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theiagen / public_health_bacterial_genomics

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task_cg_pipeline.wdl: python3 command not found with new lyveset Docker #214

Closed sam-baird closed 1 year ago

sam-baird commented 1 year ago

There was an update on 2/15/2023 to the quay.io/staphb/lyveset:1.1.4f Docker image. This appears to cause a python3: command not found error in task_cg_pipeline when I run wf_theiaprok_illumina_pe.wdl v1.1.0 on Terra. I reproduce the command not found error when I pull and run the image on my local machine. I don't get the error on my machine or on Terra when I pull the previous digest of the image: docker.io/staphb/lyveset@sha256:4ee8d93f22151f26baddf6f569ab63164806b23bbb67bf81625fb137b4825db6. (I can't pull the previous digest if I use quay.io though, I get a "manifest unkown" error).

I didn't test it, but maybe calling python (v2.7) instead of python3 could work for what the task is doing.

Thanks for developing this workflow, it's very useful! Just wanted to alert a problem I encountered with a Docker image update.

kapsakcj commented 1 year ago

Hi Sam, we appreciate you reporting the issue and apologies that you've hit this error.

We're adding python3 back to the docker image and redeploying to dockerhub and quay with the same docker image name & tag as before. Should be available shortly.

As a stop gap solution, you can use the other lyveset docker image we have available for the 2 cg-pipeline tasks, which will resolve the error.

Image name: staphb/lyveset:2.0.1

kapsakcj commented 1 year ago

Closing this issue as the original lyveset docker image has been updated w/ python3 and the TheiaProk workflows now run with out error at the cg-pipeline steps.

Please re-open if you are still having issues & thanks again for the bug report!