New OpenCGA 2.0.0 Feature. Work in progress
OpenCGA produces four different Docker images for different use cases, these are:
You can use opencga Docker image to run a complete OpenCGA platform locally. You can use the other images to deploy a whole cluster solution in a cloud environment using Kubernetes. Docker Images are deployed in Docker Hub OpenCB organisation.
All images run with the user opencga and run Java 8. Docker images are deployed in Docker Hub.
This image contains the basic installation in directory /opt
This image is based in opencga-base and runs REST web services using the REST server command-line.
This image runs the master service
all-in-one image with all OpenCGA components running
OpenCGA publishes a number of images into DockerHub for user ease. These images are based on Alpine JRE images to keep sizes as small as possible, contains OpenCGA binaries, for complete contents of image, please have a look at Dockerfile in github. A typical image name will follow the following structure :
OpenCGA has published a docker image for quick testing and playing without going through hassle to learn, wait and install each and every OpenCGA components. The docker image is available at the public docker registry under the repository opencb/opencga-demo.
The OpenCGA demo docker image contains the following components:
To download OpenCGA demo image, use the command docker pull with the OpenCB enterprise, opencga-demo repository and tag. For example :
$ docker pull opencb/opencga-demo:1.4.2
To start the OpenCGA demo container, use the command docker run. For example: (This command will pull image as well if not present in local repository)
$ docker run --name demo -d opencb/opencga-demo:1.4.2
The first time you run the OpenCGA demo container, it installs the OpenCGA catalog in mongoDB, starts the OpenCGA REST server and finally, it starts the OpenCGA daemon. In this case, no data is loaded. If you want to load some demo data, set the option load to true that instructs OpenCGA demo container to download data from Corpasome project and then, to run an ETL pipeline that loads, annotates, computes statistics and indexes data into the Solr search engine. This process roughly takes 35-40 minutes depending on the internet speed and the machine specifications. Following command starts the OpenCGA container loading demo data:
$ docker run --name demo -e load=true -d opencb/opencga-demo:1.4.2
User can also mount customise directories to store MongoDB and Solr data for ease. The following command will mount the ~/data/mongodb and ~/data/solr directories from host machine to inside container at "/data/opencga/mongodb", "/data/opencga/mongodb" respectively.
$ docker run --name demo -e load=true -v ~/data/mongodb:/data/opencga/mongodb -v ~/data/solr:/data/opencga/solr -d opencb/opencga-demo:1.4.2
In case, user has previously used mongodb and solr data outside of docker, mounted on host machine and now want to use NEW docker image and force docker to NOT install catalog, use the following command:
$ docker run --name demo -e installCatalog=false -v ~/data/mongodb:/data/opencga/mongodb -v ~/data/solr:/data/opencga/solr -d opencb/opencga-demo:1.4.2
You can connect to the OpenCGA demo container using the following command:
$ docker exec -it demo bash
To fetch the logs of the OpenCGA demo container, use the following command:
$ docker logs demo -f
In order to access to the Solr dashboard, use the following URL on your internet browser:
And to access to the OpenCGA REST webservices, use the following URL:
Distributed systems with multiple dependencies require a lot of work to setup, install, configure system and developers would like to have a quick way to test their changes locally and quickly with a system mimicking as close as possible to production systems. Following are the steps to create your own opencga demo image from modified oepncga source code :
~/appl/opencga[develop*]$ mvn clean install -DskipTests -Dopencga.war.name=opencga
Build OpenCGA Next image :
~/appl/opencga[develop*]$ docker build -t opencga-next -f opencga-app/app/cloud/docker/opencga-next/Dockerfile .
Next Build OpenCGA Demo Image :
~/appl/opencga[develop*]$ docker build -t opencga-demo -f opencga-app/app/cloud/docker/opencga-demo/Dockerfile .
Catalog installation and steps to create project, study etc are in listed in "opencga-app/app/scripts/docker/opencga-demo/init.sh" script. User can modify as per own needs for example, change the variant file etc.
Following command will run local OpenCGA Demo :
~/appl/opencga[develop*]$ docker run --name demo -d opencga-demo
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