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
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
|
#!/usr/bin/env python3
import setuptools
setuptools.setup(
name='gubbins',
version = open('VERSION').read().strip(),
description='Frontend to the Gubbins BioInformatics tool',
author='Andrew Page, Nicholas Croucher, Aidan Delaney, Christoph Puethe and Simon Harris',
author_email='n.croucher@imperial.ac.uk',
url='https://github.com/nickjcroucher/gubbins/',
packages=setuptools.find_packages(),
entry_points={
"console_scripts": [
"run_gubbins.py = gubbins.run_gubbins:main",
]
},
scripts=[
'scripts/generate_ska_alignment.py',
'scripts/extract_gubbins_clade.py',
'scripts/mask_gubbins_aln.py',
'scripts/gubbins_alignment_checker.py',
'scripts/generate_files_for_clade_analysis.py',
'scripts/count_recombinations_per_gene.py',
'scripts/extract_recombinant_sequences.py',
'../R/scripts/plot_gubbins.R'
],
tests_require=[
"pytest >= 4.6",
"wheel >= 0.34",
"biopython >= 1.59",
"dendropy >= 4.0.2",
"multiprocess >= 0.70",
"scipy >= 1.5.3",
"numpy >= 1.19",
"ska >= 1.0"
],
long_description="""\
Gubbins is a tool that generates a reconstruction of
a microbial strain's recent evolutionary history through
identifying imports of divergent sequence through recombination
and generating a phylogeny from the remaining clonal frame.
""",
classifiers=[
"License :: OSI Approved :: GNU General Public License (GPL)",
"Programming Language :: Python :: 3",
"Development Status :: 4 - Beta",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Bio-Informatics",
],
install_requires=[
"biopython >= 1.59",
"dendropy >= 4.0.2",
"multiprocess >= 0.70",
"scipy >= 1.5.3",
"numpy >= 1.19"
],
license="GPL"
)
|
