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| -rw-r--r-- | var/spack/repos/builtin/packages/bracken/package.py | 75 |
1 files changed, 75 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/bracken/package.py b/var/spack/repos/builtin/packages/bracken/package.py new file mode 100644 index 0000000000..50efea40c8 --- /dev/null +++ b/var/spack/repos/builtin/packages/bracken/package.py @@ -0,0 +1,75 @@ +############################################################################## +# 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 Bracken(Package): + """Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly + accurate statistical method that computes the abundance of species in DNA + sequences from a metagenomics sample.""" + + homepage = "https://ccb.jhu.edu/software/bracken" + url = "https://github.com/jenniferlu717/Bracken/archive/1.0.0.tar.gz" + + version('1.0.0', 'bd91805655269c5f3becb8f8028bab6d') + + depends_on('perl') + depends_on('python@2.7:') + depends_on('perl-exporter-tiny') + depends_on('perl-list-moreutils') + depends_on('perl-parallel-forkmanager') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install_tree('sample_data', prefix.sample_data) + + filter_file( + r'#!/bin/env perl', + '#!/usr/bin/env perl', + 'count-kmer-abundances.pl' + ) + + filter_file( + r'#!/usr/bin/python', + '#!/usr/bin/env python', + 'est_abundance.py' + ) + + filter_file( + r'#!/usr/bin/python', + '#!/usr/bin/env python', + 'generate_kmer_distribution.py' + ) + + files = ( + 'count-kmer-abundances.pl', + 'est_abundance.py', + 'generate_kmer_distribution.py', + ) + + chmod = which('chmod') + for name in files: + install(name, prefix.bin) + chmod('+x', join_path(self.prefix.bin, name)) |