From 88cb8b493b5a5816f501f480e8e6612289565fae Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Fri, 14 Jul 2017 13:49:46 -0700 Subject: Add package for freebayes (#4718) * Add package for freebayes * Don't include url, must use git info. * Fix flake8 complaints --- .../repos/builtin/packages/freebayes/package.py | 51 ++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 var/spack/repos/builtin/packages/freebayes/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/freebayes/package.py b/var/spack/repos/builtin/packages/freebayes/package.py new file mode 100644 index 0000000000..9fb7fd1161 --- /dev/null +++ b/var/spack/repos/builtin/packages/freebayes/package.py @@ -0,0 +1,51 @@ +############################################################################## +# 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 Freebayes(MakefilePackage): + """Bayesian haplotype-based genetic polymorphism discovery and + genotyping.""" + + homepage = "https://github.com/ekg/freebayes" + + version('1.1.0', git='https://github.com/ekg/freebayes.git', + commit='39e5e4bcb801556141f2da36aba1df5c5c60701f', + submodules=True) + + depends_on('cmake', type='build') + depends_on('zlib') + + parallel = False + + def edit(self, spec, prefix): + makefile = FileFilter('Makefile') + b = prefix.bin + makefile.filter('cp bin/freebayes bin/bamleftalign /usr/local/bin/', + 'cp bin/freebayes bin/bamleftalign {0}'.format(b)) + + @run_before('install') + def make_prefix_dot_bin(self): + mkdir(prefix.bin) -- cgit v1.2.3-70-g09d2