diff --git a/var/spack/repos/builtin/packages/canu/package.py b/var/spack/repos/builtin/packages/canu/package.py new file mode 100644 index 0000000000..fd6acfec0f --- /dev/null +++ b/var/spack/repos/builtin/packages/canu/package.py @@ -0,0 +1,61 @@ +############################################################################## +# 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 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 Canu(MakefilePackage): + """A single molecule sequence assembler for genomes large and + small.""" + + homepage = "http://canu.readthedocs.io/" + url = "https://github.com/marbl/canu/archive/v1.5.tar.gz" + + version('1.5', '65df275baa28ecf11b15dfd7343361e3') + + depends_on('gnuplot', type='run') + depends_on('jdk', type='run') + depends_on('perl', type='run') + + build_directory = 'src' + + def patch(self): + # Use our perl, not whatever is in the environment + perl = self.spec['perl'].prefix.bin.perl + filter_file(r'^#!/usr/bin/env perl', + '#!{0}'.format(perl), + 'src/pipelines/canu.pl') + + def install(self, spec, prefix): + # replicate the Makefile logic here: + # https://github.com/marbl/canu/blob/master/src/Makefile#L344 + uname = which('uname') + ostype = uname(output=str).strip() + machinetype = uname('-m', output=str).strip() + if machinetype == 'x86_64': + machinetype = 'amd64' + target_dir = '{0}-{1}'.format(ostype, machinetype) + bin = join_path(target_dir, 'bin') + + install_tree(bin, prefix.bin)