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| -rw-r--r-- | var/spack/repos/builtin/packages/vardictjava/package.py | 47 |
1 files changed, 47 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/vardictjava/package.py b/var/spack/repos/builtin/packages/vardictjava/package.py new file mode 100644 index 0000000000..e255411acc --- /dev/null +++ b/var/spack/repos/builtin/packages/vardictjava/package.py @@ -0,0 +1,47 @@ +############################################################################## +# Copyright (c) 2013-2017, 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/llnl/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 glob + + +class Vardictjava(Package): + """VarDictJava is a variant discovery program written in Java. + It is a partial Java port of VarDict variant caller.""" + + homepage = "https://github.com/AstraZeneca-NGS/VarDictJava" + url = "https://github.com/AstraZeneca-NGS/VarDictJava/releases/download/v1.5.1/VarDict-1.5.1.tar" + + version('1.5.1', '8c0387bcc1f7dc696b04e926c48b27e6') + + depends_on('java@8:', type='run') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('bin/VarDict', prefix.bin) + + mkdirp(prefix.lib) + files = [x for x in glob.glob("lib/*jar")] + for f in files: + install(f, prefix.lib) |