62927654dd
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
46 lines
1.8 KiB
Python
46 lines
1.8 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 Trimmomatic(Package):
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"""A flexible read trimming tool for Illumina NGS data."""
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homepage = "http://www.usadellab.org/cms/?page=trimmomatic"
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url = "http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip"
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# Older version aren't explicitly made available, but the URL
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# works as we'd like it to, so...
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version('0.38', sha256='d428af42b6c400a2e7ee5e6b4cab490eddc621f949b086bd7dddb698dcf1647c')
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version('0.36', sha256='4846c42347b663b9d6d3a8cef30da2aec89fc718bf291392c58e5afcea9f70fe')
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version('0.33', sha256='6968583a6c5854a44fff7d427e7ccdcb8dc17f4616082dd390a0633f87a09e3d')
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depends_on('java@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 = 'trimmomatic-{v}.jar'.format(v=self.version.dotted)
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install(jar_file, prefix.bin)
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# Put the adapter files someplace sensible
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install_tree('adapters', prefix.share.adapters)
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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__), "trimmomatic.sh")
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script = prefix.bin.trimmomatic
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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['java'].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('trimmomatic.jar', join_path(prefix.bin, jar_file),
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script, **kwargs)
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