46 lines
1.6 KiB
Python
46 lines
1.6 KiB
Python
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
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# Spack Project Developers. See the top-level COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack import *
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import os
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import glob
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class Gapfiller(Package):
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"""GapFiller is a stand-alone program for closing gaps within
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pre-assembled scaffolds.
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Note: A manual download is required for GapFiller.
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Spack will search your current directory for the download file.
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Alternatively, add this file to a mirror so that Spack can find it.
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For instructions on how to set up a mirror, see
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http://spack.readthedocs.io/en/latest/mirrors.html"""
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homepage = "https://www.baseclear.com/genomics/bioinformatics/basetools/gapfiller"
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version('1.10', '54d5e2ada131a1305a66e41c0d380382')
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def url_for_version(self, version):
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return "file://{0}/39GapFiller_v{1}_linux-x86_64.tar.gz".format(
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os.getcwd(), version.dashed)
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depends_on('perl+threads', type=('build', 'run'))
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def patch(self):
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with working_dir('.'):
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files = glob.iglob("*.pl")
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for file in files:
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change = FileFilter(file)
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change.filter('usr/bin/perl', 'usr/bin/env perl')
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change.filter('require "getopts.pl";', 'use Getopt::Std;')
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change.filter('&Getopts', 'getopts')
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change.filter('\r', '')
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set_executable(file)
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def install(self, spec, prefix):
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install_tree('bowtie', prefix.bin.bowtie)
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install_tree('bwa', prefix.bin.bwa)
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install('GapFiller.pl', prefix.bin)
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