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Diffstat (limited to 'var/spack/repos/builtin/packages/treesub/package.py')
| -rw-r--r-- | var/spack/repos/builtin/packages/treesub/package.py | 41 |
1 files changed, 41 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..99feceddf8 --- /dev/null +++ b/var/spack/repos/builtin/packages/treesub/package.py @@ -0,0 +1,41 @@ +# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +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) |