Out-of-the-box Docker build can't find the config file

[tetron]

crunch@97452befd42c:/tmp/crunch-job/project1/work$ bcbio_nextgen.py ../config/project1.yaml
Traceback (most recent call last):
File "/usr/local/bin/bcbio_nextgen.py", line 62, in
main(**kwargs)
File "/usr/local/bin/bcbio_nextgen.py", line 40, in main
run_main(**kwargs)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 31, in run_main
config, config_file = load_system_config(config_file, workdir)
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/pipeline/config_utils.py", line 60, in load_system_config
(config_file, os.path.join(base_dir, "galaxy")))
ValueError: Could not find input system configuration file bcbio_system.yaml, including inside standard directory /usr/local/share/bcbio-nextgen/galaxy

[chapmanb]

Peter;
There is a wrapper around docker called bcbio-nextgen-vm which is meant to run against the docker images:

https://github.com/chapmanb/bcbio-nextgen-vm

It keeps bcbio_system.yaml outside of the container allowing it to be edited by users, since it relates to the external system. The general idea behind the bcbio-nextgen-vm wrapper is to keep data, workflow and parallelization outside the container. All of the tools and biological logic in bcbio-nextgen is inside the container. I'd hope the bcbio-nextgen-vm wrapper is where we could abstract Arvados integration.

Let me know if this works or if better organization would make more sense. Thanks much.