search

vanheeringen-lab / genomepy

genes and genomes at your fingertips
https://vanheeringen-lab.github.io/genomepy/
MIT License
381 stars 37 forks source link

Multiple genomes option? #145

Open Ahmed-Shibl opened 3 years ago

Ahmed-Shibl commented 3 years ago

Hi genomepy team,

First, I want to say thanks for this software. Second, I have a question related to the genome install command - is there a way to install several genomes at a time instead of individually?

Thanks!

siebrenf commented 3 years ago

Hey @Ahmed-Shibl,

Glad to hear you like the tool! Genomepy can only install one genome at a time (since you may wish to specify your options for each).

If you have a list of genomes you wish to install, you could make a loop in either bash or Python. It should be simple if all genomes come from the same provider, or if you agree with our provider search order (Ensembl > UCSC > NCBI). If however you do need different options, it would get a bit more complicated.