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# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import glob
from spack.package import *
class Mitofates(Package):
"""MitoFates predicts mitochondrial presequence, a cleavable localization
signal located in N-terminal, and its cleaved position."""
homepage = "http://mitf.cbrc.jp/MitoFates/cgi-bin/top.cgi"
url = "http://mitf.cbrc.jp/MitoFates/program/MitoFates_1.2.tar.gz"
version("1.2", sha256="fafc93d8d619fe993ce747782d31ab9a89b248cd4f817e0242e4ceb5e33cf0a7")
depends_on("libsvm")
depends_on("perl", type="run")
depends_on("perl-inline-c", type="run")
depends_on("perl-perl6-slurp", type="run")
depends_on("perl-math-cephes", type="run")
# The DirichletRegulator_fast.pm sets the perl Inline directory
# to be inside the deployed source (which won't be writable by
# the end user of site wide deployed software.
# Removing that config entry will cause the inline module to auto
# create a directory in the user's homedir instead
patch("DirichletRegulator_fast.patch")
def patch(self):
perlscripts = FileFilter("MitoFates.pl")
perlscripts.filter("#!/usr/bin/perl", "#!/usr/bin/env perl")
# other perl module files probably should get this filter too
with working_dir(join_path(self.stage.source_path, "bin/modules")):
perlmodules = glob.glob("*.pm")
filter_file("#!/usr/bin/perl", "#!/usr/bin/env perl", *perlmodules)
def install(self, spec, prefix):
install_tree("bin", prefix.bin)
install("MitoFates.pl", prefix)
chmod = which("chmod")
chmod("+x", join_path(prefix, "MitoFates.pl"))
def setup_run_environment(self, env):
# We want the main MitoFates.pl script in the path
env.prepend_path("PATH", self.prefix)
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