Bundle runtimes with pathogen repos

[victorlin]

This is in early stages, so preliminary discussions are in an internal Google doc.

Mentions

• Include external tools in the Nextstrain Snakemake workflow - Nextstrain Discussion

Current workarounds

As Tom notes, we should not continue down this path and let it proliferate.

• Configure Nextstrain CLI to use the ambient environment
• Create a custom Docker image extending nextstrain/base
  • ncov-ingest
  • victorlin/nextstrain-custom-docker, used by
    • blab/flu-geo-fitness
    • nextstrain/tb
• Create a custom Conda environment extending nextstrain-base
  • zika-tutorial

[tsibley]

I wrote up some of my thoughts in my own notes to share out. (Comments in that Google doc seem too limiting for what I had to say.)

[tsibley]

That said, I think it's a bit too early to be working on this yet. While it's possible to start on it, I'd think to keep pushing on all the work for the first half of workflows as programs and solidify that more first rather than split efforts.

[tsibley]

Heads up that I added a clarification preamble to my previously-linked thoughts.