General Beagle environment variables
| Environment | Description | Example |
|---|---|---|
| BEAGLE_DB_NAME | PostgreSQL database | example_database |
| BEAGLE_DB_USERNAME | PostgreSQL user | example_user |
| BEAGLE_DB_PASSWORD | password for PostgreSQL user | example_password |
| BEAGLE_DB_PORT | PostgreSQL port | 3333 |
| BEAGLE_PORT | Beagle port ( only for container use) | 4444 |
| FLOWER_PORT | Flower port ( only for container use) | 5555 |
| BEAGLE_LOG_PATH | log file | /example/path/logs/beagle-server.log |
| BEAGLE_PATH | Path to Beagle repo ( only for container use) | /srv/services/staging_voyager/beagle/ |
| BEAGLE_URL | Url for beagle | http://your_server:4444 |
| BEAGLE_ALLOWED_HOSTS | Hosts allowed to run Beagle | localhost,your_server |
| BEAGLE_POOLED_NORMAL_FILE_GROUP | File group for pooled normals, must be a uuid | 62033c45-6c55-4d2d-bec2-9c917b4af133 |
| BEAGLE_DMP_BAM_FILE_GROUP | File group for DMP BAMS normal, must be a uuid | f62f5fb8-2dbd-45b2-8050-6dac56a4cc17 |
| BEAGLE_NOTIFIERS | List of notifiers | JIRA |
Beagle environment variables needed to interact with other services
| Environment | Description | Example |
|---|---|---|
| GIT_SSH_COMMAND | Git ssh command needed to clone private repos | ssh -i /path/to/id_rsa -o UserKnownHostsFile=/path/to/known_hosts -F /dev/null" |
| BEAGLE_AUTH_LDAP_SERVER_URI | LDAP server URI | ldaps://example.org/ |
| BEAGLE_RIDGEBACK_URL | Ridgeback URL | http://localhost:2000 |
| BEAGLE_RABIX_URL | Rabix URL | http://localhost:2001 |
| BEAGLE_RABIX_PATH | Path to Rabix binary | /path/to/rabix |
| BEAGLE_RABBITMQ_USERNAME | Rabbitmq username | example_username |
| BEAGLE_RABBITMQ_PASSWORD | Rabbitmq password | example_password |
| BEAGLE_LIMS_USERNAME | LIMS username | example_username |
| BEAGLE_LIMS_PASSWORD | LIMS password | example_password |
| BEAGLE_RUNNER_QUEUE | Rabbitmq runner queue | example.runner.queue |
| BEAGLE_DEFAULT_QUEUE | Rabbitmq default queue | example.runner.queue |
| BEAGLE_JOB_SCHEDULER_QUEUE | Rabbitmq scheduler queue | example.runner.queue |
| CELERY_EVENT_QUEUE_PREFIX | Prefix for Celery event | beagle.celery |
| CELERY_LOG_PATH | Log path for Celery | /path/to/celey.log |
| CELERY_BROKER_URL | URL to Celery broker | amqp://[RABBITMQ_USERNAME]:[RABBITMQ_PASSWORD]@localhost:5672 |
| JIRA_USERNAME | JIRA username | example_username |
| JIRA_PASSWORD | JIRA password | example_password |
| JIRA_URL | JIRA URL | http://jira.example.org:5000 |
| JIRA_PROJECT | JIRA Board | EXAMPLE_BOARD |