From 5267681abe50542bc2c9e3d17b82aab8907f51a1 Mon Sep 17 00:00:00 2001 From: Audrey Thoma Date: Wed, 20 Sep 2017 16:45:13 -0500 Subject: [PATCH] tmhmm: new package (#5335) --- .../repos/builtin/packages/tmhmm/package.py | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 var/spack/repos/builtin/packages/tmhmm/package.py diff --git a/var/spack/repos/builtin/packages/tmhmm/package.py b/var/spack/repos/builtin/packages/tmhmm/package.py new file mode 100644 index 0000000000..64953733db --- /dev/null +++ b/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)