50 lines
1.8 KiB
Python
50 lines
1.8 KiB
Python
# Copyright 2013-2022 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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from os import chmod
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from spack.package import *
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class Mirdeep2(Package):
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"""miRDeep2 is a completely overhauled tool which discovers microRNA genes
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by analyzing sequenced RNAs."""
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homepage = "https://www.mdc-berlin.de/8551903/en/"
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url = "https://www.mdc-berlin.de/system/files/migrated_files/fiona/mirdeep2_0_0_8.zip"
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version("0.0.8", sha256="eeb24ee1b0e76b49ee2f542da3ee7d46d163c80b152709e963492b79f4fca1b8")
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depends_on("perl", type=("build", "run"))
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depends_on("perl-pdf-api2", type=("build", "run"))
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depends_on("bowtie")
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depends_on("viennarna")
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depends_on("squid")
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depends_on("randfold")
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def url_for_version(self, version):
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url = "https://www.mdc-berlin.de/system/files/migrated_files/fiona/mirdeep2_{0}.zip"
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return url.format(version.underscored)
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def patch(self):
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with working_dir("src"):
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files = glob.iglob("*.pl")
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for file in files:
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chmod(file, 0o755)
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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("perl -W", "perl")
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change.filter("../Rfam_for_miRDeep.fa", "Rfam_for_miRDeep.fa")
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change.filter("../install_successful", "install_successful")
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def install(self, spec, prefix):
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install_tree("src", prefix.bin)
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install("Rfam_for_miRDeep.fa", prefix.bin)
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# miRDeep looks for the install_sucessful file to check if you used
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# their automated install script which we'll just be kind of hacking
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# around
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touch(prefix.bin.install_successful)
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