targetp: new package (#5334)

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)