openSEEK

openSEEK is the name given to the combined package including both SEEK and openBIS

The package is provided using Docker Compose, and became available with SEEK version 1.3.0

Installation and running

First you should read the guide for Docker and in particular Docker Compose

Running openSEEK is essentially the same, but you will need to use a different compose file and create an additional volume

Create the additional volume for storing the openbis state with:

docker volume create --name=openbis-state

The compose file to use is docker-compose-openseek.yml

When using Docker Compose you need to reference this compose file, for example:

docker-compose -f docker-compose-openseek.yml up -d

and

docker-compose -f docker-compose-openseek.yml down

You can reach SEEK through

http://localhost:3000

after which you will need to create the initial account and profile. The SEEK will already be setup to talk to the openBIS.

You can reach openBIS through

https://localhost:4000/openbis/

Note this uses a self-signed certificate by default. The default user is admin and password is changeit.

Standalone openBIS

You don’t need to run the combined openSEEK package to use SEEK with openBIS.

For SEEK versions following 1.3, you can use SEEK with a pre-existing openBIS which is running the 16.05.02 version. You can also install openBIS separately using the Standard openBIS installation, or a single Docker container as follows:

docker volume create name=openbis-state
docker run -p 4000:443 -v openbis-state:/home/openbis/openbis_state openbis/debian-openbis:16.05.2

More details about running the openBIS Docker container can be found on Docker Hub

Using SEEK and openBIS

For further instructions on how to use SEEK with openBIS please read our User Guide