signalp: new package (#5054)

* signalp: new package

* fixed homepage

* fixed url and phases

* refixed phase

* improved readability

* making path in execuatble adaptable to new versions

1 files changed, 61 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/signalp/package.py b/var/spack/repos/builtin/packages/signalp/package.py
new file mode 100644
index 0000000000..78caa33452
--- /dev/null
+++ b/var/spack/repos/builtin/packages/signalp/package.py
@@ -0,0 +1,61 @@
+##############################################################################
+# Copyright (c) 2013-2016, 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 Signalp(Package):
+    """SignalP predicts the presence and location of signal peptide cleavage
+       sites in amino acid sequences from different organisms: Gram-positive
+       bacteria, Gram-negative bacteria, and eukaryotes.
+       Note: A manual download is required for SignalP.
+       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/SignalP/"
+    url      = "file://{0}/signalp-4.1f.Linux.tar.gz".format(os.getcwd())
+
+    version('4.1f', 'a9aeb66259202649c959846f3f4d9744')
+
+    depends_on('perl', type=('build', 'run'))
+    depends_on('gnuplot')
+
+    def patch(self):
+        edit = FileFilter('signalp')
+        edit.filter("ENV{SIGNALP} = .*",
+                    "ENV{SIGNALP} = '%s'" % self.prefix)
+
+    def install(self, spec, prefix):
+        mkdirp(prefix.share.man)
+        install('signalp', prefix)
+        install('signalp.1', prefix.share.man)
+        install_tree('bin', prefix.bin)
+        install_tree('lib', prefix.lib)
+        install_tree('syn', prefix.syn)
+
+    def setup_environment(self, spack_env, run_env):
+        run_env.prepend_path('PATH', prefix)