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| -rw-r--r-- | var/spack/repos/builtin/packages/shortbred/package.py | 51 |
1 files changed, 51 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/shortbred/package.py b/var/spack/repos/builtin/packages/shortbred/package.py new file mode 100644 index 0000000000..aeccfa9378 --- /dev/null +++ b/var/spack/repos/builtin/packages/shortbred/package.py @@ -0,0 +1,51 @@ +############################################################################## +# 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/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 Shortbred(Package): + """ShortBRED is a system for profiling protein families of interest at + very high specificity in shotgun meta'omic sequencing data.""" + + homepage = "https://huttenhower.sph.harvard.edu/shortbred" + url = "https://bitbucket.org/biobakery/shortbred/get/0.9.4.tar.gz" + + version('0.9.4', 'ad3dff344cbea3713e78b384afad28fd') + + depends_on('blast-plus@2.2.28:') + depends_on('cdhit@4.6:') + depends_on('muscle@3.8.31:') + depends_on('python@2.7.9:') + depends_on('py-biopython') + depends_on('usearch@6.0.307:') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install('shortbred_identify.py', prefix.bin) + install('shortbred_quantify.py', prefix.bin) + install_tree('src', prefix.src) + + def setup_environment(self, spack_env, run_env): + run_env.prepend_path('PYTHONPATH', self.prefix) |