Update MEDI to new DB builder and NCBI Taxonomy

[cdiener]

TODO:

• update architeuthis
• explain need for Kraken2 patches
• document the new Docker image
• provide a small example DB

[szimmerman92]

Hello. I have been making some edits to MEDI to fix the rsync issues caused by making to many requests to download genomes. I switched rsync to databases CLI like as done in this pull request, but I noticed the dehydrate option was not included if I am reading your commits correctly.

If you do something like

datasets download genome accession --inputfile accessions.txt --dehydrated --filename my-genomes.zip
unzip my-genomes.zip -d my-genomes
datasets rehydrate --directory my-genomes/

the genomes download very fast, compared to not using the dehydrated/rehydrate commands.

I hope this helps.

Best,
Sam