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authorJustin Stanley <molecuul@users.noreply.github.com>2019-02-07 16:53:30 -0600
committerPeter Scheibel <scheibel1@llnl.gov>2019-02-07 16:53:30 -0600
commitec6de8326e1884307dc167395b128645397596ba (patch)
treefaca70b307e433e9e6fa06c41aa5e27184ba72f4 /var
parent76feb0205d49ade45a813ead9fea0bc259e78175 (diff)
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repeatmasker package: add variant for cross_match engine (#10534)
Diffstat (limited to 'var')
-rw-r--r--var/spack/repos/builtin/packages/repeatmasker/package.py14
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'