C. Titus Brown

https://www.biorxiv.org/content/10.1101/2021.06.22.449360v2

...as alternate/additional contamination analysis per https://github.com/ctb/2022-sourmash-sens-spec/issues/1

update `env-reporting.yml` version pins

3

[env-reporting.yml](https://github.com/dib-lab/charcoal/blob/latest/charcoal/conf/env-reporting.yml) is the largest and most complex conda environment we have in charcoal, and it pins a lot of things... and it's pretty out of date. this is causing trouble...

ref https://github.com/dib-lab/charcoal/issues/212, https://github.com/sourmash-bio/sourmash/pull/2255 this would be a good time to think about prototyping https://github.com/sourmash-bio/sourmash/issues/1005 maybe 😆

add test requirements to ...environment? pip install? something?

1

currently, pytest and pytest_dependency both need to be installed manually.

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006277 https://twitter.com/StevenSalzberg1/status/1391484373648781314

create a bioconda package and/or install charcoal within the environment.yml

1

now that we provide our own (non-snakemake) entry point, charcoal itself needs to be installed in order to run stuff. in the short term, I think we can use the...

https://www.biorxiv.org/content/10.1101/2022.01.24.477489v1

With the merge of https://github.com/sourmash-bio/sourmash/pull/1543 and https://github.com/sourmash-bio/sourmash/pull/1651, among others, we have a lot of ~duplicated functionality between charcoal and sourmash. We should change charcoal over to using sourmash functions where...

This PR updates snakemake to 6.10.0. There are a few other misc changes - - limit Python to < 3.10 for now - add a print statement that makes genome...