Mulled Version 3 / BioContainers for non-standard channels

[jmchilton]

We've made a decision to heard developers into a fixed set of "best practice" channels, I think it has been a fine choice. As a result the mulled hash that maps package lists to containers doesn't allow specifying channels (they are assumed to be the "best practice" channels). But other prominent platforms give developers the option to select channels when defining tools / workflows:

• Snakemake allows Conda environment specifications that include channel lists (http://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#integrated-package-management) and has for some time.
• Nextflow recently added Conda support Add the support for Bioconda nextflow-io/nextflow#493 that likewise allows Conda environment specifications (https://github.com/nextflow-io/nextflow/blob/master/docs/conda.rst#use-conda-environment-files) that includes a list of channels.

This is a not the route we took, but it would be nice if the the plumbing we developed would work with such specifications - the mulled-* tools, galaxy-lib dependency and container resolution, multi-package-containers, planemo-monitor, etc... One can imagine a new mulled hash that also incorporated the list of channels in the computation would be all that would needed here right?

I think making our tooling and such compatible with these other platforms is a good goal in its own right, but it might also help current supported tool formats also? I'm not sure I'd want to fight to expose this functionality in Galaxy tools, but for CWL resolution - it would be nice to have a modality that matched the Snakemake / Nextflow paradigm (in addition to the Galaxy paradigm already supported by cwltool and Toil).