a164b0b3e6
* metaeuk: new package * sepp: new package * busco: adding version 5.4.3 * busco: adding maintainers * metauk: more accurate cmake dep * sepp: adding missing dep and accurate python dep * sepp: remove install_tree * sepp: extend python
60 lines
2.0 KiB
Python
60 lines
2.0 KiB
Python
# Copyright 2013-2022 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)
|