41 lines
1.5 KiB
Python
41 lines
1.5 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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from glob import glob
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class PerlStarFusion(Package):
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"""STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis
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Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate
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fusion transcripts supported by Illumina reads. STAR-Fusion further
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processes the output generated by the STAR aligner to map junction reads
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and spanning reads to a reference annotation set."""
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homepage = "https://github.com/STAR-Fusion/STAR-Fusion"
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git = "https://github.com/STAR-Fusion/STAR-Fusion.git"
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version('master', commit='8c5a541')
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extends('perl')
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depends_on('star', type=('build', 'run'))
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depends_on('perl', type=('build', 'run'))
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depends_on('perl-intervaltree', type=('build', 'run'))
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depends_on('perl-dbi', type=('build', 'run'))
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depends_on('perl-dbfile', type=('build', 'run'))
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depends_on('perl-uri-escape', type=('build', 'run'))
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def install(self, spec, prefix):
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mkdirp(prefix.bin)
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install('STAR-Fusion', prefix.bin)
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mkdirp(perl_lib_dir)
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with working_dir('PerlLib'):
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for pm in glob("*.pm"):
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install(pm, perl_lib_dir)
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with working_dir('util'):
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for files in glob("*"):
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install(files, prefix.bin)
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