Docker build error about singe HOT 2 CLOSED

Thanks for testing the Dockerfile @adyprat.

I checked out v0.3.0 and can reproduce this error when I run docker build --no-cache -t singe -f docker/Dockerfile . I did not see this earlier in my local testing because the image caches were skipping this build step. The same was true in our Travis CI builds because we build using the tmp tagged image from Docker Hub:

I'll troubleshoot this issue and work on an updated Dockerfile. This romaricp/kit-starter-symfony-4-docker#10 (comment) seems to fix the problem for me, but I want to test it more.

In the bigger picture, the next SINGE release (v0.4.0) will likely be the first one that is ready to integrate directly into BEELINE. Are there any BEELINE-related deadlines or timelines that we should be aware of that would require accelerating our next release?

Release v0.3.0 had a proof-of-concept of running SINGE inside Docker, but it was not set up for easy general use on new input data. The next release will make it much easier to run SINGE with user-provided data. To run the complete SINGE algorithm (multiple GLG runs with different hyperparameters and subsamples of the data followed by aggregation) we'll have syntax that is something like:

docker run agitter/singe standalone data gene_list outdir hyperparameter_file

where standalone is a SINGE mode that runs the full pipeline. We also plan a GLG and aggregate mode in case users want to parallelize the GLG calls across multiple servers (like we do).

Would that interface work for BEELINE?

from singe.

@adyprat I made a pull request to fix this specific problem and close this issue. However, we can still use this issue to discuss SINGE, Docker, and BEELINE more generally.

from singe.