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broadinstitute / PANOPLY

Repository for the Broad Institute Proteogenomic Data Analysis Center (PGDAC) established by the NIH Clinical Proteomics Tumor Analysis Consortium (CPTAC)
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Initialization cell in PANOPLY-startup-notebook never finishes #35

Closed wnojopra closed 2 years ago

wnojopra commented 2 years ago

Hi,

Thanks for creating these workspaces in Terra. They've been a great resource.

I'm following the tutorial and I and a few others teammates are getting stuck initializing the notebook. After cloning the workspace and starting a cloud environment with the broadcptac/panda:1_0 container image, I try to run the first cell in the PANOPLY-startup-notebook. This cell seems to hang and never finish, even after waiting for several hours.

A teammate opened up the terminal this afternoon and it looks like it's in an endless loop, presumably because the broadcptac/panda:1_0 image is missing a package, and thus it's never able to load:

image Any suggestions for how we can move past this step? Thanks!

drmani commented 2 years ago

The docker takes too long to download, and hence the compute environment does not initialize properly. We have fixed the issue, and we are in the process of updating documentation. Please use gcr.io/broadcptac/panda:1_2 as the docker. This is an updated docker stored on GCR, and should work more reliably.

wnojopra commented 2 years ago

Thank you @drmani ! After updating the docker image version I was able to succesfully run the initialize code. I'm looking forward to the documentation update but in the meantime I'll try and spread the word to my team.