51 lines
1.9 KiB
Python
51 lines
1.9 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 spack.package import *
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class Mitofates(Package):
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"""MitoFates predicts mitochondrial presequence, a cleavable localization
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signal located in N-terminal, and its cleaved position."""
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homepage = "http://mitf.cbrc.jp/MitoFates/cgi-bin/top.cgi"
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url = "http://mitf.cbrc.jp/MitoFates/program/MitoFates_1.2.tar.gz"
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version("1.2", sha256="fafc93d8d619fe993ce747782d31ab9a89b248cd4f817e0242e4ceb5e33cf0a7")
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depends_on("libsvm")
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depends_on("perl", type="run")
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depends_on("perl-inline-c", type="run")
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depends_on("perl-perl6-slurp", type="run")
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depends_on("perl-math-cephes", type="run")
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# The DirichletRegulator_fast.pm sets the perl Inline directory
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# to be inside the deployed source (which won't be writable by
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# the end user of site wide deployed software.
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# Removing that config entry will cause the inline module to auto
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# create a directory in the user's homedir instead
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patch("DirichletRegulator_fast.patch")
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def patch(self):
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perlscripts = FileFilter("MitoFates.pl")
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perlscripts.filter("#!/usr/bin/perl", "#!/usr/bin/env perl")
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# other perl module files probably should get this filter too
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with working_dir(join_path(self.stage.source_path, "bin/modules")):
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perlmodules = glob.glob("*.pm")
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filter_file("#!/usr/bin/perl", "#!/usr/bin/env perl", *perlmodules)
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def install(self, spec, prefix):
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install_tree("bin", prefix.bin)
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install("MitoFates.pl", prefix)
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chmod = which("chmod")
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chmod("+x", join_path(prefix, "MitoFates.pl"))
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def setup_run_environment(self, env):
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# We want the main MitoFates.pl script in the path
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env.prepend_path("PATH", self.prefix)
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