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LMToolKit_Setup.py
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LMToolKit_Setup.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jan 22 10:19:44 2021
@author: sb069
"""
import os
import errno
from os.path import expanduser
os.system("sudo apt-get update")
os.system("sudo apt install nvidia-cuda-toolkit")
os.system("sudo apt install python3.8")
os.system("conda install flye")
try:
os.system("mkdir -p ~/Documents/LMToolkit")
except OSError as e:
if e.errno != errno.EEXIST:
raise
try:
os.system("mkdir -p ~/Documents/LMToolkit/MinionOut")
except OSError as e:
if e.errno != errno.EEXIST:
raise
try:
os.system("mkdir -p ~/Documents/LMToolkit/Assembly_Out")
except OSError as e:
if e.errno != errno.EEXIST:
raise
#Downloads=str(os.environ['_'])
#Downloads=Download.replace('/LMToolkit_Setup.py','')
#print("THIS IS A TEST " + Downloads)
#os.chdir(Downloads)
#print("mv LMToolKit.py ~/Documents/LMToolkit")
try:
os.system("mv LMToolkit.py ~/Documents/LMToolkit/LMToolkit.py")
except OSError as e:
if e.errno != errno.EEXIST:
raise
try:
os.system("mv README.md ~/Documents/LMToolkit/README.md")
except OSError as e:
if e.errno != errno.EEXIST:
raise
try:
os.system("mv LMToolKit_License ~/Documents/LMToolkit/LMToolKit_License")
except OSError as e:
if e.errno != errno.EEXIST:
raise
def main():
hdir=os.path.expanduser('~')
os.chdir(hdir+'/Documents/LMToolkit')
with open("config.txt", 'w') as config1:
Basecall=input("What is the path of your guppy basecaller (ont-guppy/bin/guppy_basecaller)?: ")
config1.write(Basecall)
config1.close()
with open("guppyconfig.txt", "w") as config2:
Basecallconfig=input("What is the path of your guppy basecaller config file (ont-guppy/data/config) please read readme for details )?: ")
config2.write(Basecallconfig)
config2.close()
print("LMToolKit is now setup! Happy Basecalling!")
main()