Galaxy Beacon import

Utility to import variants from specific galaxy histories to a beacon instance.

Try it locally

1. Set up galaxy

You will need a galxy instance where you have admin privileges. You can for example clone galaxy and run it with the included run.sh script.

• To select VCF files in the galaxy frontend enable the setting enable_beacon_integration in your galaxy.yml
• To get api access add your email in the setting admin_users

2. Provide a dataset

Perform the following actions in your local galaxy (http://localhost:8080)

• Log in as any user
• Go to User -> Preferences and select Manage Beacon
• In the Modal, press the green button to enable beacon for this user
• Use the button to switch to your beacon history
• Upload any .vcf file to the history

3. Start beacon-python

Beacon python is an implementation of beacon in python. It will be the target of the import.

Beacon 1

The project also comes with a docker-compose.yml so starting a local instance is pretty straight forward.

git clone https://github.com/CSCfi/beacon-python.git
cd beacon-python/deploy
docker-compose up -d

Beacon 2

git clone https://github.com/EGA-archive/beacon2-ri-tools.git
cd beacon2-ri-tools
docker-compose up -d

4. Prepare import script

Thus far the script has been tested under Python 3.8.10. It requires some modules that can be installed from requirements.txt.

git clone https://github.com/Paprikant/galaxy-beacon-import.git
cd galaxy-beacon-import
pip3 install -r requirements.txt

5. Run the import

Beacon 1

./beacon-import.py -k <api-key-from-step-2>

Beacon 2

./beacon2-import.py -k <api-key-from-step-2>