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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 os
class Targetp(Package):
"""TargetP predicts the subcellular location of eukaryotic protein sequences.
Note: A manual download is required for TargetP.
Spack will search your current directory for the download file.
Alternatively, add this file to a mirror so that Spack can find it.
For instructions on how to set up a mirror, see
http://spack.readthedocs.io/en/latest/mirrors.html"""
homepage = "http://www.cbs.dtu.dk/services/TargetP/"
url = "file://{0}/targetp-1.1b.Linux.tar.gz".format(os.getcwd())
manual_download = True
version('1.1b', '80233d0056e11abfd22a4ce73d1808c6')
depends_on('perl', type='run')
depends_on('awk', type='run')
depends_on('chlorop')
depends_on('signalp')
def patch(self):
targetp = FileFilter('targetp')
targetp.filter('TARGETP=', '#TARGETP=')
targetp.filter('CHLOROP=/usr/cbs/bio/bin/chlorop',
self.spec['chlorop'].prefix.bin.chlorop)
targetp.filter('SIGNALP=/usr/cbs/bio/bin/signalp',
self.spec['signalp'].prefix.signalp)
targetp.filter('TMP=/scratch', 'TMP=/tmp')
def install(self, spec, prefix):
install_tree('bin', prefix.bin)
install_tree('etc', prefix.etc)
install_tree('how', prefix.how)
install_tree('test', prefix.test)
install_tree('tmp', prefix.tmp)
install('targetp', prefix.targetp)
def setup_run_environment(self, env):
env.set('TARGETP', self.prefix)
env.prepend_path('PATH', self.prefix)
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