From 0dddb988696f3c90ea3c14c48346c265d744e2f2 Mon Sep 17 00:00:00 2001 From: Eric Date: Sun, 6 May 2018 10:56:03 -0500 Subject: [PATCH] metabat: Create new package (#7991) * metabat: Create new package * fix Perl script shebangs and BOOST_ROOT environment * add perl script fix function * add perl dependency and fix positional argument for Python 2.6 --- .../repos/builtin/packages/metabat/package.py | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 var/spack/repos/builtin/packages/metabat/package.py diff --git a/var/spack/repos/builtin/packages/metabat/package.py b/var/spack/repos/builtin/packages/metabat/package.py new file mode 100644 index 0000000000..3d00c2dbe6 --- /dev/null +++ b/var/spack/repos/builtin/packages/metabat/package.py @@ -0,0 +1,54 @@ +############################################################################## +# Copyright (c) 2013-2018, 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 Metabat(SConsPackage): + """MetaBAT, an efficient tool for accurately reconstructing single + genomes from complex microbial communities.""" + + homepage = "https://bitbucket.org/berkeleylab/metabat" + url = "https://bitbucket.org/berkeleylab/metabat/get/v2.12.1.tar.gz" + + version('2.12.1', 'c032f47a8b24e58a5a9fefe52cb6e0f8') + + depends_on('boost@1.55.0:', type=('build', 'run')) + depends_on('perl', type='run') + + def setup_environment(self, spack_env, run_env): + spack_env.set('BOOST_ROOT', self.spec['boost'].prefix) + + def install_args(self, spec, prefix): + return ["PREFIX={0}".format(prefix)] + + @run_after('build') + def fix_perl_scripts(self): + filter_file(r'#!/usr/bin/perl', + '#!/usr/bin/env perl', + 'aggregateBinDepths.pl') + + filter_file(r'#!/usr/bin/perl', + '#!/usr/bin/env perl', + 'aggregateContigOverlapsByBin.pl')