fix user issue

IMP

@@ -3,6 +3,7 @@ from lib.docopt import docopt
 from lib.path import Path
 import subprocess
 import os
+import getpass
 import json
 import shlex
 from copy import deepcopy
@@ -68,6 +69,12 @@ def yes_or_no(question):
         return yes_or_no("Please enter ")
 
 
+def format_command(cmd, dir):
+    # get group id and username of the user
+    username = getpass.getuser()
+    return ' /bin/bash -c "{c} ; useradd {u} && chown -R {u} {d} && chmod 755 {d}"'.format(c=cmd, u=username, d=dir)
+
+
 def init(args):
     CURRENT_PATH = Path(__file__).parent.abspath()
     # start docker container to index files and setup prokka
@@ -76,10 +83,11 @@ def init(args):
     cmd = [
         'docker', 'run', '--rm',
         '-v %s:/code' % CURRENT_PATH,
-        '-v %s:/databases' % db_path, container_name, 'snakemake -s /code/init.rule'
+        '-v %s:/databases' % db_path, container_name
     ]
-    print("Executing", '"', ' '.join(cmd), '"')
-    subprocess.call(shlex.split(' '.join(cmd)))
+    cmd = ' '.join(cmd) + format_command('snakemake -s /code/init.rule', '/databases')
+    print("Executing", '"', cmd, '"')
+    subprocess.call(cmd, shell=True)
 
 
 def run(args):
@@ -136,14 +144,15 @@ def run(args):
     if args['--enter']:
         cmd += ['-it']
     # add container name and commands to pass to snakemake
-    cmd += [container_name] + args['COMMANDS']
+    cmd += [container_name]
     # if --enter flag is specified, change the command
     if args['--enter']:
         cmd += ['/bin/bash']
-    # parse CL correctly
-    cmd = shlex.split(' '.join(cmd))
-    print("Executing", '"', ' '.join(cmd), '"')
-    subprocess.call(cmd)
+
+    cmd = ' '.join(cmd) + format_command(' '.join(args['COMMANDS']), '/output')
+
+    print("Executing", '"', cmd, '"')
+    subprocess.call(cmd, shell=True)
 
 
 def validate(args):