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| author | Justin Stanley <molecuul@users.noreply.github.com> | 2019-02-07 16:53:30 -0600 |
|---|---|---|
| committer | Peter Scheibel <scheibel1@llnl.gov> | 2019-02-07 16:53:30 -0600 |
| commit | ec6de8326e1884307dc167395b128645397596ba (patch) | |
| tree | faca70b307e433e9e6fa06c41aa5e27184ba72f4 | |
| parent | 76feb0205d49ade45a813ead9fea0bc259e78175 (diff) | |
| download | spack-ec6de8326e1884307dc167395b128645397596ba.tar.gz spack-ec6de8326e1884307dc167395b128645397596ba.tar.bz2 spack-ec6de8326e1884307dc167395b128645397596ba.tar.xz spack-ec6de8326e1884307dc167395b128645397596ba.zip | |
repeatmasker package: add variant for cross_match engine (#10534)
| -rw-r--r-- | var/spack/repos/builtin/packages/repeatmasker/package.py | 14 |
1 files changed, 13 insertions, 1 deletions
diff --git a/var/spack/repos/builtin/packages/repeatmasker/package.py b/var/spack/repos/builtin/packages/repeatmasker/package.py index 746162e8e4..f91f71aaba 100644 --- a/var/spack/repos/builtin/packages/repeatmasker/package.py +++ b/var/spack/repos/builtin/packages/repeatmasker/package.py @@ -16,12 +16,18 @@ class Repeatmasker(Package): version('4.0.7', '4dcbd7c88c5343e02d819f4b3e6527c6') + 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('phrap-crossmatch-swat', type=('build', 'run'), + when='+crossmatch') + def url_for_version(self, version): url = 'http://www.repeatmasker.org/RepeatMasker-open-{0}.tar.gz' return url.format(version.dashed) @@ -48,7 +54,13 @@ class Repeatmasker(Package): '%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'] + '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' |