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repeatmasker: add 4.0.9, refactor interactive config (#11385)

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Justin S 2019-05-14 15:16:32 -05:00 committed by Levi Baber
parent 5cd593743e
commit c6d34076dc
1 changed files with 23 additions and 10 deletions
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33
var/spack/repos/builtin/packages/repeatmasker/package.py
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@ -4,7 +4,6 @@
# SPDX-License-Identifier: (Apache-2.0 OR MIT) # SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import * from spack import *
import inspect
class Repeatmasker(Package): class Repeatmasker(Package):
@ -14,6 +13,7 @@ class Repeatmasker(Package):
homepage = "http://www.repeatmasker.org" homepage = "http://www.repeatmasker.org"
url = "http://www.repeatmasker.org/RepeatMasker-open-4-0-7.tar.gz" url = "http://www.repeatmasker.org/RepeatMasker-open-4-0-7.tar.gz"
version('4.0.9', sha256='8d67415d89ed301670b7632ea411f794c6e30d8ed0f007a726c4b0a39c8638e5')
version('4.0.7', '4dcbd7c88c5343e02d819f4b3e6527c6') version('4.0.7', '4dcbd7c88c5343e02d819f4b3e6527c6')
variant('crossmatch', description='Enable CrossMatch search engine', variant('crossmatch', description='Enable CrossMatch search engine',
@ -50,24 +50,37 @@ def install(self, spec, prefix):
# Repeatmasker? (Y/N) # Repeatmasker? (Y/N)
# Add a Search Engine: Done # Add a Search Engine: Done
config_answers = ['\n', '%s\n' % self.spec['perl'].command.path, config_answers = []
'%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']
if spec.satisfies('@4.0.9:'):
# 4.0.9 removes a bunch of the interactive options
config_answers.append('')
else:
config_answers.extend(['',
self.spec['perl'].command.path,
self.stage.source_path,
self.spec['trf'].prefix.bin.trf])
# add crossmatch search
if '+crossmatch' in spec: if '+crossmatch' in spec:
crossmatch = self.spec['phrap-crossmatch-swat'].prefix.bin crossmatch = self.spec['phrap-crossmatch-swat'].prefix.bin
config_answers.extend(['1\n', '%s\n' % crossmatch, 'N\n']) config_answers.extend(['1', crossmatch, 'N'])
config_answers.append('5\n') # set default BLAST search
config_answers.extend(['2',
self.spec['ncbi-rmblastn'].prefix.bin,
'Y'])
# end configuration
config_answers.append('5')
config_answers_filename = 'spack-config.in' config_answers_filename = 'spack-config.in'
with open(config_answers_filename, 'w') as f: with open(config_answers_filename, 'w') as f:
f.writelines(config_answers) f.write('\n'.join(config_answers))
with open(config_answers_filename, 'r') as f: with open(config_answers_filename, 'r') as f:
inspect.getmodule(self).perl('configure', input=f) perl = which('perl')
perl('configure', input=f)
install_tree('.', prefix.bin) install_tree('.', prefix.bin)