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Diffstat (limited to 'var/spack/repos/builtin/packages/fast-gbs/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/fast-gbs/package.py | 54 |
1 files changed, 0 insertions, 54 deletions
diff --git a/var/spack/repos/builtin/packages/fast-gbs/package.py b/var/spack/repos/builtin/packages/fast-gbs/package.py deleted file mode 100644 index feddf105d9..0000000000 --- a/var/spack/repos/builtin/packages/fast-gbs/package.py +++ /dev/null @@ -1,54 +0,0 @@ -############################################################################## -# 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 * - - -class FastGbs(Package): - """A bioinformatic pipeline designed to extract a high-quality SNP catalog - starting from FASTQ files obtained from sequencing - genotyping-by-sequencing (GBS) libraries.""" - - homepage = "https://bitbucket.org/jerlar73/fast-gbs" - git = "https://bitbucket.org/jerlar73/fast-gbs.git" - - version('2017-01-25', commit='3b3cbffa84d269419692067c6a3de08b3b88849c') - - depends_on('parallel', type='run') - depends_on('python@2.7:', type='run') - depends_on('sabre', type='run') - depends_on('py-cutadapt', type='run') - depends_on('bwa', type='run') - depends_on('samtools', type='run') - depends_on('platypus', type='run') - depends_on('py-pyvcf', type='run') - - def install(self, spec, prefix): - mkdirp(prefix.bin) - install('fastgbs.sh', prefix.bin) - install('parameters.txt', prefix.bin) - install('makeDir.sh', prefix.bin) - install('makeBarcodeSabre.py', prefix.bin) - install('vcf2txt.py', prefix.bin) - install('txt2unix.sh', prefix.bin) |