diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/redundans/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/redundans/package.py | 35 |
1 files changed, 11 insertions, 24 deletions
diff --git a/var/spack/repos/builtin/packages/redundans/package.py b/var/spack/repos/builtin/packages/redundans/package.py index 71f83f623a..17aed51ee1 100644 --- a/var/spack/repos/builtin/packages/redundans/package.py +++ b/var/spack/repos/builtin/packages/redundans/package.py @@ -1,27 +1,8 @@ -############################################################################## -# 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 * @@ -36,16 +17,22 @@ class Redundans(Package): depends_on('python', type=('build', 'run')) depends_on('py-pyscaf', type=('build', 'run')) depends_on('py-fastaindex', type=('build', 'run')) + depends_on('py-numpy', type=('build', 'run')) depends_on('perl', type=('build', 'run')) depends_on('sspace-standard') depends_on('bwa') depends_on('last') depends_on('gapcloser') depends_on('parallel') - depends_on('snap-berkeley') + depends_on('snap-berkeley@1.0beta.18:', type=('build', 'run')) def install(self, spec, prefix): + sspace_location = join_path(spec['sspace-standard'].prefix, + 'SSPACE_Standard_v3.0.pl') mkdirp(prefix.bin) + filter_file(r'sspacebin = os.path.join(.*)$', + 'sspacebin = \'' + sspace_location + '\'', + 'redundans.py') install('redundans.py', prefix.bin) with working_dir('bin'): install('fasta2homozygous.py', prefix.bin) |