45 lines
1.7 KiB
Python
45 lines
1.7 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 glob
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import os.path
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class Hisat2(MakefilePackage):
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"""HISAT2 is a fast and sensitive alignment program for mapping
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next-generation sequencing reads (whole-genome, transcriptome, and
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exome sequencing data) against the general human population (as well as
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against a single reference genome)."""
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homepage = "http://ccb.jhu.edu/software/hisat2"
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url = "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.1.0-source.zip"
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version('2.1.0', '8b566d1b7e6c5801c8ae9824ed2da3d0')
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def install(self, spec, prefix):
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install_tree('doc', prefix.doc)
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install_tree('example', prefix.example)
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install_tree('hisatgenotype_modules', prefix.hisatgenotype_modules)
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install_tree('hisatgenotype_scripts', prefix.hisatgenotype_scripts)
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install_tree('scripts', prefix.scripts)
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mkdirp(prefix.bin)
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install('hisat2', prefix.bin)
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install('hisat2-align-s', prefix.bin)
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install('hisat2-align-l', prefix.bin)
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install('hisat2-build', prefix.bin)
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install('hisat2-build-s', prefix.bin)
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install('hisat2-build-l', prefix.bin)
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install('hisat2-inspect', prefix.bin)
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install('hisat2-inspect-s', prefix.bin)
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install('hisat2-inspect-l', prefix.bin)
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files = glob.iglob('*.py')
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for file in files:
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if os.path.isfile(file):
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install(file, prefix.bin)
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def setup_environment(self, spack_env, run_env):
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run_env.prepend_path('PATH', self.spec.prefix)
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