53 lines
1.9 KiB
Python
53 lines
1.9 KiB
Python
# Copyright 2013-2024 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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import glob
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import os
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from spack.package import *
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class SspaceStandard(Package):
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"""SSPACE standard is a stand-alone program for scaffolding pre-assembled
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contigs using NGS paired-read data
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Note: A manual download is required for SSPACE-Standard.
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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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https://spack.readthedocs.io/en/latest/mirrors.html"""
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homepage = "https://www.baseclear.com/genomics/bioinformatics/basetools/SSPACE"
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url = "file://{0}/41SSPACE-STANDARD-3.0_linux-x86_64.tar.gz".format(os.getcwd())
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manual_download = True
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version("3.0", md5="7e171b4861b9d514e80aafc3d9cdf554")
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depends_on("perl+threads", type=("build", "run"))
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depends_on("perl-perl4-corelibs", type=("build", "run"))
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def install(self, spec, prefix):
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rootscript = "SSPACE_Standard_v{0}.pl".format(self.version)
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scripts = [rootscript]
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scripts.extend(glob.glob("tools/*.pl"))
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scripts.extend(glob.glob("bwa/*.pl"))
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for s in scripts:
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filter_file("/usr/bin/perl", "/usr/bin/env perl", s, string=True)
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filter_file('require "getopts.pl";', "use Getopt::Std;", s, string=True)
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filter_file("&Getopts(", "getopts(", s, string=True)
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install_tree("bin", prefix.bin)
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install_tree("bowtie", prefix.bowtie)
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install_tree("bwa", prefix.bwa)
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install_tree("dotlib", prefix.dotlib)
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install_tree("tools", prefix.tools)
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install(rootscript, prefix)
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def setup_run_environment(self, env):
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env.set("SSPACE_HOME", self.prefix)
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env.prepend_path("PATH", self.prefix)
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