setup

#!/usr/bin/env python3
################################################################
#  This file part of GALA Gap-free Long-reads Assembler        #
#  Auther: Mohamed awad                                        #
#  Company: Xiangchao Gan lab (MPIPZ)                          #
#  Released under the (MIT) license (see LICENSE file)         #
################################################################
import os
a=['ccm','comp','mdm','newgenome','gala','readsep','reformat','seprator']
for i in a:
    b=os.getcwd()
    os.system('mkdir -p bin')
    c=''.join(list(open(i)))
    c=c.replace('path=os.getcwd()','path="'+b+'/bin"')
    d=open('bin/'+i,'w')
    d.writelines(c)
    d.close()
    os.system('cp -avr scr bin/' )
    os.system('chmod +x bin/'+i )
    print(i+'\tSuccsessfully installed')

home='/home/'
a=os.listdir(home)
fil=home+a[0]+'/'+'.bashrc'
fil2=home+a[0]+'/'+'.bash_profile'
try:
    b=open(fil,'rw')
except:
    b=open(fil,'w')
try:
    bb=open(fil2,'rw')
except:
    bb=open(fil2,'w')
path=os.getcwd()
c='export PATH="'+os.getcwd()+'/bin:$PATH"'
os.system("echo '"+c+"\n' >> "+fil)
os.system("echo '"+c+"\n' >> "+fil2)
os.system('sh '+fil)
os.system('sh '+fil2)