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wustl-oncology / cloud-workflows

Infrastructure and tooling required to get genomic workflows running in the cloud
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Use a release of analysis WDLs instead of pulling main #37

Closed malachig closed 7 months ago

malachig commented 1 year ago

Currently when the Cromwell VM is initialized it is set up to pull the latest commit from main.

This is controlled by: https://github.com/wustl-oncology/cloud-workflows/blob/1e55fbd4acb4bf5647b466fe802529c0cd360724/manual-workflows/start.sh#L146

And then:

https://github.com/wustl-oncology/cloud-workflows/blob/1e55fbd4acb4bf5647b466fe802529c0cd360724/manual-workflows/server_startup.py#L92C30-L92C90

We could change this to have a hard coded release being cloned instead of the current state of the default branch (main in this case). And then allow the user to over-ride this default with a different release of their choice.

malachig commented 1 year ago

At the same time we could update the clone path to reference wustl-oncology instead of griffithlab

malachig commented 7 months ago

To clone a particular release of the analysis-wdls repo: https://github.com/wustl-oncology/analysis-wdls/releases

git clone git@github.com:wustl-oncology/analysis-wdls.git --branch v1.1.4
tmooney commented 7 months ago

Might be neat if you could choose which version to checkout, perhaps by having the startup script read the selected version from the metadata like: https://cloud.google.com/compute/docs/instances/startup-scripts/linux#accessing-metadata

malachig commented 7 months ago

A solution has been tested and merged.