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KarchinLab / open-cravat

A modular annotation tool for genomic variants
MIT License
113 stars 27 forks source link

check that reqired annotators installed (in .yml) fails #59

Closed EugeneEA closed 3 years ago

EugeneEA commented 3 years ago

Hi, I have a custom annotator which, relyes on multiple of other annotators, everything works fine (thanks a lot!), but there is an issue with dependancies.

According to manual (https://open-cravat.readthedocs.io/en/latest/Annotator-Reference.html) I'm inserting necessary rows in yml file:

requires:
- clinvar
- ...etc

but even if I'm listing there missing (or non existing) annotators everything works perfectly (offcourse untill I actlually try to fetch missing data with secondary_inputs:). Am I doing something wrong or this functionality does not work? PS later I also like to specify versions of the annotators (to avoid these issues https://github.com/KarchinLab/open-cravat/issues/48). I'm fin if oc would just crashes of the version is incorrect, the real annotator-verson control is probably different stroy.

Best, Eugene

rkimoakbioinformatics commented 3 years ago

Hi Eugene,

When you develop a module inside the modules directory, requires is not used for the module's functionality. When the module is published and installed with oc module install, then the modules defined in requires will be installed also. If a non-existing module is defined under requires, that wrong module will be ignored in the installation.

EugeneEA commented 3 years ago

Ok, thanks for the clarification! Best, Eugene