/code

IMP

@@ -16,7 +16,6 @@ __doc__ = """Integrated Metaomic Pipeline.
 
 Usage:
   IMP -m MG1 -m MG2 -t MT1 -t MT2 -o OUTPUT [--enter] [--norm] [-n CONTAINER] [-d DBPATH] [-e ENV] ... [COMMANDS ...]
-  IMP (-m MG1 -m MG2 | -t MT1 -t MT2) -o OUTPUT [--enter] [--norm] [-n CONTAINER] [-d DBPATH] [-e ENV] ... [COMMANDS ...]
   IMP --init [-d DBPATH]
   IMP (-h | --help)
   IMP --version
@@ -73,8 +72,8 @@ def init(args):
     db_path = Path(args['-d']).abspath()
     cmd = [
         'docker', 'run', '--rm',
-        '-v %s:/home/imp/integrated-metaomic-pipeline' % CURRENT_PATH,
-        '-v %s:/databases' % db_path, container_name, 'snakemake -s /home/imp/integrated-metaomic-pipeline/init.rule'
+        '-v %s:/code' % CURRENT_PATH,
+        '-v %s:/databases' % db_path, container_name, 'snakemake -s /code/init.rule'
     ]
     print("Executing", '"', ' '.join(cmd), '"')
     subprocess.call(shlex.split(' '.join(cmd)))
@@ -106,7 +105,7 @@ def run(args):
     # configure IMP mount point to the docker container
     mount_points = [
         '-v %s:/data' % common_path,
-        '-v %s:/home/imp/integrated-metaomic-pipeline' % CURRENT_PATH,
+        '-v %s:/code' % CURRENT_PATH,
         '-v %s:/output' % output,
         '-v %s:/databases' % db_path,
     ]

docker/Dockerfile

@@ -214,6 +214,6 @@ RUN echo "`snakemake --bash-completion`" >> ~/.bashrc \
 ######################
 ENV PATH /home/imp/lib/trinityrnaseq_r20140717:/home/imp/lib/Platypus_0.8.1:/home/imp/lib/megahit:$PATH
 
-VOLUME ["/data", "/output"]
-WORKDIR /home/imp/integrated-metaomic-pipeline
+VOLUME ["/data", "/output", "/databases", "/code"]
+WORKDIR /code
 CMD ["snakemake", "ALL"]