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popsim-consortium / analysis2

Analysis for the second consortium paper.
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now computing stats on subwindows within focal #92

Closed mufernando closed 1 year ago

mufernando commented 1 year ago

@nspope

mufernando commented 1 year ago

I added the VCF output to this PR @andrewkern

andrewkern commented 1 year ago

looks like the conda requirements have been moved to a different file? can you put everything into just the environment.yml file?

andrewkern commented 1 year ago

running into an issue where i don't have the reqs to run the sweep stuff as part of the main analysis2 env

andrewkern commented 1 year ago

okay I pushed a small change to your branch @mufernando and now this is ready, I think

mufernando commented 1 year ago

this is fully working now! we had to downgrade protobuf to stop the weird seg faults we were getting.

andrewkern commented 1 year ago

i believe that @dschride is currently trying to run this pipeline on the UNC cluster to see if it works on their scheduler.

@mufernando do you reckon we are ready to merge?

mufernando commented 1 year ago

if it works fine in @dschride's cluster I think we can safely merge this.

dschride commented 1 year ago

I'm having all kinds of issues trying to run jobs of any kind on our cluster today so it may be a while longer before I can confirm this for you...

andrewkern commented 1 year ago

@dschride was able to confirm that this workflow ran to completion on his cluster

dschride commented 1 year ago

Yay!