- create a feature branch in git
- look at https://github.com/UCSC-MedBook/MedBook-JobRunner/blob/f-gsea-new/webapp/server/classes/RunLimmaGSEA.js
- create a new class
- Add new class and its args to primary-collections repo collections/Jobs.js
- add adapters (importers and exporters) to convert from MedBook objects to files that tools understand and store check them into external-tools
- add external code to external-tools repo (or mechanism to install it)
- add pointers to external code in your personal settings.json for use while testing
- also add these pointers in the MedBook main repo docker-compose.yml METEOR_SETTINGS environment variable
- add gui to appropriate MedBook app, that initiates job by inserting into jobs collection for example: Jobs.insert({ name: "UpDownGenes", status: "waiting", user_id: user._id, collaborations: [ user.personalCollaboration() ], args });
- read errors from jobs.error_description