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metabat: Create new package (#7991)

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* 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
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Eric 2018-05-06 10:56:03 -05:00 committed by Adam J. Stewart
parent c451644f12
commit 0dddb98869
1 changed files with 54 additions and 0 deletions
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var/spack/repos/builtin/packages/metabat/package.py Normal file
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##############################################################################
# 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')