A new package: lumpy-sv. (#7009)

1 files changed, 43 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/lumpy-sv/package.py b/var/spack/repos/builtin/packages/lumpy-sv/package.py
new file mode 100644
index 0000000000..a2ffca2b8e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/lumpy-sv/package.py
@@ -0,0 +1,43 @@
+##############################################################################
+# 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 LumpySv(MakefilePackage):
+    """A probabilistic framework for structural variant discovery."""
+
+    homepage = "https://github.com/arq5x/lumpy-sv"
+    url      = "https://github.com/arq5x/lumpy-sv/archive/0.2.13.tar.gz"
+
+    version('0.2.13', '36929d29fc3a171d3abbe1d93f9f3b50')
+
+    depends_on('htslib')
+
+    def edit(self, spec, prefix):
+        makefile = FileFilter('Makefile')
+        makefile.filter('export CXX .*', '')
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)