MedBook-JobRunner

Runs and monitors Jobs (Current UNIX processes, Galaxy and other Environments coming)

steps to adding a new tools

1. create a feature branch in git
2. look at https://github.com/UCSC-MedBook/MedBook-JobRunner/blob/f-gsea-new/webapp/server/classes/RunLimmaGSEA.js
3. create a new class
4. Add new class and its args to primary-collections repo collections/Jobs.js
5. add adapters (importers and exporters) to convert from MedBook objects to files that tools understand and store check them into external-tools
6. add external code to external-tools repo (or mechanism to install it)
7. 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

6. 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 });
7. read errors from jobs.error_description