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authorGeorge Hartzell <hartzell@alerce.com>2017-03-28 19:27:20 -0700
committerAdam J. Stewart <ajstewart426@gmail.com>2017-03-28 21:27:20 -0500
commitbdf0baead75573deaeff425a7cd148ad9a60b4c3 (patch)
tree4a5a014706dd5ece29d2abd378ea214fe9fa6375 /var
parent81a0881a572885f0a356005c62b1b0a8ddd0cefd (diff)
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New package: mummer (#3606)
* Add package for mummer Blocked on https://github.com/LLNL/spack/pull/3555. * Make "check" step optional and flake8 cleanups
Diffstat (limited to 'var')
-rw-r--r--var/spack/repos/builtin/packages/mummer/package.py55
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
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+++ b/var/spack/repos/builtin/packages/mummer/package.py
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+##############################################################################
+# 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:]))