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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)
from spack.package import *
class Sepp(Package):
"""SEPP stands for SATe-enabled phylogenetic placement"""
homepage = "https://github.com/smirarab/sepp"
url = "https://github.com/smirarab/sepp/archive/refs/tags/4.5.1.tar.gz"
maintainers("snehring")
version("4.5.1", sha256="51e052569ae89f586a1a94c804f09fe1b7910a3ffff7664e2005f18c7d3f717b")
depends_on("python@3.6:", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-dendropy@4:", type=("build", "run"))
depends_on("java@1.8:", type="run")
depends_on("pasta@1:", type="run")
depends_on("blast-plus@2.10.1:", type="run")
extends("python")
def install(self, spec, prefix):
dirs = ["sepp", "tools"]
for d in dirs:
install_tree(d, join_path(prefix, d))
files = ["default.main.config", "*.py"]
for f in files:
install(f, prefix)
with working_dir(prefix):
prefix_string = "--prefix=" + prefix
python("setup.py", "config", "-c")
python("setup.py", "install", prefix_string)
python("setup.py", "upp", "-c")
for f in ["merge_script.py", "run_ensemble.py"]:
install(f, prefix.bin)
set_executable(join_path(prefix.bin, f))
remove_files = [
"merge_script.py",
"run_ensemble.py",
"run_sepp.py",
"run_upp.py",
"setup.py",
"split_sequences.py",
"distribute_setup.py",
"home.path",
"default.main.config",
]
for f in remove_files:
force_remove(f)
dirs = ["sepp", "tools", "build", "dist", "__pycache__", "sepp.egg-info"]
for d in dirs:
remove_linked_tree(d)
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