Installing InjectTool

Installing docker and docker compose

InjectTool is developed inside a docker-compose instance. You need to install both docker and docker compose in order to run InjectTool. Please follow your platform documentation to install docker.

Note

if you want to interact with docker using your user and not root, you need to do the following (only applies to Linux machines):

$ sudo groupadd docker
$ sudo usermod -aG docker <your user>
# login again

Docker compose is a tool for defining and running multi-container Docker applications. Please follow your platform documentation to install docker-compose.

Download and install InjectTool

A detailed description on how to install InjectTool is described in github README. There also a set or ansible roles which help the user to automate the configuration and installation process.

Switch to BioSamples production environment

By default InjectTool works by submitting data to BioSamples test servers. In order to switch to the BioSamples production environment, you have to define the production URLs in the .env file, like this:

BIOSAMPLE_URL=https://www.ebi.ac.uk/biosamples/samples
EBI_AAP_API_AUTH=https://api.aai.ebi.ac.uk/auth
BIOSAMPLE_API_ROOT=https://submission.ebi.ac.uk/api/

This is enough to ovverride the default API endpoints defined in pyUSIrest, which is the main module for BioSamples submission. For more information, please refer to Biosample App documentation.

Note

remember to re-create countainers since those variables are esported as environment variables.

Warning

The EBI Auth server is different from the test server. You will need to register your users through the new environment. The resulting group names will be incompatible from test to production, you have to clean up each biosample account data in database