Docker mmpdb.py error

[MKCarter]

Hey,

Trying to run this, but I seem to be unable to run the mmpdb.py when running the docker compose up command. This is the error I am obtaining:

matcher-backend-1   | python: can't open file '/opt/./mmpdb/mmpdb.py': [Errno 2] No such file or directory
matcher-backend-1   | ERROR conda.cli.main_run:execute(49): `conda run python ./mmpdb/mmpdb.py fragment ./initialize_db/quick_structures.smi -o ./initialize_db/quick_structures.fragments --cut-smarts matcher_alpha` failed. (See above for error)
matcher-backend-1 exited with code 1

Do you have any thoughts on how to fix this?

[hooveran]

Hey @MKCarter,

It seems like you may not have downloaded the required mmpdb submodule. You can check whether this is the case by looking in the matcher/backend/mmpdb directory, in your local matcher repository.

The contents of this mmpdb directory (submodule) are not automatically downloaded when cloning the matcher repository; these additional steps are necessary:

1. Navigate to your local matcher repository (the parent matcher folder)
2. Execute git submodule init, and then git submodule update. This should download all the mmpdb code into the location matcher/backend/mmpdb

The below commands are only necessary if you've already run docker-compose, and you want to update your docker setup with the new code. If you hadn't previously run docker-compose, the below steps wouldn't be necessary.

3. Rebuild your local docker images to incorporate this newly downloaded code: docker-compose build (this command comprehensively rebuilds all images from source, although it is likely that only the backend container needs to be rebuilt)
4. Launch a fresh set of containers from the updated images: docker-compose up --force-recreate

Please let us know if there are further issues. Thanks!