hapcut2: new package (#5238)

var/spack/repos/builtin/packages/hapcut2/package.py

@@ -0,0 +1,44 @@
+##############################################################################
+# 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 Hapcut2(MakefilePackage):
+    """HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes
+       from DNA sequence reads, designed to 'just work' with excellent speed
+       and accuracy."""
+
+    homepage = "https://github.com/vibansal/HapCUT2"
+    url      = "https://github.com/vibansal/HapCUT2"
+
+    version('2017-07-10', git='https://github.com/vibansal/HapCUT2.git',
+            commit='2966b94c2c2f97813b757d4999b7a6471df1160e', submodules=True)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.bin)
+        with working_dir('build'):
+            install('extractFOSMID', prefix.bin)
+            install('extractHAIRS', prefix.bin)
+            install('HAPCUT2', prefix.bin)