54 lines
2.0 KiB
Python
54 lines
2.0 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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from spack import *
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import os
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import glob
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class SspaceStandard(Package):
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"""SSPACE standard is a stand-alone program for scaffolding pre-assembled
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contigs using NGS paired-read data
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Note: A manual download is required for SSPACE-Standard.
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Spack will search your current directory for the download file.
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Alternatively, add this file to a mirror so that Spack can find it.
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For instructions on how to set up a mirror, see
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http://spack.readthedocs.io/en/latest/mirrors.html"""
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homepage = "https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE"
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url = "file://{0}/41SSPACE-STANDARD-3.0_linux-x86_64.tar.gz".format(os.getcwd())
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manual_download = True
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version('3.0', '7e171b4861b9d514e80aafc3d9cdf554')
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depends_on('perl+threads', type=('build', 'run'))
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depends_on('perl-perl4-corelibs', type=('build', 'run'))
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def install(self, spec, prefix):
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rootscript = 'SSPACE_Standard_v{0}.pl'.format(self.version)
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scripts = [rootscript]
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scripts.extend(glob.glob('tools/*.pl'))
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scripts.extend(glob.glob('bwa/*.pl'))
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for s in scripts:
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filter_file('/usr/bin/perl', '/usr/bin/env perl',
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s, string=True)
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filter_file('require "getopts.pl";', 'use Getopt::Std;',
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s, string=True)
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filter_file('&Getopts(', 'getopts(', s, string=True)
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install_tree('bin', prefix.bin)
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install_tree('bowtie', prefix.bowtie)
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install_tree('bwa', prefix.bwa)
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install_tree('dotlib', prefix.dotlib)
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install_tree('tools', prefix.tools)
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install(rootscript, prefix)
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def setup_run_environment(self, env):
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env.set('SSPACE_HOME', self.prefix)
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env.prepend_path('PATH', self.prefix)
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