improved documentation for configuring conf.yml

[clb21565]

hi there, might be me, but i'm having a hard time knowing how to format the conf.yml file to run sourmash with settings other than defaults

i found this link
https://github.com/dib-lab/genome-grist/blob/latest/genome_grist/conf/defaults.conf

which looks to be the defaults in the correct format?

metagenome_trim_memory: 10e9
sourmash_compute_ksizes:

• 21
• 31
• 51
  sourmash_scaled: 1000

by default, leave stuff in /tmp

tempdir:

• /tmp

cache genbank genome info in ./genbank_cache/ by default

genbank_cache: ./genbank_cache/

allow automatic download from SRA

prevent_sra_download: false

in any case, would be maybe helpful to have some additional documentation on it

[ctb]

hi @clb21565 - do these docs help?

https://dib-lab.github.io/genome-grist/configuring/#reference-the-complete-set-of-config-file-options

note that it's in YAML format - see https://yaml.org/. Happy to answer specific or general questions here or elsewhere as you need!

there's a gitter channel here where you can get realtime support too :) sourmash-bio/sourmash#1686

[ctb]

(also happy to get suggestions on how to improve findability of docs!)

[clb21565]

ahah! i didn't scroll far enough and i don't think it was in the ToC at the top, but, this is great thank you!

[clb21565]

nevermind i was just blind

[ctb]

no worries at all, never hesitate to ask! it helps us improve!

[ctb]

I need to add it to the ToC on top 🤔