741bb9bafe
* install/install_tree: glob support * Add unit tests * Update existing packages * Raise error if glob finds no files, document function raises
43 lines
1.8 KiB
Python
43 lines
1.8 KiB
Python
# Copyright 2013-2020 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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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 = "https://daehwankimlab.github.io/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('2.2.0', sha256='0dd55168853b82c1b085f79ed793dd029db163773f52272d7eb51b3b5e4a4cdd',
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url='https://cloud.biohpc.swmed.edu/index.php/s/hisat2-220-source/download',
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extension='zip')
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version('2.1.0', sha256='89a276eed1fc07414b1601947bc9466bdeb50e8f148ad42074186fe39a1ee781')
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def install(self, spec, prefix):
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if spec.satisfies('@:2.1.0'):
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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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install('*.py', prefix.bin)
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def setup_run_environment(self, env):
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env.prepend_path('PATH', self.spec.prefix)
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