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informatics-isi-edu / protein-database

Deriva Protein Database Project
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common deployment workflow #223

Open tgarello opened 1 month ago

tgarello commented 1 month ago

https://github.com/informatics-isi-edu/protein-database/blob/d2576fd33b3e2d2cf8d108daca0fbd8fc31d77a9/scripts/ubuntu/workflow-common/deploy-common.sh#L30C1-L30C33

hello,

I attempted to follow scripts/ubuntu/workflow-dev.

I encountered the following error in the above deployment command : cp: cannot stat '/home/isrddev/python-ihm/util/make-mmcif.py': No such file or directory

After check, there was a breaking change in python-ihm. util/make-mmcif.py has been renamed to _ihm/util/makemmcif.py

cf. https://github.com/ihmwg/python-ihm/commit/b476d4dea3d3b3d3ce5ea3877eff5f46cdac8ca7

tgarello commented 1 month ago

also the isrd software library is missing for the deploy-common.sh it supposed to be here : /isrddev/protein-database/scripts/ubuntu/lib/pdb-software-lib.sh

but I imagine it may be deliberate

hongsudt commented 1 month ago

The goal for the deployment workflow is to cover the deployment of backend processing pipeline, not the deriva software stack. If you are interested in setting up the dependencies of tools used in processing pipeline, then this is the place to look (e.g. if we are going to replicate the tools in here with model archive).