
We'd like to use a consistent checksum scheme everywhere so that we can: a) incorporate archive checksums into our specs and have a consistent hashing algorithm across all specs. b) index mirrors with a consistent type of checksum, and not one that is dependent on how spack packages are written. - [x] convert existing md5, sha224, sha512, sha1 checksums to sha256
44 lines
1.9 KiB
Python
44 lines
1.9 KiB
Python
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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import os.path
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class RnaSeqc(Package):
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"""RNA-SeQC is a java program which computes a series of quality control
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metrics for RNA-seq data."""
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homepage = "http://archive.broadinstitute.org/cancer/cga/rna-seqc"
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url = "http://www.broadinstitute.org/cancer/cga/tools/rnaseqc/RNA-SeQC_v1.1.8.jar"
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version('1.1.8', sha256='0a6a8cc885e77c7e7b75dafcfd2152e0d1031fa7aba2565250a46fbd98979793', expand=False)
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version('1.1.7', sha256='78e043a2973fed8d567e16bd1f68b1bd78dafe536a41cee07c32e3148e1f1ff3', expand=False)
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version('1.1.6', sha256='76f1497b275c801d18a1b403336569552853dd248d94aa625862ea08c6ba25f6', expand=False)
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version('1.1.5', sha256='1da100182037f46c61f93a063083e3be579da2678b0441fbc3fc8b58120e52c9', expand=False)
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version('1.1.4', sha256='eac437061157036dddf496be8e05fe62b011fb95d34e9079c93ee4001710f1c6', expand=False)
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depends_on('jdk@8:', type='run')
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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jar_file = 'RNA-SeQC_v{0}.jar'.format(self.version.dotted)
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install(jar_file, prefix.bin)
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# Set up a helper script to call java on the jar file,
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# explicitly codes the path for java and the jar file.
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script_sh = join_path(os.path.dirname(__file__), "rna-seqc.sh")
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script = join_path(prefix.bin, "rna-seqc")
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install(script_sh, script)
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set_executable(script)
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# Munge the helper script to explicitly point to java and the
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# jar file.
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java = self.spec['jdk'].prefix.bin.java
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kwargs = {'ignore_absent': False, 'backup': False, 'string': False}
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filter_file('^java', java, script, **kwargs)
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filter_file('RNA-SeQC_v{0}.jar', join_path(prefix.bin, jar_file),
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script, **kwargs)
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