diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/sspace-standard/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/sspace-standard/package.py | 46 |
1 files changed, 21 insertions, 25 deletions
diff --git a/var/spack/repos/builtin/packages/sspace-standard/package.py b/var/spack/repos/builtin/packages/sspace-standard/package.py index 2724c1022f..9275b200ea 100644 --- a/var/spack/repos/builtin/packages/sspace-standard/package.py +++ b/var/spack/repos/builtin/packages/sspace-standard/package.py @@ -1,29 +1,11 @@ -############################################################################## -# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. -# Produced at the Lawrence Livermore National Laboratory. +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. # -# 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 -############################################################################## +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + from spack import * import os +import glob class SspaceStandard(Package): @@ -41,15 +23,29 @@ class SspaceStandard(Package): version('3.0', '7e171b4861b9d514e80aafc3d9cdf554') - depends_on('perl', type=('build', 'run')) + 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('SSPACE_Standard_v{0}.pl'.format(self.version), prefix) + install(rootscript, prefix) def setup_environment(self, spack_env, run_env): run_env.set('SSPACE_HOME', prefix) |