1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
|
# 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 PyDrep(PythonPackage):
"""dRep is a python program for rapidly comparing large numbers of genomes.
dRep can also "de-replicate" a genome set by identifying groups of highly
similar genomes and choosing the best representative genome for each
genome set."""
homepage = "https://github.com/MrOlm/drep"
pypi = "drep/drep-3.4.0.tar.gz"
version("3.4.0", sha256="a6533eb585122c1ee66ae622b1b97450a3e1e493a3c3c1d55e79a580d5c46d40")
variant("fastani", default=True, description="Enable fastANI support")
variant("py-checkm-genome", default=True, description="Enable CheckM support")
variant("anicalculator", default=True, description="Enable gDNA support")
variant("prodigal", default=True, description="Used with both checkM and gANI")
depends_on("py-setuptools", type="build")
depends_on("py-numpy", type=("build", "run"))
depends_on("py-pandas", type=("build", "run"))
depends_on("py-seaborn", type=("build", "run"))
depends_on("py-matplotlib", type=("build", "run"))
depends_on("py-biopython", type=("build", "run"))
depends_on("py-scikit-learn", type=("build", "run"))
depends_on("py-tqdm", type=("build", "run"))
depends_on("py-pytest", type=("build", "run"))
# Non-python dependencies
# https://drep.readthedocs.io/en/latest/installation.html#dependencies
# essential dependencies
depends_on("mash@1.1.1:", type="run")
depends_on("mummer@3.23:", type="run")
# recommended dependencies
depends_on("fastani", type="run", when="+fastani")
depends_on("py-checkm-genome@1.0.7:", type="run", when="+py-checkm-genome")
depends_on("anicalculator@1:", type="run", when="+anicalculator")
depends_on("prodigal@2.6.3:", type="run", when="+prodigal")
|
