diff options
Diffstat (limited to 'var/spack/repos/builtin/packages/gapfiller/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/gapfiller/package.py | 47 |
1 files changed, 20 insertions, 27 deletions
diff --git a/var/spack/repos/builtin/packages/gapfiller/package.py b/var/spack/repos/builtin/packages/gapfiller/package.py index 43e6eeaac0..883874007b 100644 --- a/var/spack/repos/builtin/packages/gapfiller/package.py +++ b/var/spack/repos/builtin/packages/gapfiller/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 Gapfiller(Package): @@ -44,9 +26,20 @@ class Gapfiller(Package): return "file://{0}/39GapFiller_v{1}_linux-x86_64.tar.gz".format( os.getcwd(), version.dashed) - depends_on('perl', type=('build', 'run')) + depends_on('perl+threads', type=('build', 'run')) + + def patch(self): + with working_dir('.'): + files = glob.iglob("*.pl") + for file in files: + change = FileFilter(file) + change.filter('usr/bin/perl', 'usr/bin/env perl') + change.filter('require "getopts.pl";', 'use Getopt::Std;') + change.filter('&Getopts', 'getopts') + change.filter('\r', '') + set_executable(file) def install(self, spec, prefix): - install_tree('bowtie', prefix.bowtie) - install_tree('bwa', prefix.bwa) - install('GapFiller.pl', prefix) + install_tree('bowtie', prefix.bin.bowtie) + install_tree('bwa', prefix.bin.bwa) + install('GapFiller.pl', prefix.bin) |