50 lines
1.6 KiB
Python
50 lines
1.6 KiB
Python
# Copyright 2013-2022 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 os import symlink
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from spack import *
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class Homer(Package):
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"""Software for motif discovery and next generation sequencing analysis"""
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homepage = "http://homer.ucsd.edu/homer"
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url = "http://homer.ucsd.edu/homer/data/software/homer.v4.9.1.zip"
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version('4.9.1', sha256='ad1303b0b0400dc8a88dbeae1ee03a94631977b751a3d335326c4febf0eec3a9')
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depends_on('perl', type=('build', 'run'))
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depends_on('r-biocgenerics', type='run')
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depends_on('r-biocparallel', type='run')
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depends_on('r-edger', type='run')
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depends_on('r-deseq2', type='run')
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variant('data', default=False,
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description='Download genome data packages')
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def install(self, spec, prefix):
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# initialize homer directories
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basedir = join_path(prefix.lib, 'homer')
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mkdirp(basedir)
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install_tree('.', basedir)
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# symlink bin so it is included in the PATH
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symlink(join_path(basedir, 'bin'), prefix.bin)
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# override homer base directory in configure script
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filter_file('my $homeDir = $1;',
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'my $homeDir = \"{0}\";'.format(basedir),
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'configureHomer.pl', string=True)
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# compile/prepare binaries and perl scripts with the correct paths
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perl = which('perl')
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perl('configureHomer.pl', '-local')
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# download extra data if requested
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if '+data' in spec:
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perl('configureHomer.pl', '-install', '-all')
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