies('@4.0.9:'):
config_answers.extend(['3',
self.spec['hmmer'].prefix.bin,
'N'])
else:
config_answers.extend(['4',
self.spec['hmmer'].prefix.bin,
'N'])
# end configuration
config_answers.append('5')
config_answers_filename = 'spack-config.in'
with open(config_answers_filename, 'w') as f:
f.write('\n'.join(config_answers))
with open(config_answers_filename, 'r') as f:
perl = which('perl')
perl('configure', input=f)
# fix perl paths
# every sbang points to perl, so a regex will suffice
for f in glob.glob('*.pm'):
filter_file('#!.*', '#!%s' % spec['perl'].command, f)
install_tree('.', prefix.bin)
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