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monarch-initiative / pheval.exomiser

Exomiser plugin for PhEval.
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Add docker mounted volume paths to constants.py #16

Closed yaseminbridges closed 1 year ago

yaseminbridges commented 1 year ago

When passing paths to be mounted to a docker volume, that path to which the path is being specified, e.g., /path/to/input-data/:/exomiser-input-data specifically exomiser-input-data should be specified as a constant as this is used in several places within the code.

I think what I mean here is the TARGETDIRECTORY which is what I want to specify in the constants so a volume I am mounting:

docker run -v /path/to/testdata/phenopacketdir/:TARGETDIRECTORY

This TARGETDIRECTORY is something that is required for the methods to write out the input commands for exomiser, as well as in the actual running of exomiser where I am using the docker package for Python to run the Exomiser docker image

matentzn commented 1 year ago

Ok, so this is only related to internal stuff in pheval.exomiser? As long as none of this bleeds into pheval its ok, because we should not have any docker specific configurations in there..

yaseminbridges commented 1 year ago

Yes, only for pheval.exomiser