diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/rna-seqc/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/rna-seqc/package.py | 49 |
1 files changed, 34 insertions, 15 deletions
diff --git a/var/spack/repos/builtin/packages/rna-seqc/package.py b/var/spack/repos/builtin/packages/rna-seqc/package.py index feb50d4b93..56fc66d98f 100644 --- a/var/spack/repos/builtin/packages/rna-seqc/package.py +++ b/var/spack/repos/builtin/packages/rna-seqc/package.py @@ -13,19 +13,39 @@ class RnaSeqc(Package): metrics for RNA-seq data.""" homepage = "http://archive.broadinstitute.org/cancer/cga/rna-seqc" - url = "http://www.broadinstitute.org/cancer/cga/tools/rnaseqc/RNA-SeQC_v1.1.8.jar" - - version('1.1.8', sha256='0a6a8cc885e77c7e7b75dafcfd2152e0d1031fa7aba2565250a46fbd98979793', expand=False) - version('1.1.7', sha256='78e043a2973fed8d567e16bd1f68b1bd78dafe536a41cee07c32e3148e1f1ff3', expand=False) - version('1.1.6', sha256='76f1497b275c801d18a1b403336569552853dd248d94aa625862ea08c6ba25f6', expand=False) - version('1.1.5', sha256='1da100182037f46c61f93a063083e3be579da2678b0441fbc3fc8b58120e52c9', expand=False) - version('1.1.4', sha256='eac437061157036dddf496be8e05fe62b011fb95d34e9079c93ee4001710f1c6', expand=False) - - depends_on('java@8:', type='run') + url = "http://www.broadinstitute.org/cancer/cga/tools/rnaseqc/RNA-SeQC_v1.1.8.jar" + + version( + "1.1.8", + sha256="0a6a8cc885e77c7e7b75dafcfd2152e0d1031fa7aba2565250a46fbd98979793", + expand=False, + ) + version( + "1.1.7", + sha256="78e043a2973fed8d567e16bd1f68b1bd78dafe536a41cee07c32e3148e1f1ff3", + expand=False, + ) + version( + "1.1.6", + sha256="76f1497b275c801d18a1b403336569552853dd248d94aa625862ea08c6ba25f6", + expand=False, + ) + version( + "1.1.5", + sha256="1da100182037f46c61f93a063083e3be579da2678b0441fbc3fc8b58120e52c9", + expand=False, + ) + version( + "1.1.4", + sha256="eac437061157036dddf496be8e05fe62b011fb95d34e9079c93ee4001710f1c6", + expand=False, + ) + + depends_on("java@8:", type="run") def install(self, spec, prefix): mkdirp(prefix.bin) - jar_file = 'RNA-SeQC_v{0}.jar'.format(self.version.dotted) + jar_file = "RNA-SeQC_v{0}.jar".format(self.version.dotted) install(jar_file, prefix.bin) # Set up a helper script to call java on the jar file, @@ -37,8 +57,7 @@ class RnaSeqc(Package): # Munge the helper script to explicitly point to java and the # jar file. - java = self.spec['java'].prefix.bin.java - kwargs = {'ignore_absent': False, 'backup': False, 'string': False} - filter_file('^java', java, script, **kwargs) - filter_file('RNA-SeQC_v{0}.jar', join_path(prefix.bin, jar_file), - script, **kwargs) + java = self.spec["java"].prefix.bin.java + kwargs = {"ignore_absent": False, "backup": False, "string": False} + filter_file("^java", java, script, **kwargs) + filter_file("RNA-SeQC_v{0}.jar", join_path(prefix.bin, jar_file), script, **kwargs) |