Closed jotech closed 1 year ago
I am hesitant to add every possible database to the download rule, maybe users don't want them but making them local is devenitively a good idea. Do you want to make a PR? Or shuld I implement the changes? download busco is not used for now.
great thank you for your feedback! I opened a PR
Our slurm cluster only works in offline mode, so there is no possibility of downloading files when executing jobs. Although the atlas pipeline has a downloading step, some resources are not downloaded. Especially the rules
download_gunc
anddram_download
fail when submitted as jobs by snakemake.As an ad-hoc fix, I modified
atlas/workflow/rules/download.smk
by addingdownload_gunc
to thelocalrules
block. Similarly, I added a localrules block withdram_download
for dram inatlas/workflow/rules/dram.smk
. My question is, does this approach make sense, or are there other ways to do it?Could it make sense to move the steps to
atlas download
? (potentially includingbusco_download
, but I haven't encountered an error with it, yet.)