New package: mummer (#3606)

* Add package for mummer

Blocked on https://github.com/LLNL/spack/pull/3555.

* Make "check" step optional and flake8 cleanups

1 files changed, 55 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/mummer/package.py b/var/spack/repos/builtin/packages/mummer/package.py
new file mode 100644
index 0000000000..49533ed95e
--- /dev/null
+++ b/var/spack/repos/builtin/packages/mummer/package.py
@@ -0,0 +1,55 @@
+##############################################################################
+# 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 LICENSE file 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 Mummer(Package):
+    """MUMmer is a system for rapidly aligning entire genomes."""
+
+    homepage = "http://mummer.sourceforge.net/"
+    url      = "https://sourceforge.net/projects/mummer/files/mummer/3.23/MUMmer3.23.tar.gz/download"
+
+    version('3.23', 'f2422b3d2638dba4baedb71b1acdffa2')
+
+    depends_on('gnuplot')
+
+    def install(self, spec, prefix):
+        if self.run_tests:
+            make('check')
+        make('install')
+        mkdirp(prefix.bin)
+
+        bins = ["show-tiling", "show-snps", "show-coords", "show-aligns", 
+                "show-diff", "delta-filter", "combineMUMs", "mummer", 
+                "repeat-match", "annotate", "mgaps", "gaps", "dnadiff", 
+                "nucmer2xfig", "run-mummer3", "mummerplot", "promer", 
+                "run-mummer1", "nucmer", "mapview", "exact-tandems"]
+        aux_bins = ["aux_bin/postnuc", "aux_bin/postpro",
+                    "aux_bin/prenuc", "aux_bin/prepro"]
+                  
+        for b in bins:
+            install(b, join_path(prefix.bin, b))
+        for b in aux_bins:
+            install(b, join_path(prefix.bin, b[8:]))