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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 os
from spack.package import *
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
https://spack.readthedocs.io/en/latest/mirrors.html"""
homepage = "https://www.cbs.dtu.dk/services/TargetP/"
url = "file://{0}/targetp-1.1b.Linux.tar.gz".format(os.getcwd())
manual_download = True
version("1.1b", md5="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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