61 lines
2.3 KiB
Python
61 lines
2.3 KiB
Python
##############################################################################
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# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
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# Produced at the Lawrence Livermore National Laboratory.
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#
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# This file is part of Spack.
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# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
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# LLNL-CODE-647188
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#
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# For details, see https://github.com/spack/spack
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# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
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#
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# This program is free software; you can redistribute it and/or modify
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# it under the terms of the GNU Lesser General Public License (as
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# published by the Free Software Foundation) version 2.1, February 1999.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
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# conditions of the GNU Lesser General Public License for more details.
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#
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# You should have received a copy of the GNU Lesser General Public
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# License along with this program; if not, write to the Free Software
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# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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##############################################################################
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from spack import *
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class Canu(MakefilePackage):
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"""A single molecule sequence assembler for genomes large and
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small."""
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homepage = "http://canu.readthedocs.io/"
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url = "https://github.com/marbl/canu/archive/v1.5.tar.gz"
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version('1.5', '65df275baa28ecf11b15dfd7343361e3')
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depends_on('gnuplot', type='run')
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depends_on('jdk', type='run')
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depends_on('perl', type='run')
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build_directory = 'src'
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def patch(self):
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# Use our perl, not whatever is in the environment
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filter_file(r'^#!/usr/bin/env perl',
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'#!{0}'.format(self.spec['perl'].command.path),
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'src/pipelines/canu.pl')
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def install(self, spec, prefix):
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# replicate the Makefile logic here:
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# https://github.com/marbl/canu/blob/master/src/Makefile#L344
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uname = which('uname')
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ostype = uname(output=str).strip()
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machinetype = uname('-m', output=str).strip()
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if machinetype == 'x86_64':
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machinetype = 'amd64'
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target_dir = '{0}-{1}'.format(ostype, machinetype)
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bin = join_path(target_dir, 'bin')
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install_tree(bin, prefix.bin)
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