From bdf0baead75573deaeff425a7cd148ad9a60b4c3 Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Tue, 28 Mar 2017 19:27:20 -0700 Subject: New package: mummer (#3606) * Add package for mummer Blocked on https://github.com/LLNL/spack/pull/3555. * Make "check" step optional and flake8 cleanups --- var/spack/repos/builtin/packages/mummer/package.py | 55 ++++++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 var/spack/repos/builtin/packages/mummer/package.py 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:])) -- cgit v1.2.3-70-g09d2