diff options
Diffstat (limited to 'var')
| -rw-r--r-- | var/spack/repos/builtin/packages/treesub/package.py | 61 | ||||
| -rwxr-xr-x | var/spack/repos/builtin/packages/treesub/treesub | 2 |
2 files changed, 63 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/treesub/package.py b/var/spack/repos/builtin/packages/treesub/package.py new file mode 100644 index 0000000000..6cec60fa22 --- /dev/null +++ b/var/spack/repos/builtin/packages/treesub/package.py @@ -0,0 +1,61 @@ +############################################################################## +# Copyright (c) 2013-2018, 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 os + + +class Treesub(Package): + """A small program (which glues together other programs) that + allows a user to input a codon alignment in FASTA format and + produce an annotated phylogenetic tree showing which substitutions + occurred on a given branch. Originally written for colleagues at + the MRC NIMR.""" + + homepage = "https:/github.com/tamuri/treesub" + url = "https://github.com/tamuri/treesub/archive/v0.2.tar.gz" + + version('0.2', sha256='58b0d2638cf9ae1ad8705df26a57c32b52a69f50e7954debbd678c82772fdc56') + version('0.1', sha256='c083ecc5f7e9f11645a7e768f6a09fefcbb254b526212003527b4b8dd14723f1') + + depends_on('jdk', type='run') + depends_on('ant', type='build') + depends_on('paml', type='run') + depends_on('raxml', type='run') + depends_on('figtree', type='run') + + def install(self, spec, prefix): + ant = self.spec['ant'].command + ant('jar') + + mkdirp(prefix.bin) + install_tree('dist', prefix.bin) + + mkdirp(prefix.lib) + install_tree('lib', prefix.lib) + + execscript = join_path(self.package_dir, 'treesub') + os.chmod(execscript, 0o775) + install(execscript, prefix.bin) diff --git a/var/spack/repos/builtin/packages/treesub/treesub b/var/spack/repos/builtin/packages/treesub/treesub new file mode 100755 index 0000000000..8be7cb73e6 --- /dev/null +++ b/var/spack/repos/builtin/packages/treesub/treesub @@ -0,0 +1,2 @@ +#!/bin/sh +java -jar $(dirname $0)/treesub.jar |