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| -rw-r--r-- | var/spack/repos/builtin/packages/guidance/package.py | 66 |
1 files changed, 66 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/guidance/package.py b/var/spack/repos/builtin/packages/guidance/package.py new file mode 100644 index 0000000000..6cb4e0cfc6 --- /dev/null +++ b/var/spack/repos/builtin/packages/guidance/package.py @@ -0,0 +1,66 @@ +############################################################################## +# 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/spack/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 glob + + +class Guidance(MakefilePackage): + """Guidance: Accurate detection of unreliable alignment regions accounting + for the uncertainty of multiple parameters.""" + + homepage = "http://guidance.tau.ac.il/ver2/" + url = "http://guidance.tau.ac.il/ver2/guidance.v2.02.tar.gz" + + version('2.02', 'aa6ae2168e8e0237ee56bc2ac81202cf') + + depends_on('perl', type=('build', 'run')) + depends_on('perl-bio-perl', type=('build', 'run')) + depends_on('ruby') + depends_on('prank') + depends_on('clustalw') + depends_on('mafft') + depends_on('muscle') + + conflicts('%gcc@6.2.0:') + + def edit(self, spec, prefix): + for dir in 'Guidance', 'Selecton', 'bioSequence_scripts_and_constants': + with working_dir(join_path('www', dir)): + files = glob.iglob('*.pl') + for file in files: + perl = FileFilter(file) + perl.filter('#!/usr/bin/perl -w', '#!/usr/bin/env perl') + + def install(self, spac, prefix): + mkdir(prefix.bin) + install_tree('libs', prefix.bin.libs) + install_tree('programs', prefix.bin.programs) + install_tree('www', prefix.bin.www) + with working_dir(join_path('www', 'Guidance')): # copy without suffix + install('guidance.pl', join_path(prefix.bin.www.Guidance, + 'guidance')) + + def setup_environment(self, spack_env, run_env): + run_env.prepend_path('PATH', prefix.bin.www.Guidance) |