45784af7f2
This also adds the tcl, tk, and libx11 dependencies to ruby. All other changes are new packages.
91 lines
3.8 KiB
Python
91 lines
3.8 KiB
Python
##############################################################################
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# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/spack/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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import distutils.dir_util
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class Biopieces(Package):
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"""The Biopieces are a collection of bioinformatics tools that can be
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pieced together in a very easy and flexible manner to perform both
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simple and complex tasks."""
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homepage = "http://maasha.github.io/biopieces/"
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url = "https://github.com/maasha/biopieces/archive/2.0.tar.gz"
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version('2016-04-12', commit='982f80f7c55e2cae67737d80fe35a4e784762856',
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git='https://github.com/maasha/biopieces.git', submodules=True)
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depends_on('perl', type=('build', 'run'))
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depends_on('perl-module-build', type=('build', 'run'))
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depends_on('perl-bit-vector', type=('build', 'run'))
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depends_on('perl-svg', type=('build', 'run'))
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depends_on('perl-term-readkey', type=('build', 'run'))
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depends_on('perl-time-hires', type=('build', 'run'))
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depends_on('perl-dbi', type=('build', 'run'))
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depends_on('perl-xml-parser', type=('build', 'run'))
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depends_on('perl-carp-clan', type=('build', 'run'))
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depends_on('perl-class-inspector', type=('build', 'run'))
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depends_on('perl-html-parser', type=('build', 'run'))
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depends_on('perl-lwp', type=('build', 'run'))
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depends_on('perl-soap-lite', type=('build', 'run'))
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depends_on('perl-uri', type=('build', 'run'))
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depends_on('perl-inline', type=('build', 'run'))
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depends_on('perl-inline-c', type=('build', 'run'))
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depends_on('perl-parse-recdescent', type=('build', 'run'))
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depends_on('perl-version', type=('build', 'run'))
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depends_on('perl-dbfile', type=('build', 'run'))
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depends_on('perl-dbd-mysql', type=('build', 'run'))
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depends_on('ruby@1.9:')
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depends_on('ruby-gnuplot')
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depends_on('ruby-narray')
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depends_on('ruby-rubyinline')
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depends_on('ruby-terminal-table')
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depends_on('python@2.6:', type=('build', 'run'))
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depends_on('blast-plus')
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depends_on('muscle')
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depends_on('mummer')
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depends_on('blat')
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depends_on('vmatch')
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depends_on('bowtie')
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depends_on('bwa')
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depends_on('usearch')
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depends_on('velvet')
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depends_on('idba')
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depends_on('ray')
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depends_on('scan-for-matches')
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def install(self, spec, prefix):
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distutils.dir_util.copy_tree(".", prefix)
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def setup_environment(self, spack_env, run_env):
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# Note: user will need to set environment variables on their own,
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# dependent on where they will want data to be located:
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# BP_DATA - Contains genomic data etc.
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# BP_TMP - Required temporary directory
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# BP_LOG - Required log directory
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run_env.prepend_path('BP_DIR', prefix)
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