From bcb8615fb0d009ad4e7899b9e91701333dc56990 Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Tue, 20 Jun 2017 16:34:42 -0500 Subject: Add abyss package (#4555) * abyss * abyss: deleting attemped test from script * abyss: adding new package abyss * abyss: partially fixing mpi dependency issue * abyss: added mpi provider conflicts --- var/spack/repos/builtin/packages/abyss/package.py | 54 +++++++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 var/spack/repos/builtin/packages/abyss/package.py (limited to 'var/spack/repos/builtin/packages/abyss') diff --git a/var/spack/repos/builtin/packages/abyss/package.py b/var/spack/repos/builtin/packages/abyss/package.py new file mode 100644 index 0000000000..9f4a31a47e --- /dev/null +++ b/var/spack/repos/builtin/packages/abyss/package.py @@ -0,0 +1,54 @@ +############################################################################## +# 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 Abyss(AutotoolsPackage): + """ABySS is a de novo, parallel, paired-end sequence assembler + that is designed for short reads. The single-processor version + is useful for assembling genomes up to 100 Mbases in size.""" + + homepage = "http://www.bcgsc.ca/platform/bioinfo/software/abyss" + url = "http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/2.0.2/abyss-2.0.2.tar.gz" + + version('2.0.2', '1623f55ad7f4586e80f6e74b1f27c798') + + depends_on('mpi') + depends_on('boost@:1.50.0,1.53.0:') + depends_on('sparsehash') + depends_on('sqlite') + + conflicts('^intel-mpi') + conflicts('^intel-parallel-studio+mpi') + conflicts('^mvapich2') + conflicts('^spectrum-mpi') + + def configure_args(self): + args = ['--with-boost=%s' % self.spec['boost'].prefix, + '--with-sqlite=%s' % self.spec['sqlite'].prefix, + '--with-mpi=%s' % self.spec['mpi'].prefix] + if self.spec['mpi'].name == 'mpich': + args.append('--enable-mpich') + return args -- cgit v1.2.3-60-g2f50