bsipos
commented
6 years ago Hello,
I assume you are still mounting a data directory to your container. If that is writable a simple workaround would be to check out the repository under that. This would allow you to edit the config file. Let me know if this works for you.
Regards, Botond
rusalkaguy
Good docker container practices say that I shouldn't have to modify the container to use it to run my analysis. There should be a run/exec command where I specify an external location for my config.mk, and all temp files and results are also outside the container.
Context: I work in an academic translational research lab. We use the university's HPC cluster. They do not support docker (for security reasons), but they do support Singularity, which enforces read-only contianers. So, I had no trouble using your Dockerfile to build a docker container and then build a singularity container from that, and I can start it up on my cluster. But now I'm a little stuck, as I can't modify config.mk.
Perhaps there's a flag I haven't found to run it with an externalized config.mk? (it would be nice to have a simple example worked out in the README.md, perhaps with a small amount of test data to validate everything is functioning, etc).