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# Copyright 2013-2021 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)
from spack import *
import glob
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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