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##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, see https://github.com/spack/spack
# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License (as
# published by the Free Software Foundation) version 2.1, February 1999.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
# conditions of the GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
##############################################################################
from spack import *
import os
import glob
class SspaceStandard(Package):
"""SSPACE standard is a stand-alone program for scaffolding pre-assembled
contigs using NGS paired-read data
Note: A manual download is required for SSPACE-Standard.
Spack will search your current directory for the download file.
Alternatively, add this file to a mirror so that Spack can find it.
For instructions on how to set up a mirror, see
http://spack.readthedocs.io/en/latest/mirrors.html"""
homepage = "https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE"
url = "file://{0}/41SSPACE-STANDARD-3.0_linux-x86_64.tar.gz".format(os.getcwd())
version('3.0', '7e171b4861b9d514e80aafc3d9cdf554')
depends_on('perl+threads', type=('build', 'run'))
depends_on('perl-perl4-corelibs', type=('build', 'run'))
def install(self, spec, prefix):
rootscript = 'SSPACE_Standard_v{0}.pl'.format(self.version)
scripts = [rootscript]
scripts.extend(glob.glob('tools/*.pl'))
scripts.extend(glob.glob('bwa/*.pl'))
for s in scripts:
filter_file('/usr/bin/perl', '/usr/bin/env perl',
s, string=True)
filter_file('require "getopts.pl";', 'use Getopt::Std;',
s, string=True)
filter_file('&Getopts(', 'getopts(', s, string=True)
install_tree('bin', prefix.bin)
install_tree('bowtie', prefix.bowtie)
install_tree('bwa', prefix.bwa)
install_tree('dotlib', prefix.dotlib)
install_tree('tools', prefix.tools)
install(rootscript, prefix)
def setup_environment(self, spack_env, run_env):
run_env.set('SSPACE_HOME', prefix)
run_env.prepend_path('PATH', prefix)
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