new package: Glfmultiples (#7055)

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
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+++ b/var/spack/repos/builtin/packages/glfmultiples/package.py
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+##############################################################################
+# 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')