Solution to slow download speeds for GTDB

[jcmcnch]

Hi,

For one of the steps where ATLAS is downloading the partial GTDB files, it's incredibly slow (see here for description of issue on GTDB's github issue page). This seems to be system-dependent, so users on Windows may not notice it but I'm on Linux and it's painfully slow (kb/sec) which slows the whole workflow down.

Here's how I solved it:

#edit download snakemake file
vi ~/miniconda3/envs/atlasenv/lib/python3.10/site-packages/atlas/workflow/rules/download.smk

#replace line 21 with the following (this is GTDB's mirror of the ecogenomic.org link)
GTDB_DATA_URL = "https://data.ace.uq.edu.au/public/gtdb/data/releases/release220/220.0/auxillary_files/gtdbtk_package"

I then deactivated the conda env, restarted and now getting reasonable download speeds of Mb/sec.

Hope this can help someone else who is seeing ATLAS slow down without an obvious explanation. Devs, perhaps consider changing in the main branch if not done already?

Jesse