Mount the current IMP codebase via --current option

IMP

@@ -21,8 +21,8 @@ __doc__ = """Integrated Metaomic Pipeline.
 (____)(_/\/\_)(__)
 
 Usage:
-  IMP [-m MG1 -m MG2] [-t MT1 -t MT2] -o OUTPUT [--enter] [--norm] [-r REPO] [-n CONTAINER] [-v VERSION] [-c CONFIGFILE] [-d DBPATH] [-a ASSEMBLER] [-e ENV] ... [COMMANDS ...]
-  IMP --init [-d DBPATH] [-n CONTAINER] [-v VERSION] [-r REPO]
+  IMP [-m MG1 -m MG2] [-t MT1 -t MT2] -o OUTPUT [--enter] [--norm] [--current] [-r REPO] [-n CONTAINER] [-v VERSION] [-c CONFIGFILE] [-d DBPATH] [-a ASSEMBLER] [-e ENV] ... [COMMANDS ...]
+  IMP --init [--current] [-d DBPATH] [-n CONTAINER] [-v VERSION] [-r REPO]
   IMP (-h | --help)
   IMP --version
 
@@ -32,6 +32,7 @@ Options:
   --init            Initialize IMP databases (Take a while).
   --norm            Don't delete the container after use. Useful for debugging.
   --ask             Ask to create directory if it doesn't exist.
+  --current         Use the current version of the IMP codebase (what you have pulled).
   -c CONFIG         Pass a user defined config file. Default: conf/userconfig.imp.json
   -h --help         Show this help and exit
   -m MG             Path to the metagenomics paired files (must be 2 files).
@@ -54,6 +55,8 @@ Typical use:
     ./IMP --init -d /path/to/databases_directory
     ./IMP -m input/mg.r1.fq -m input/mg.r2.fq -t input/mt.r1.fq -t input/mt.r2.fq -o output_directory -d /path/to/databases_directory
 
+    # use the IMP code you have pulled instead of the one shipped inside the container.
+    ./IMP -m input/mg.r1.fq -m input/mg.r2.fq -t input/mt.r1.fq -t input/mt.r2.fq -o output_directory --current
 
 """.format(
     name=IMP_IMAGE_NAME,
@@ -140,16 +143,22 @@ def init(args):
     Must be run at least once.
     """
     CURRENT_PATH = Path(__file__).parent.abspath()
-    version = args['-v']
-    container_name = args['-n']
     database_path = Path(args['-d']).abspath()
-
-    docker_cmd = 'docker run --rm -v {p}:/code -v {d}:/databases {n}:{v}'.format(
-        p=CURRENT_PATH,
-        d=database_path,
-        n=args['-n'],
-        v=args['-v']
-    )
+    # prepare docker command
+    docker_cmd = 'docker run --rm -v {d}:/databases {n}:{v}'
+    formatting_args = {
+        'd': database_path,
+        'n': args['-n'],
+        'v': args['-v']
+    }
+    # override docker command if the user want to mount a specific version of IMP codebase.
+    if args[--'current']:
+        formatting_args['p'] = CURRENT_PATH
+        docker_cmd = 'docker run --rm -v {p}:/code -v {d}:/databases {n}:{v}'
+
+    # format docker command
+    docker_cmd.format(**formatting_args)
+    # IMP command + user mapping (see https://github.com/docker/docker/pull/12648)
     cmd = docker_cmd + map_user('snakemake -s /code/rules/init', '/databases')
     print("Executing", '"', cmd, '"')
     subprocess.call(cmd, shell=True)
@@ -183,12 +192,14 @@ def run(args):
     # configure IMP mount point to the docker container
     mount_points = [
         '-v %s:/data' % common_path,
-        '-v %s:/code' % CURRENT_PATH,
         '-v %s:/output' % output,
         '-v %s:/databases' % database_path,
     ]
+    # add code mount point if the user want to mount a specific version of IMP codebase.
+    if args[--'current']:
+        mount_points.append('-v %s:/code' % CURRENT_PATH)
 
-    # environement variables: add MG and MT data and config if specified
+    # environment variables: add MG and MT data and config if specified
     envs = ['-e {}="{}"'.format(*e.split('=')) for e in args['-e']]
 
     # prepare MG and MT data