diff options
| -rw-r--r-- | var/spack/repos/builtin/packages/glfmultiples/package.py | 49 |
1 files changed, 49 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/glfmultiples/package.py b/var/spack/repos/builtin/packages/glfmultiples/package.py new file mode 100644 index 0000000000..001e842264 --- /dev/null +++ b/var/spack/repos/builtin/packages/glfmultiples/package.py @@ -0,0 +1,49 @@ +############################################################################## +# 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 Glfmultiples(MakefilePackage): + """glfMultiples is a GLF-based variant caller for next-generation + sequencing data. It takes a set of GLF format genotype likelihood + files as input and generates a VCF-format set of variant calls + as output. """ + + homepage = "https://genome.sph.umich.edu/wiki/GlfMultiples" + url = "http://www.sph.umich.edu/csg/abecasis/downloads/generic-glfMultiples-2010-06-16.tar.gz" + + version('2010-06-16', '64bf6bb7c76543f4c8fabce015a3cb11') + + depends_on('zlib') + + def edit(self, spec, prefix): + makefile = FileFilter('Makefile') + makefile.filter('CXX=.*', 'CXX = ' + env['CXX']) + makefile.filter('CFLAGS=.*', + 'CFLAGS=-O2 -I./libsrc -I./pdf ' + + '-D_FILE_OFFSET_BITS=64 -D__USE_LONG_INT') + + def install(self, spec, prefix): + make('INSTALLDIR=%s' % prefix, 'install') |