mefit: Create new package. (#6700)

1 files changed, 47 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/mefit/package.py b/var/spack/repos/builtin/packages/mefit/package.py
new file mode 100644
index 0000000000..7f4c555bd8
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mefit/package.py
@@ -0,0 +1,47 @@
+##############################################################################
+# 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 *
+import distutils.dir_util
+
+
+class Mefit(Package):
+    """This pipeline will merge overlapping paired-end reads, calculate
+    merge statistics, and filter reads for quality."""
+
+    homepage = "https://github.com/nisheth/MeFiT"
+    url      = "https://github.com/nisheth/MeFiT.git"
+
+    version('1.0', git='https://github.com/nisheth/MeFiT.git', commit='0733326d8917570bbf70ff5c0f710bf66c13db09')
+
+    depends_on('py-numpy')
+    depends_on('py-htseq')
+    depends_on('jellyfish')
+    depends_on('casper %gcc@4.8.5')
+
+    def install(self, spec, prefix):
+        distutils.dir_util.copy_tree(".", prefix)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', self.prefix)