This repository contains the source code for the Harmonizome.
- BD2K-LINCS Data Coordination and Integration Center
- Illuminating the Druggable Genome, Knowledge Management Center
Please acknowledge the Harmonizome in your publications by citing the following reference:
Certain environment variables are necessary to connect to the database. Typically this can be handled with a gradle.properties
file of the form:
DB_URL=jdbc:mysql://yourhost/yourdb
DB_USER=youruser
DB_PASS=yourpass
HARMONIZOME_PREFIX=Harmonizome
TOMCAT_PORT=8080
Gradle is used to fetch dependencies, build and debug the project. The two commands below in different terminals can be used to automatically rebuild/deploy the project to an embedded tomcat server for a continuous development experience.
# Continuous build (rebuilds on file change)
gradle build -t
# Tomcat development server (reflects file changes)
gradle tomcatRun
Gradle is used to assemble a war file to be deployed with a tomcat8-base docker image.
# Build and assemble war file
gradle war
# Construct docker image
docker build -t maayanlab/harmonizome:latest .
When you run the image you'll need to provide the environment variables:
docker run \
-e DB_URL=jdbc:mysql://yourhost/yourdb \
-e DB_USER=youruser \
-e DB_PASS=yourpass \
-p 8080:8080
-it maayanlab/harmonizome:latest