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from setuptools import setup
import os
import sys
if sys.version_info < (3,5):
print("This python version is not supported:")
print(sys.version)
print("pVACtools requires python 3.5 or greater")
sys.exit(1)
pvacseq_data_files = []
for dirpath, dirnames, filenames in os.walk("tools/pvacseq/example_data"):
for filename in filenames:
if not (filename.endswith(".py") or filename.endswith(".pyc")):
pvacseq_data_files.append(os.path.join(os.path.relpath(dirpath, 'tools/pvacseq'), filename))
pvacfuse_data_files = []
for dirpath, dirnames, filenames in os.walk("tools/pvacfuse/example_data"):
for filename in filenames:
if not (filename.endswith(".py") or filename.endswith(".pyc")):
pvacfuse_data_files.append(os.path.join(os.path.relpath(dirpath, 'tools/pvacseq'), filename))
pvacvector_data_files = []
for dirpath, dirnames, filenames in os.walk("tools/pvacvector/example_data"):
for filename in filenames:
if not (filename.endswith(".py") or filename.endswith(".pyc")):
pvacvector_data_files.append(os.path.join(os.path.relpath(dirpath, 'tools/pvacseq'), filename))
for dirpath, dirnames, filenames in os.walk("tools/pvacseq/VEP_plugins"):
for filename in filenames:
if not (filename.endswith(".py") or filename.endswith(".pyc")):
pvacseq_data_files.append(os.path.join(os.path.relpath(dirpath, 'tools/pvacseq'), filename))
for dirpath, dirnames, filenames in os.walk("tools/pvacseq/iedb_alleles"):
for filename in filenames:
if not (filename.endswith(".py") or filename.endswith(".pyc")):
pvacseq_data_files.append(os.path.join(os.path.relpath(dirpath, 'tools/pvacseq'), filename))
server_data = []
for dirpath, dirnames, filenames in os.walk("utils/pvacapi"):
for filename in filenames:
if not (filename.endswith(".py") or filename.endswith(".pyc")):
server_data.append(os.path.join(
os.path.relpath(
dirpath,
'utils/pvacapi'
),
filename
))
client_data = []
for dirpath, dirnames, filenames in os.walk("utils/pvacviz/client"):
for filename in filenames:
if not (filename.endswith(".py") or filename.endswith(".pyc")):
client_data.append(os.path.join(
os.path.relpath(
dirpath,
'utils/pvacapi/client'
),
filename
))
setup(
name="pvactools",
version="1.1.1",
packages=[
"tools",
"tools.pvacfuse",
"tools.pvacvector",
"tools.pvacseq",
"lib",
"utils.pvacapi",
"utils.pvacapi.controllers",
"utils.pvacviz"
],
entry_points={
"console_scripts":[
"pvactools = tools.main:main",
"pvacseq = tools.pvacseq.main:main",
"pvacfuse = tools.pvacfuse.main:main",
"pvacvector = tools.pvacvector.main:main",
"pvacapi = utils.pvacapi.app:main [API]",
"pvacviz = utils.pvacviz.app:main [API]"
]
},
install_requires=[
'PyVCF',
'requests',
'PyYAML',
'connexion==1.4.2',
'biopython',
'networkx',
'simanneal',
'pandas',
'wget',
'mhcflurry',
'mhcnuggets',
'pysam',
'tensorflow==1.8.0'
],
package_data={
'tools.pvacseq': pvacseq_data_files,
'tools.pvacfuse': pvacfuse_data_files,
'tools.pvacvector': pvacvector_data_files,
'utils.pvacapi': server_data,
'utils.pvacviz': client_data,
},
extras_require={
'API':[
'connexion==1.4.2',
'py-postgresql',
'watchdog',
'flask-cors',
'bokeh==0.13.0',
'tornado==5.0.2',
'swagger-spec-validator==2.1.0',
]
},
classifiers=[
'Development Status :: 4 - Beta',
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering :: Bio-Informatics',
"Programming Language :: Python :: 3.5"
],
author = "Jasreet Hundal, Susanna Kiwala, Joshua McMichael, Yang-Yang Feng, Christopher A. Miller, Aaron Graubert, Amber Wollam, Connor Liu, Jonas Neichin, Megan Neveau, Jason Walker, Elaine R. Mardis, Obi L. Griffith, Malachi Griffith",
author_email = "help@pvactools.org",
description = "A cancer immunotherapy tools suite",
license = "NPOSL-3.0",
keywords = "antigens neoantigens cancer sequencing variant variants fusion fusions",
#This needs to be the url where the code is being hosted
url = "https://github.com/griffithlab/pVACtools",
)