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Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/transdecoder/package.py | 50 |
1 files changed, 50 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/transdecoder/package.py b/var/spack/repos/builtin/packages/transdecoder/package.py new file mode 100644 index 0000000000..4c23afbf2a --- /dev/null +++ b/var/spack/repos/builtin/packages/transdecoder/package.py @@ -0,0 +1,50 @@ +############################################################################## +# Copyright (c) 2013-2016, 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 * + + +class Transdecoder(MakefilePackage): + """TransDecoder identifies candidate coding regions within transcript + sequences, such as those generated by de novo RNA-Seq transcript + assembly using Trinity, or constructed based on RNA-Seq alignments to + the genome using Tophat and Cufflinks.""" + + homepage = "http://transdecoder.github.io/" + url = "https://github.com/TransDecoder/TransDecoder/archive/v3.0.1.tar.gz" + + version('3.0.1', 'f62b86a15fcb78b1dada9f80cc25f300') + + depends_on('perl', type=('build', 'run')) + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('TransDecoder.LongOrfs', prefix) + install('TransDecoder.Predict', prefix) + install_tree('PerlLib', prefix.PerlLib) + install_tree('util', prefix.util) + + def setup_environment(self, spack_env, run_env): + run_env.prepend_path('PATH', prefix.util.bin) + run_env.prepend_path('PATH', prefix) |