diff --git a/var/spack/repos/builtin/packages/targetp/package.py b/var/spack/repos/builtin/packages/targetp/package.py new file mode 100644 index 0000000000..24bee3aa6b --- /dev/null +++ b/var/spack/repos/builtin/packages/targetp/package.py @@ -0,0 +1,67 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the NOTICE and LICENSE files for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +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()) + + 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_environment(self, spack_env, run_env): + run_env.set('TARGETP', self.prefix) + run_env.prepend_path('PATH', self.prefix)