We have a database file in LFS (Large File Storage), so you first need to install git-lfs. After that, you can run the following commands, to get the repository's content, and install the LFS hooks.
git clone https://github.com/EGA-archive/beacon-2.x.git beacon
cd beacon
git lfs install
We use a postgres image, for the database, and separate images for the Beacon, the (fake) permissions server and the identity provider.
If you instantiate directly the containers, the images will be automatically downloaded.
If you are not on the master branch, you should (re-)create the images for the Beacon locally. Run the following command in the current directory:
docker-compose build beacon
At boot time, the database pre-loads some data from the Genome in a bottle project.
This takes only a few seconds. Instantiate a container with
docker-compose up -d db
You can look at what is happening in the container with docker-compose logs -f db.
We can point the web browser to localhost, on some given port,
which docker will redirect to the relevant container. That part is
fine, but when a docker container A needs to call another container B
using a URL pointing to localhost, it will look at itself (ie,
packets don't get out of A), and won't find the service running on the
chosen port.
We cannot circumvent this issue by adding DNS entries, to point to
the other containers. This issue is to change an already existing one
inside the container, namely localhost.
A simple solution is to update your local machine's DNS resolution by
adding to /etc/hosts, the following entries:
127.0.0.1 idp
127.0.0.1 beacon
127.0.0.1 beacon-permissions
That way, you can make your browser point to http://idp:8080 and
http://beacon:5050, and they'll redirect to the right container. The
same is true from within those containers (because they either
already have a DNS entry, or they don't, would get out of the
container and then use the above newly added entries).
The pre-configured settings assume the above.
We have already adjusted the settings for the network and the different connection parameters.
docker-compose up -d
The beacon is now ready. You can query it on beacon (port 5050). For example:
- /api
- /api/g_variants?assemblyId=GRCh37.p1&referenceName=MT&referenceBases=T&alternateBases=C&start=150&includeDatasetResponses=ALL
- /api/g_variants?assemblyId=GRCh37.p1&referenceName=MT&start=1&end=200
- /api/biosamples
and point you browser to beacon:5050 for the UI.
The -d flag runs the containers detached, ie we get the prompt back. You can check the logs with:
docker-compose logs -f
Tear down the system and remove the database volume, with:
docker-compose down -v
We use Keycloak in a container, connected to a Postgres database. We import a pre-configured realm, with a beacon client and 2 users:
| Username | Password | |
|---|---|---|
| admin | secret | |
| john | john | john.smith@beacon.ga4gh |
| jane | jane | jane.smith@beacon.ga4gh |
Exporting the settings can be done with:
docker-compose exec idp /opt/jboss/keycloak/bin/standalone.sh \
-Djboss.socket.binding.port-offset=100 \
-Dkeycloak.migration.action=export \
-Dkeycloak.migration.provider=singleFile \
-Dkeycloak.migration.realmName=Beacon \
-Dkeycloak.migration.usersExportStrategy=REALM_FILE \
-Dkeycloak.migration.file=/tmp/export-beacon-realm.json
Once it has run, you can stop the above command and copy out the file from the container
docker cp idp:/tmp/export-beacon-realm.json <destination-path>