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# Copyright 2013-2023 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)
import os
from spack.package import *
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("java", type=("build", "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)
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