Administrator side

Most maintenance operations can be carried out directly via biomaj-cli (documentation here), however it is possible to automate and visualize a number of tasks.

How to update banks?

Standalone version : cron tasks


  • release service (biomaj-release)(auto-schedule of banks): Scan every day remote banks release modifications and send stats to prometheus and influxdb about new release detection. When a new release is detected, according to minimal delay configuration (in global or bank properties), a new bank update is sent.
  • Cron service, manageable via biomaj-watcher (web ui)

BioMAJ watcher overview:




An email is sent to bank owner with update/removal status and log extract, then log can be analysed in log dir (one log per session/command).

How to search basic informations on banks?

Elasticsearch can index bank update session information for search on banks. This indexing is activated via configuration.

How to get BioMAJ running statistics?


  • It is possible to get stats of BioMAJ with influxdb 
  • Influxdb is a time series database designed to analyse and store time-series data.

Do not forget to create influxdb database manually. You will first have to run the CLI influxdb in the influxdb container and then create a biomaj database:

docker exec -it biomajdocker_biomaj-influxdb_1 influx
#Connected to http://localhost:8086 version 1.3.0
#InfluxDB shell version: 1.3.0
create database biomaj



  • BioMAJ collects metrics with prometheus (time based metrics on execution time of downloads and executions, there are available for biomaj-daemon, biomaj-process and biomaj-download).


An example of the configuration for prometheus is available here :




  • Grafana is a dashboard that will get the data in influxdb and prometheus. It provides a visualization interface for timeseries records on update, current and past downloads, disk space used per bank, etc.

Grafana for BioMAJ GenOuest:

How to use it?

Add this service to the docker-compose.yml of BioMAJ (find the example here)

 image: grafana/grafana
 - "3000:3000"



Other services

  • Status info page on public-proxy http://public-proxy/status/index.html
  • Graylog: centralisation of the logs of docker containers
  • Zipkin: shows per workflow step info (dependency, time) (Start optional zipkin server and use –trace option on a bank update command)


What to check in case of a BioMAJ bug?

  • Bank logs (<rootdir>/log/bank/version/execution)
  • Check the bank status: --config --status --bank alu
  • Check per process logs (logs generated by process or docker logs)