PanDrugs Docker

A Dockerfile to generate an all-in-one PanDrugs server.

Latest version available: 2024.06

Requirements

To be fully functional, in addition to building the pandrugs2 Docker image as explained below, this PanDrugs server requires:

• An additional Docker image for running VEP. Check this instructions to build and configure the image and see how
• An additional Docker image for running PharmCat. The official image pgkb/pharmcat:2.1.2 is used to run the additional scripts.

Versions of PanDrugs components included in this image

• Front-end: 2.2.0
• Back-end: 2.3.0
• Perl variant analysis module: v20
• Database: 20240612

These versions are packed into the 2024.06 release.

Versions of databases used by PanDrugs and included this image

The database sources can be found in the pandrugs-db project.

Building the image

Edit the context.xml file in order to configure the mail system (see SMTP Configuration Properties for configuration details).

<Resource name="mail/session"
        auth="Container"
        type="javax.mail.Session"
        mail.smtp.host="sing.ei.uvigo.es"
        mail.smtp.port="25"
        mail.smtp.auth="false"
/>

Note that the versions of the PanDrugs components are are taken from the following environment variables declared in the Dockerfile:

• APP_BACKEND_VERSION
• APP_FRONTEND_VERSION
• APP_DB_SCHEMA_VERSION
• APP_DB_DATA_VERSION

The available releases for these versions are:

• latest (points to 2024.06)
• 2024.06
• 2024.05
• 2023.03

Then, inside the cloned repository:

docker build -t pandrugs2 .

This process should be relatively fast as database files are downloaded when the server is started for the first time and VEP database files are part of the pandrugs2-vep Docker image. The pandrugs2 image should be about 1.41GB.

Starting the server

docker run -d -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp -v [your_local_dir_for_data OR volume_name]:/pandrugs2-backend_data -p 80:8080 --name pandrugs2 pandrugs2

This command will:

• Make your server available via the port 80 at the container machine.
• Allow the container executing Docker.
• Share the host /tmp directory with the container.
• Create a Docker managed volume named pandrugs2-backend_data if using -v pandrugs2-backend_data:/pandrugs2-backend_data

The first time the container is started, it will download the database files and import them into the MySQL DB. Therefore, this process may take a while and its progress can be monitored with:

docker logs -f pandrugs2

As noted in the VEP configuration, create the following symbolic link in the host: ln -s /var/lib/docker/volumes/pandrugs2-backend_data/_data /pandrugs2-backend_data (replace pandrugs2-backend_data with the actual name of your Docker managed volume). This is because the Docker run commands (created in the run-pandrugs-vep-*-on-docker.sh scripts) will use references to directories inside /pandrugs2-backend_data. As these commands are executed in the host, such path must exist and point to the actual location of the data (which in this case is the location of the corresponding managed Docker volume).

Accessing the server

The frontend will be serving at: http://yourhost

The backend will be serving at: http://yourhost/pandrugs-backend

Accessing the database

docker exec -it pandrugs2 /usr/bin/mysql -uroot

Getting the pandrugs tomcat log

docker exec -it pandrugs2 tail -f /pandrugsdb.log

Stopping the server

docker stop pandrugs2