forked from artic-network/civet
-
Notifications
You must be signed in to change notification settings - Fork 0
/
setup.py
63 lines (61 loc) · 2.11 KB
/
setup.py
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
60
61
62
63
from setuptools import setup, find_packages
from setuptools.command.build_py import build_py
import glob
import os
import pkg_resources
# Note: the _program variable is set in __init__.py.
# it determines the name of the package/final command line tool.
from civet import __version__, _program
class NPMInstall(build_py):
def run(self):
self.run_command('npm install -g markdown-pdf --ignore-scripts')
build_py.run(self)
setup(name='civet',
version=__version__,
packages=find_packages(),
scripts=["civet/scripts/Snakefile",
"civet/scripts/assess_input_file.smk",
"civet/scripts/find_closest_cog.smk",
"civet/scripts/cluster_civet.smk",
"civet/scripts/process_collapsed_trees.smk",
"civet/scripts/just_collapse_trees.smk",
"civet/scripts/find_snps.smk",
"civet/scripts/make_report.py",
"civet/scripts/local_scale_analysis.py",
"civet/scripts/check_cog_db.py",
"civet/scripts/civet_template.pmd",
"civet/scripts/parse_closest.py",
"civet/scripts/mapping.py",
"civet/scripts/civetfunks.py"],
package_data={"civet":["data/*","data/headers/*","data/mapping_files/*","data/vega_templates/*"]},
install_requires=[
"biopython>=1.70",
"dendropy>=4.4.0",
"pytools>=2020.1",
'pandas>=1.0.1',
'pysam>=0.15.4',
"matplotlib>=3.2.1",
"pweave>=0.30.3",
"scipy>=1.4.1",
"numpy>=1.13.3",
"geopandas>=0.7.0",
"descartes>=1.1.0",
"adjustText>=0.7.3",
"grip>=4.5.2",
"tabulate>=0.8.7",
"snipit>=1.0.3"
],
cmdclass={
'npm_install': NPMInstall
},
description='Cluster Investivation & Virus Epidemiology Tool',
url='https://github.com/aineniamh/civet',
author='Aine OToole, Verity Hill',
author_email='aine.otoole@ed.ac.uk',
entry_points="""
[console_scripts]
{program} = civet.command:main
""".format(program = _program),
include_package_data=True,
keywords=[],
zip_safe=False)