thehyve/cbioportal-staging

Name: cbioportal-staging

Owner: The Hyve

Description: Staging app for automatically loading studies into cBioPortal

Created: 2018-01-11 16:28:25.0

Updated: 2018-02-21 17:10:25.0

Pushed: 2018-02-28 11:51:47.0

Homepage: null

Size: 196

Language: Java

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README

cbioportal-staging

Staging app for automatically executing E(extract)T(transform)L(load) steps on study files stored in a central location (like a file share or S3) and meant to be loaded as studies in cBioPortal. This app executes the following workflow:

1. Extract files from central location
2. Transform files into cBioPortal study staging files
3. Validate the study staging files generated by step 2
4. Load the staging files into cBioPortal as new studies, or overwriting existing studies.

Build status:

Setup

Configure your custom settings in src/main/resources/application.properties. See provided example file src/main/resources/application.properties.EXAMPLE. Be sure to at least configure cloud.aws.region.static there.

Build

To build and run tests execute:

clean install

You can skip tests with extra argument -DskipTests.

Run

To run use:

rget/cbioportal-staging-*.jar

You can overwrite application properties at runtime by adding them as parameters, for example:

rget/cbioportal-staging-*.jar --scan.cron="* * * * * *"