tmhmm: new package (#5335)

var/spack/repos/builtin/packages/tmhmm/package.py

@@ -0,0 +1,56 @@
+##############################################################################
+# 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 Tmhmm(Package):
+    """Transmembrane helices in proteins
+
+       Note: A manual download is required for TMHMM.
+       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/cgi-bin/nph-sw_request?tmhmm"
+    url      = "file://{0}/tmhmm-2.0c.Linux.tar.gz".format(os.getcwd())
+
+    version('2.0c', '359db0c4ecf84d1ade5786abe844d54e')
+
+    depends_on('perl', type='run')
+
+    def patch(self):
+        with working_dir('bin'):
+            tmhmm = FileFilter('tmhmmformat.pl')
+            tmhmm.filter('#!/usr/local/bin/perl -w',
+                         '#!/usr/bin/env perl')
+            tmhmm = FileFilter('tmhmm')
+            tmhmm.filter('#!/usr/local/bin/perl',
+                         '#!/usr/bin/env perl')
+
+    def install(self, spec, prefix):
+        install_tree('bin', prefix.bin)
+        install_tree('lib', prefix.lib)