[MRG] workflow for gtdb-rs214 genomic

[bluegenes]

This PR adapts the genbank release process to use wort signatures to build databases.

Components:

• README.md - instructions for running
• environment.yml - file for conda environment
• config.yml - configuration file, with all information specific to gtdb-rs214
• make-gtdb-taxonomy.py- python file to build a taxonomic lineages file from GTDB's bacteria, archea metadata files. This script was written during a session with @mr-eyes @ccbaumler @jeanzzhao
• Snakefile:
  • downloads GTDB metadata and builds taxonomic lineages file (including 'representative' information)
  • builds database zipfiles (with abundance) by checking for signatures in wort
• releases.smk:
  • builds non-abundance zip, sbt, lca databases from the zipfiles

Notes:

• For this release, I manually ran an extra sig extract step on the abundance zipfiles because of sig cat selection relies on md5sum, which can pull in unwanted sigs with duplicated md5 sourmash#2617
  e.g. - sourmash sig extract gtdb-rs214-k21.abund.bak.zip -o gtdb-rs214-k21.abund.zip --picklist gtdb-rs214.manifest.csv:name:name --ksize 21. I have not included that here because it required code in [MRG] modify signature filtering to avoid identical md5sum issues with sig grep, sig extract sourmash#2602, and it will hopefully be solved by the next release.
• As mentioned in we should flatten genome signatures during release process. #1, non-abund zip building feels a bit redundant (as it doesn't save much space) and could potentially be eliminated in a future release.

[bluegenes]

Resources used to build release databases from abundance zipfile.

Full

db	ksize	type	h:m:s	max_vms
gtdb-rs214	21	zip	0:56:07	13286.50
gtdb-rs214	31	zip	0:56:07	13255.00
gtdb-rs214	51	zip	0:56:11	13286.28
gtdb-rs214	21	lca	0:54:09	25892.92
gtdb-rs214	31	lca	0:53:48	28379.27
gtdb-rs214	51	lca	0:54:34	29132.74
gtdb-rs214	21	sbt	1:56:33	46175.95
gtdb-rs214	31	sbt	1:55:51	46084.80
gtdb-rs214	51	sbt	1:56:24	46200.57

Reps

db	ksize	type	h:m:s	max_vms
gtdb-rs214-reps	21	zip	0:10:15	2581.86
gtdb-rs214-reps	31	zip	0:10:19	2582.69
gtdb-rs214-reps	51	zip	0:10:16	2581.24
gtdb-rs214-reps	21	lca	0:11:21	7991.74
gtdb-rs214-reps	31	lca	0:11:58	11023.45
gtdb-rs214-reps	51	lca	0:12:09	11433.45
gtdb-rs214-reps	21	sbt	0:15:04	8962.50
gtdb-rs214-reps	31	sbt	0:15:17	9108.70
gtdb-rs214-reps	51	sbt	0:15:16	9097.23

[bluegenes]

ok @sourmash-bio/devs ready for review

I can also commit the full benchmark table here if desired.