From c4613b8e1f798f0c2fd1c09b98c4dcaf843d95b5 Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Tue, 21 Nov 2017 09:04:08 -0600 Subject: [PATCH] mira: new package (#6385) --- .../repos/builtin/packages/mira/package.py | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 var/spack/repos/builtin/packages/mira/package.py diff --git a/var/spack/repos/builtin/packages/mira/package.py b/var/spack/repos/builtin/packages/mira/package.py new file mode 100644 index 0000000000..2a67276588 --- /dev/null +++ b/var/spack/repos/builtin/packages/mira/package.py @@ -0,0 +1,52 @@ +############################################################################## +# 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 Mira(AutotoolsPackage): + """MIRA is a multi-pass DNA sequence data assembler/mapper for whole genome + and EST/RNASeq projects.""" + + homepage = "http://sourceforge.net/projects/mira-assembler/" + url = "https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira-4.0.2.tar.bz2" + + version('4.0.2', '1921b426910653a34a6dbb37346f28ea') + + depends_on('boost@1.46:') + depends_on('expat@2.0.1:') + depends_on('gperftools') + + conflicts('%gcc@6:', when='@:4.0.2') + + def patch(self): + with working_dir(join_path('src', 'progs')): + edit = FileFilter('quirks.C') + edit.filter('#include ', + '#include \n#include ') + + def configure_args(self): + args = ['--with-boost=%s' % self.spec['boost'].prefix, + '--with-expat=%s' % self.spec['expat'].prefix] + return args