c56f03a3ba
* The perl-uri-escape package duplicates perl-uri
The Perl URI::Escape module is in the Perl URI package so the Spack
perl-uri-escape package is a duplicate of the perl-uri package. This PR
does the following:
- replace `depends_on('perl-uri-escape')` with `depends_on('perl-uri')`
in packages that dependend on perl-uri-escape
- add the version from perl-uri-escape to perl-uri
- remove the unneeded dependency from perl-uri
- remove the perl-uri-escape package
* Reinstated perl-test-needs dependency
Put the perl-test-needs dependency for perl-uri back in but set it to
type='test'.
* For tests to succeed the type must be ('build', 'test')
35 lines
1.4 KiB
Python
35 lines
1.4 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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class Transdecoder(MakefilePackage):
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"""TransDecoder identifies candidate coding regions within transcript
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sequences, such as those generated by de novo RNA-Seq transcript
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assembly using Trinity, or constructed based on RNA-Seq alignments to
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the genome using Tophat and Cufflinks."""
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homepage = "http://transdecoder.github.io/"
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url = "https://github.com/TransDecoder/TransDecoder/archive/TransDecoder-v5.5.0.tar.gz"
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version('5.5.0', sha256='c800d9226350817471e9f51267c91f7cab99dbc9b26c980527fc1019e7d90a76')
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version('3.0.1', 'f62b86a15fcb78b1dada9f80cc25f300',
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url='https://github.com/TransDecoder/TransDecoder/archive/v3.0.1.tar.gz')
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depends_on('perl', type=('build', 'run'))
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depends_on('perl-uri', type='run')
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def install(self, spec, prefix):
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mkdirp(prefix.util)
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install('TransDecoder.LongOrfs', prefix)
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install('TransDecoder.Predict', prefix)
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install_tree('PerlLib', prefix.PerlLib)
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install_tree('util', prefix.util)
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def setup_environment(self, spack_env, run_env):
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run_env.prepend_path('PATH', prefix)
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run_env.prepend_path('PATH', prefix.util)
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