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genome-nexus / genome-nexus-annotation-pipeline

Library and tool for annotating MAF files using Genome Nexus Webserver API
MIT License
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Use core module only #161

Closed inodb closed 3 years ago

inodb commented 3 years ago

Using the core module instead of the entire portal package somehow solves the problem. That did lack some deps such as log4j and mysql. A quick hack was to just include the log4j dep from cbioportal. Instead of the mysql package, I think we can use vanilla sql according to this stackoverflow answer: https://stackoverflow.com/a/27582891/1894184.

WARNING: we tried to include only the core module before and that caused some issue for a pipeline package downstream (see https://github.com/genome-nexus/genome-nexus-annotation-pipeline/pull/107). That might still be an issue. Maybe we can figure out a way to change these downstream deps to not depend on the entire portal package CC @averyniceday ?

ao508 commented 3 years ago

@inodb I confirmed that the CVR fetcher works with your GNAP changes here. I may want to run my own testing with the importers and standalone annotation pipeline first before moving forward with this PR. I will keep you posted.