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repeatmasker package: add variant for cross_match engine (#10534)

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Justin Stanley 2019-02-07 16:53:30 -06:00 committed by Peter Scheibel
parent 76feb0205d
commit ec6de8326e
1 changed files with 13 additions and 1 deletions
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14
var/spack/repos/builtin/packages/repeatmasker/package.py
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@ -16,12 +16,18 @@ class Repeatmasker(Package):
version('4.0.7', '4dcbd7c88c5343e02d819f4b3e6527c6') version('4.0.7', '4dcbd7c88c5343e02d819f4b3e6527c6')
variant('crossmatch', description='Enable CrossMatch search engine',
default=False)
depends_on('perl', type=('build', 'run')) depends_on('perl', type=('build', 'run'))
depends_on('perl-text-soundex', type=('build', 'run')) depends_on('perl-text-soundex', type=('build', 'run'))
depends_on('hmmer') depends_on('hmmer')
depends_on('ncbi-rmblastn') depends_on('ncbi-rmblastn')
depends_on('trf') depends_on('trf')
depends_on('phrap-crossmatch-swat', type=('build', 'run'),
when='+crossmatch')
def url_for_version(self, version): def url_for_version(self, version):
url = 'http://www.repeatmasker.org/RepeatMasker-open-{0}.tar.gz' url = 'http://www.repeatmasker.org/RepeatMasker-open-{0}.tar.gz'
return url.format(version.dashed) return url.format(version.dashed)
@ -48,7 +54,13 @@ def install(self, spec, prefix):
'%s\n' % self.stage.source_path, '%s\n' % self.stage.source_path,
'%s\n' % self.spec['trf'].prefix.bin.trf, '2\n', '%s\n' % self.spec['trf'].prefix.bin.trf, '2\n',
'%s\n' % self.spec['ncbi-rmblastn'].prefix.bin, '%s\n' % self.spec['ncbi-rmblastn'].prefix.bin,
'Y\n', '5\n'] 'Y\n']
if '+crossmatch' in spec:
crossmatch = self.spec['phrap-crossmatch-swat'].prefix.bin
config_answers.extend(['1\n', '%s\n' % crossmatch, 'N\n'])
config_answers.append('5\n')
config_answers_filename = 'spack-config.in' config_answers_filename = 'spack-config.in'