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:
Rouillard AD, Gundersen GW, Fernandez NF, Wang Z, Monteiro CD, McDermott MG, Ma'ayan A. The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. Database (Oxford). 2016 Jul 3;2016. pii: baw100.
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 install # 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