BIIGLE Distribution

This is the production configuration of the "BIIGLE laptop" of Biodata Mining Group. You can adapt this configuration to install BIIGLE on your own device in a local network. See the setup instructions to get started.

This is the production setup of BIIGLE (fork of biigle-distribution).

Installation

Perform these steps on the machine that should run BIIGLE. Check out the wiki for an example of how to prepare a new machine for the installation of BIIGLE. You also need to configure Docker to authenticate to the GitHub package registry.

Create a user for BIIGLE and find out the user and group ID:

$ sudo useradd biigle -U
$ id -u biigle
<user_id>
$ id -g biigle
<group_id>

Change the owner of the storage directory:
```
$ sudo chown -R biigle:biigle storage/
```
Move .env.example to .env.
Now set the configuration variables in .env:
- USER_ID should be <user_id>.
- GROUP_ID should be <group_id>.
Move build/.env.example to build/.env.
Now set the build configuration variables in build/.env:
- GITHUB_OAUTH_TOKEN is an OAuth token of your GitHub account.
- APP_KEY is the secret encryption key. Generate one with: head -c 32 /dev/urandom | base64. Then set APP_KEY=base64:<your_key>.
- APP_URL is https://<your_domain>.
- ADMIN_EMAIL is the email address of the administrator(s) of the application.
If you use an external database system (outside Docker), remove the database block from docker-compose.yaml and configure the DB_* variables in build/.env.
Put the SSL keychain (fullchain.pem) and private key (privkey.pem) to certificate/. See here for a description of the required contents of the keychain file.
Now build the Docker images for production: cd build && ./build.sh. You can build the images on a separate machine, too, and transfer them to the production machine using docker save and docker load. build.sh also supports an optional argument to specify the version tag of the Docker containers to build (e.g. v2.8.0). Default is latest.
Go back and run the containers: cd .. && docker-compose up -d.
Apply the database migrations: ./artisan migrate.
Create the first user: ./artisan user:new.

Updating

Get the newest versions of the Docker images:

docker pull docker.pkg.github.com/biigle/core/app:latest
docker pull docker.pkg.github.com/biigle/core/web:latest
docker pull docker.pkg.github.com/biigle/core/worker:latest

Run cd build && ./build.sh. This will fetch and install the newest versions of the BIIGLE modules, according to the version constraints configured in build.sh. Again, you can do this on a separate machine, too (see above). In this case the images mentioned above are not required on the production machine.
If the update requires a database migration, do this:
1. Put the application in maintenance mode: ./artisan down.
2. Do a database backup. This might look along the lines of:
```
docker exec -i $(docker-compose ps -q database) pg_dump -U biigle -d biigle > biigle_db.dump
```
Update the running Docker containers: docker-compose up -d.
If the update requires a database migration, do this:
1. Run the migrations ./artisan migrate
2. Turn off the maintenance mode: ./artisan up
Run docker image prune to delete old Docker images that are no longer required after the update.

Common tasks

BIIGLE runs as an ensemble of multiple Docker containers (called "services" by Docker Compose).

app runs the BIIGLE PHP application that handles user interactions.
web accepts HTTP requests, forwards them to the PHP application or serves static files.
worker executes jobs from the asynchronous queue which are submitted by app. This is the only service that runs multiple Docker containers in parallel.
scheduler runs recurring tasks (similar to cron jobs).
cache provides the Redis cache that BIIGLE uses.
database provides the PostgreSQL database that BIIGLE uses.

To interact with these services rather than individual Docker containers, you have to use Docker Compose. Here are some common tasks a maintainer of a BIIGLE instance might perform using Docker Compose.

Inspect the logs of running containers

docker-compose logs [service]

This shows the log file of the [service] service. You can use --tail=[n] to show only the last [n] lines of the log file and -f to follow the log file in real time.

Restart all services

docker-compose restart

This may be required if a service crashed or if file system mounts changed.

Run an artisan command

./artisan [command]

This runs the artisan command [command] in the worker service.

Access the interactive shell

./artisan tinker

This opens the interactive PHP shell that you can use to manipulate BIIGLE. The shell only runs in the worker service as a debugging mechanism.

Change the number of worker containers

docker-compose up -d --scale worker=[n]

Set the number of worker containers running in parallel to [n]. If you want this to persist, set scale: [n] for the worker service in docker-compose.yaml.

biigle / laptop

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