STATegra EMS Docker Image

The STATegra EMS Docker Image is an easy distributable full-fledged STATegra EMS installation.

STATegra EMS is an Experiment Management System (EMS) for omics experiments that supports different types of sequencing-based assays, proteomics and metabolomics data. STATegra EMS was developed as part of the STATegra Project, which has received funding from the European Union’s FP7 research and innovation programme.

• Citation:

Hernández-de-Diego R, Boix-Chova N, Gómez-Cabrero D, Tegner J, Abugessaisa I, and Conesa A. STATegra EMS: an Experiment Management System for complex next-generation omics experiments. BMC Syst Biol. 2014;8 Suppl 2:S9. doi: 10.1186/1752-0509-8-S2-S9.

Build the image

The docker image for STATegra EMS can be found in the docker hub. However, you can rebuild is manually by running docker build.

sudo docker build -t stategraems .

Note that the current working directory must contain the Dockerfile file.

Running the Container

The recommended way for running your STATegra EMS docker is using the provided docker-compose script that resolves the dependencies and make easier to customize your instance. Alternatively you can run the docker manually. In both cases the first time that you access to your STATegra EMS instance the system will be auto-installed. You can easily customize the installation by changing some system variables, you can find the list of available variables in the next section.

Quickstart

This procedure starts STATegra EMS in a standard virtualised environment.

• Install docker for your system if not previously done.
• docker run -it -p 8080:80 fikipollo/stategraems
• STATegra EMS will be available at http://localhost:8080/

Using the docker-compose file

Launching your STATegra EMS docker is really easy using docker-compose. Just download the docker-compose.yml file and customize the content according to your needs. There are few settings that should be change in the file, follow the instructions in the file to configure your container. To launch the container, type:

sudo docker-compose up

Using the -d flag you can launch the containers in background.

In case you do not have the Container stored locally, docker will download it for you.

Run manually

You can run manually your containers using the following commands:

sudo docker run --name stategraems-mysql -v /your/data/location/mysql:/var/lib/mysql -e MYSQL_ROOT_PASSWORD=yoursecretpass -d mysql
sudo docker run --name stategraems-tomcat -e MYSQL_ROOT_PASSWORD=yoursecretpass --link stategraems-mysql -v /your/data/location:/data -p 8080:8080 -d fikipollo/stategraems

In case you do not have the Container stored locally, docker will download it for you.

A short description of the parameters would be:

• docker run will run the container for you.

• -p 8080:8080 will make the port 8080 (inside of the container) available on port 8080 on your host. Inside the container an Tomcat Webserver is running on port 8080 and that port can be bound to a local port on your host computer. With this parameter you can access to the STATegraEMS instance via http://localhost:8080 immediately after executing the command above.

• fikipollo/stategraems is the Image name, which can be found in the docker hub.

• -d will start the docker container in daemon mode.

• -e VARIABLE_NAME=VALUE changes the default value for a system variable. The STATegra EMS docker accepts the following variables that modify the INSTALLATION of the system in the docker. Note that all the values are optional but the MYSQL_ROOT_PASSWORD which must be the same password for the MySQL container.

• EMS_ADMIN_USER, the email for the admin account (default value is emsadminuser@email.com).

• EMS_ADMIN_PASSWORD, the password for the admin account (default value is emsadminuser@email.com).

• MYSQL_ROOT_USER, the root user for the MySQL instance (default value is root).

• MYSQL_ROOT_PASSWORD, the password for the MySQL root user (mandatory).

• MYSQL_DATABASE_NAME, the name for the MySQL database (default value is STATegraDB).

• MYSQL_HOST, the name for the MySQL container (default value is stategraems-mysql).

• MYSQL_EMS_USER, the name for the MySQL user that will be used for administrate the databases (default value is emsuser).

• MYSQL_EMS_PASS, the password for the MySQL user (default value is autogenerated).

For an interactive session, you can execute :

sudo docker exec -it stategraems-tomcat bash

First configuration for STATegra EMS

The first time that you access to your STATegra EMS instance you will need to configure some of the main settings.

Version log

• v0.8 March 2017: First version of the docker.