Docker

[kaitj]

Proposed changes

This updates the Docker file so everything is contained within the singularity image (allowing it to be directly run from the container), with the container itself being around 6GB.

Should be ready for a review of the code, but needs to be tested on actual data prior to merging. Would also like to hold off on merging this so that a 0.1.0 version can first be released (basically everything that was used as part of the OHBM abstract) Also planning to, in a future PR, update all of the containers to make use of this new container.

Resolves #23 and #41.

One thing I would like to do here is to merge this, and before creating the next release update the config with the next docker version so that the workflow actually uses the self-contained with updated dependencies.

Types of changes

What types of changes does your code introduce? Put an x in the boxes that apply

• [ ] Bugfix (non-breaking change which fixes an issue)
• [x] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
• [ ] Other (if none of the other choices apply)

Checklist

Put an x in the boxes that apply. You can also fill these out after creating the PR. If you are unsure about any of the choices, don't hesitate to ask!

• [ ] Changes have been tested to ensure that fix is effective or that a feature works.
• [ ] Changes pass the unit tests
• [ ] Code has been run through the poe quality task
• [x] I have included necessary documentation or comments (as necessary)
• [ ] Any dependent changes have been merged and published

Notes

All PRs will undergo the unit testing before being reviewed. You may be requested to explain or make additional changes before the PR is accepted.

[kaitj]

Would propose holding this off until #44 and #43 are merged in, and this is rebased following the name change. This would be more of a v0.1.1 release.

[kaitj]

@tkkuehn Mind taking another look at this when you get a chance? The Dockerfile was updated and there were some workflow updates as a result as well.