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# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Biopieces(Package):
"""The Biopieces are a collection of bioinformatics tools that can be
pieced together in a very easy and flexible manner to perform both
simple and complex tasks."""
homepage = "https://maasha.github.io/biopieces/"
git = "https://github.com/maasha/biopieces.git"
version('2016-04-12', commit='982f80f7c55e2cae67737d80fe35a4e784762856',
submodules=True)
depends_on('perl', type=('build', 'run'))
depends_on('perl-module-build', type=('build', 'run'))
depends_on('perl-bit-vector', type=('build', 'run'))
depends_on('perl-svg', type=('build', 'run'))
depends_on('perl-termreadkey', type=('build', 'run'))
depends_on('perl-time-hires', type=('build', 'run'))
depends_on('perl-dbi', type=('build', 'run'))
depends_on('perl-xml-parser', type=('build', 'run'))
depends_on('perl-carp-clan', type=('build', 'run'))
depends_on('perl-class-inspector', type=('build', 'run'))
depends_on('perl-html-parser', type=('build', 'run'))
depends_on('perl-libwww-perl', type=('build', 'run'))
depends_on('perl-soap-lite', type=('build', 'run'))
depends_on('perl-uri', type=('build', 'run'))
depends_on('perl-inline', type=('build', 'run'))
depends_on('perl-inline-c', type=('build', 'run'))
depends_on('perl-parse-recdescent', type=('build', 'run'))
depends_on('perl-perl-version', type=('build', 'run'))
depends_on('perl-db-file', type=('build', 'run'))
depends_on('perl-dbd-mysql', type=('build', 'run'))
depends_on('ruby@1.9:')
depends_on('ruby-gnuplot')
depends_on('ruby-narray')
depends_on('ruby-rubyinline')
depends_on('ruby-terminal-table')
depends_on('python@2.6:', type=('build', 'run'))
depends_on('blast-plus')
depends_on('muscle')
depends_on('mummer')
depends_on('blat')
depends_on('vmatch')
depends_on('bowtie')
depends_on('bwa')
depends_on('usearch')
depends_on('velvet')
depends_on('idba')
depends_on('ray')
depends_on('scan-for-matches')
def install(self, spec, prefix):
install_tree('.', prefix)
def setup_run_environment(self, env):
# Note: user will need to set environment variables on their own,
# dependent on where they will want data to be located:
# BP_DATA - Contains genomic data etc.
# BP_TMP - Required temporary directory
# BP_LOG - Required log directory
env.prepend_path('BP_DIR', self.prefix)
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