[WIP] update utils for building databases

[bluegenes]

Joint effort to update methods for building databases

@mr-eyes @ccbaumler

[ccbaumler]

Here are some notes I took -> https://hackmd.io/RkYRWP8gS1Kad0oENNJc7Q?both

The most relevant would be the new direction database updates are being handled:

1. get two metadata files (ar and bac) from https://data.gtdb.ecogenomic.org/releases/release214/214.0/
2. use the updated make-gtdb-taxonomy.py (which was renamed to get-gtdb-release-diff.py) to create a csv file containing ident (GCA_#) and taxonomy
3. compare with previous database using ident columns this is now also done with get-gtdb-release-diff.py script
   • /group/ctbrowngrp/sourmash-db/gtdb-rs207/gtdb-res207.taxonomy.csv
   • wort manifest
4. Use snakefile download-sketch.smk on the new accessions that need sketching
5. ...