docker-compose.yml-EXAMPLE

# docker-elabftw configuration file
# use : "docker-compose up -d" to start containers
# this config file contains all the possible configuration options, shown with default values
# https://hub.docker.com/r/elabftw/elabimg/
# https://www.elabftw.net

# this is the "compose project name"
# see: https://docs.docker.com/compose/compose-file/04-version-and-name/
name: elabftw

# the internal elabftw network on which both containers will run
networks:
  elabftw-net:

# the services are the elabftw container (webservice) and MySQL (database)
services:
  # our first container is nginx + php-fpm + elabftw
  web:
    # About tags (the part after the :)
    # stable points to the latest stable version
    # latest points to the latest version, including alpha/beta
    # use a specific version tag to pin the image
    # example: elabftw/elabimg:4.0.5
    # default value: elabftw/elabimg:stable
    image: elabftw/elabimg:stable
    # this ensures the container will be restarted after a reboot of the server
    # default value: always
    restart: always
    # comment this out if you use several containers with redis, as you can't have several containers with the same name
    # default value: elabftw
    container_name: elabftw
    # make sure we wait for mysql to be available before starting
    # comment this out if you're not using a mysql container
    # note: the mysql container needs an healthcheck block for this to work
    depends_on:
      mysql:
        condition: service_healthy

    # limit number of processes
    # this option is commented out because it is not in v3 of compose files, only v2
    # even though it works as expected in a v3 file with recent docker-compose
    #pids_limit: 42

    # add a security flag to prevent a process gaining new privileges
    security_opt:
      - no-new-privileges:true

    # restrict capabilities of the root user to the strict minimum
    # see CIS Docker Benchmark v1.5 5.3
    # see ANSSI-FT-082 23/09/2020 R8
    # WARNING: for Centos7/8, comment out these lines (cap_drop and cap_add)
    # If you get this error in the logs:
    # nginx: [emerg] bind() to 0.0.0.0:443 failed (13: Permission denied)
    # comment out these lines!
    cap_drop:
        - ALL
    cap_add:
        - CHOWN
        - SETGID
        - SETUID
        - FOWNER
        - DAC_OVERRIDE

    # environment variables passed to the container to configure options at run time (when container is started)
    # commented variables are optional
    environment:
        #######################
        # MYSQL CONFIGURATION #
        #######################
        # name of the MySQL server (by default "mysql" the name of the mysql container in default elabftw Docker configuration)
        # you can put here the IP address of an existing MySQL server if you already have one running
        # default value: mysql
        - DB_HOST=mysql

        # port on which the MySQL server is listening
        # you probably don't need to modify this value
        # default value: 3306
        - DB_PORT=3306

        # name of the MySQL database
        # you probably don't need to modify this value
        # default value: elabftw
        - DB_NAME=elabftw

        # MySQL user with write access to the previously named database
        # you probably don't need to modify this value
        # default value: elabftw
        - DB_USER=elabftw

        # MySQL password; a random password has been generated for you but feel free to change it if needed
        # default value: generated randomly if you get the config from get.elabftw.net
        - DB_PASSWORD=secr3t

        # Mysql Cert path: you only need this if you connect to a mysql server with tls
        # Use a volume that points to /mysql-cert in the container
        # optional
        #- DB_CERT_PATH=/mysql-cert/cert.pem

        #####################
        # PHP CONFIGURATION #
        #####################
        # the timezone in which the server is
        # better if changed (see list of available values: http://php.net/manual/en/timezones.php
        - PHP_TIMEZONE=Europe/Paris
        # again
        - TZ=Europe/Paris

        # optional: set the limit of simultaneous request that will be served
        # see http://php.net/manual/en/install.fpm.configuration.php
        # default value: 50
        #- PHP_MAX_CHILDREN=50

        # optional: adjust the max execution time of PHP scripts, in seconds
        # default value: 120
        #- PHP_MAX_EXECUTION_TIME=120

        # optional: adjust the amount of memory available to PHP, increase it if you run into issues
        # information: 2G of memory available to PHP might seem a lot. But realize this: it's not 2003 anymore. PHP is not just a few "if" and "foreach" in some html page.
        # We use it to generate huge PDF files and archives, to manipulate potentially big images, and do complicated operations on thousands of objects fast.
        # So yeah, the conservative 128 Mb default is obsolete when a simple photo taken with a phone can be 10 Mb.
        # Most of the servers that run eLabFTW will run ONLY eLab and will easily have at least 4 Gb of RAM dedicated to this task.
        # What is the point of having 4 Gb of RAM and let the main application use only a few percents of it...
        # This doesn't mean that eLabFTW will consume that much memory all the time. 99% of the time it will have very low memory footprint.
        # But from time to time, users will export many entries at once in PDF with big images in them and that's when you want to have some headroom!
        # example value: 4G
        # default value: 2G
        #- MAX_PHP_MEMORY=2G

        # optional: set a password to get access to /php-status, which will display various metrics about the php-fpm processes
        # also works for /nginx-status, for metrics about nginx process
        # if this is not set, a random password will be generated but never displayed, effectively disabling access to this endpoint
        # the enpdoint can be accessed with the "elabftw" user, and the password you set below
        # example value: my-cool-password
        # default value: not set
        #- STATUS_PASSWORD=

        #########################
        # ELABFTW CONFIGURATION #
        #########################
        # The secret key is used for encrypting the SMTP and Timestamping passwords
        # A random one has been generated for you, if you wish to change it you can
        # get another secret key from https://get.elabftw.net/?key
        # if you don't want to get it from an external source you can also do that:
        # docker run --rm -t --entrypoint '/bin/sh' elabftw/elabimg -c "php -d memory_limit=10M -d open_basedir='' bin/init tools:genkey"
        # Note: the value MUST be generated as shown in the methods above.
        # default value: generated randomly if you get the config from get.elabftw.net
        - SECRET_KEY=

        # The canonical URL to the website, including port if not standard
        # Use the user-facing URL here.
        # example value: https://elab.uni-delta.fr
        # example value: https://elab.uni-delta.fr:3148
        - SITE_URL=

        # optional: adjust maximum size of uploaded files
        # default value: 100M
        #- MAX_UPLOAD_SIZE=100M

        # optional: adjust maximum time for uploading files, in milliseconds
        # default value: 900000
        #- MAX_UPLOAD_TIME=900000

        # optional: s3 storage credentials
        #- ELAB_AWS_ACCESS_KEY=
        #- ELAB_AWS_SECRET_KEY=

        #######################
        # NGINX CONFIGURATION #
        #######################
        # change to your server name in nginx config
        # default value: localhost
        # example value: elab.uni.edu
        - SERVER_NAME=localhost

        # optional: disable https, use this to have an http server listening on port 443
        # useful if the SSL stack is handled by haproxy or something alike
        # default value: false
        - DISABLE_HTTPS=false

        # set to true to use letsencrypt or other certificates
        # note: does nothing if DISABLE_HTTPS is set to true
        # default value: false
        - ENABLE_LETSENCRYPT=false

        # optional: enable ipv6 (make sure you have an AAAA dns record!)
        # default value: false
        #- ENABLE_IPV6=false

        # optional: adjust the user/group that will own the uploaded files (and run the webserver)
        # useful if your files are stored on an NFS mount point where the files ownership are imposed by the NFS server
        # default value: nginx
        # example value: nobody
        #- ELABFTW_USER=nginx
        # default value: nginx
        # example value: nobody
        #- ELABFTW_GROUP=nginx
        # default value: 101
        # example value: 65534
        #- ELABFTW_USERID=101
        # default value: 101
        # example value: 65534
        #- ELABFTW_GROUPID=101

        # optional: enable if you want nginx to be configured with set_real_ip_from directives
        # default value: false
        #- SET_REAL_IP=false
        # the IP address/addresses. Separate them with a , AND A SPACE. Several set_real_ip_from lines will be added to the nginx config. One for each.
        # this does nothing if SET_REAL_IP is set to false
        #- SET_REAL_IP_FROM=192.168.31.48, 192.168.0.42, 10.10.13.37

        # optional: modify connection persistence for MySQL
        # pdo doc: https://www.php.net/manual/en/pdo.connections.php
        # default: true
        # example value: false
        #- USE_PERSISTENT_MYSQL_CONN=true

        # optional: adjust the number of worker processes nginx will spawn
        # default value: auto
        # if auto doesn't work for you, use the number of cores available on the server (or less)
        #- NGINX_WORK_PROC=auto

        # optional: allow javascript code to call the API from an external service
        # this will add a response header Access-Control-Allow-Origin with content of the env var as value
        # mdn doc: https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers/Access-Control-Allow-Origin
        # default: header not set (empty value)
        # example value: app.example.org
        # example value: *
        #- ALLOW_ORIGIN=

        # optional: define methods allowed to javascript code calling the API from an external service
        # this will add a response header Access-Control-Allow-Methods with content of the env var as value
        # mdn doc: https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers/Access-Control-Allow-Methods
        # default: header not set (empty value)
        # example value: OPTIONS, GET, POST, PATCH, DELETE
        #- ALLOW_METHODS=

        # optional: define headers allowed to javascript code calling the API from an external service
        # this will add a response header Access-Control-Allow-Headers with content of the env var as value
        # mdn doc: https://developer.mozilla.org/en-US/docs/Web/HTTP/Headers/Access-Control-Allow-Headers
        # default: header not set (empty value)
        # example value: Content-Type, Authorization
        #- ALLOW_HEADERS=

        # optional: modify the keepalive_timeout value
        # nginx doc: http://nginx.org/en/docs/http/ngx_http_core_module.html#keepalive_timeout
        # default: 10s
        # example value: 5s
        #- KEEPALIVE_TIMEOUT=10s

        #######################
        # REDIS CONFIGURATION #
        #######################
        # optional: use a redis server to store the PHP sessions
        # default value: false
        #- USE_REDIS=false
        # optional: set an IP or hostname for the redis server
        # default value: redis
        #- REDIS_HOST=redis
        # optional: set a custom port for redis
        # default value: 6379
        #- REDIS_PORT=6379
        # optional: set a username for redis
        # default value: <empty>
        #- REDIS_USERNAME=
        # optional: set a password for redis
        # default value: <empty>
        #- REDIS_PASSWORD=

        ######################
        # LDAP CONFIGURATION #
        ######################
        # optional: configure ldap certificate verification behavior: will create /etc/openldap/ldap.conf with TLS_REQCERT config line
        # default value: false
        # possible values: never, allow, try
        #- LDAP_TLS_REQCERT=false

        #################
        # MISCELLANEOUS #
        #################
        # optional: be less verbose during init
        # default value: false
        #- SILENT_INIT=false

        # optional: automatically install the database structure on container start
        # default value: false
        #- AUTO_DB_INIT=false

        # optional: automatically update the database structure on container start
        # default value: false
        #- AUTO_DB_UPDATE=false

        # set to true to set the instance in demo mode, with autologin for demo users
        # default value: false
        #- DEMO_MODE=false

        # set to true to set the instance in maintenance mode, displaying an informative page, thereby disabling all user interaction
        # default value: false
        #- MAINTENANCE_MODE=false

        ###########
        # PLUGINS #
        ###########
        # Activating these plugins is highly recommended for all labs
        # See below the configuration necessary to deploy them.
        # optional: define chemistry/biology plugin services domain name + port
        # IMPORTANT: end url values with trailing slash!
        #
        # This service is necessary for the Chemical structure editor (Ketcher)
        #- USE_INDIGO=false
        #- INDIGO_URL=http://chem-plugin/
        # The fingerprinter is necessary to create a fingerprint of chemical compounds so we can do sub-structure search
        #- USE_FINGERPRINTER=false
        #- FINGERPRINTER_URL=http://chem-plugin:8000/
        # If your fingerprinter service needs to use the generic app proxy, set this to true
        #- FINGERPRINTER_USE_PROXY=false
        # This is for the integration of the DNA Cloning tool
        #- USE_OPENCLONING=false
        #- OPENCLONING_URL=http://opencloning-plugin:8000/

        #######
        # DEV #
        #######
        # set to true in a development environment.
        # This will remove php cache, serve assets directly (instead of the brotli/gzip version) and make composer available.
        # default value: false
        #- DEV_MODE=false

    ports:
        # Important note about exposing ports: due to the way Docker deals with the host firewall, it is recommended to use '127.0.0.1:1234:443'
        # if you only want to expose the service locally (on port 1234 in this example). See https://github.com/moby/moby/issues/22054
        # Another option is to use the "expose" directive instead of "ports" and let your reverse proxy figure things out.
        #
        # if you want elabftw to run on a different port, change the first number
        # host:container
        - '443:443'
        # if you are aiming for running multiple instances of this container you can put a range like so:
        # - "3100-3200:443"
        # use redis for session storage if that is the case, or configure your load balancer with sticky sessions
    volumes:
        # this is where you will keep the uploaded files persistently
        # for Windows users it might look like this
        # - D:\Users\Nico\elab-data\web:/elabftw/uploads
        # host:container
        - /var/elabftw/web:/elabftw/uploads
        #
        # TLS configuration
        #
        # Note: if your certificate is not from letsencrypt, make sure to have those two files:
        #
        #       /etc/letsencrypt/live/SERVER_NAME/fullchain.pem
        #       /etc/letsencrypt/live/SERVER_NAME/privkey.pem
        #
        # in the folder /etc/letsencrypt (or any folder you like as long as you adapt the line below
        # replace SERVER_NAME with the value of SERVER_NAME of course.
        #
        # if you have enabled letsencrypt, uncomment the line below
        # path to the folder with TLS certificate + private key
        # host:container
        #- /etc/letsencrypt:/ssl
        #
        # MYSQL cert path
        #- /path/to/cert/folder:/mysql-cert
        #
        # Exports: bind mount this folder so exported files are saved outside
        # of the container. Useful if you have several containers or expect
        # many users to export data and don't want your containers to grow too
        # much or be stateful.
        #- /path/to/big_partition:/elabftw/exports

    # This part is just an example for having a custom DNS entry in /etc/hosts of the container
    # Use it if DNS resolution cannot work for some reason
    # The "extra_hosts" key must be aligned at the same indentation level as "ports" or "volumes" or "networks" blocks.
    #
    # extra_hosts:
    #   - internal.s3.example.org:10.12.34.56

    networks:
      - elabftw-net

  # the mysql database image
  # Note: if you already have a MySQL server running, you don't need to use this image, as you can use the already existing one
  # In this case, add the IP address of the server in DB_HOST and comment out or remove this block
  # Upgrading from 8.0 note: if you're updating from 8.0 and used to have the mysql_native_password option, see this doc:
  # https://doc.elabftw.net/sysadmin-guide.html#fix-deprecation-warning-for-old-password-storage
  mysql:
    image: mysql:8.4
    restart: always
    container_name: mysql
    # add an healthcheck block so the web container knows when it is ready to accept connections
    # use double $ here so env vars are correctly found
    healthcheck:
      test: "/usr/bin/mysql --user=$$MYSQL_USER --password=$$MYSQL_PASSWORD --execute 'SHOW DATABASES;'"
      interval: 5s
      timeout: 5s
      retries: 42
    # drop some capabilities
    cap_drop:
        - AUDIT_WRITE
        - MKNOD
        - SYS_CHROOT
        - SETFCAP
        - NET_RAW
    cap_add:
        - SYS_NICE
    environment:
        # need to change
        - MYSQL_ROOT_PASSWORD=secr3t
        # no need to change
        - MYSQL_DATABASE=elabftw
        # no need to change
        - MYSQL_USER=elabftw
        # need to change IMPORTANT: this should be the same password as DB_PASSWORD from the elabftw container
        - MYSQL_PASSWORD=secr3t
        # need to change, this is your timezone, see PHP_TIMEZONE from the elabftw container
        - TZ=Europe/Paris
        # Update this if you want to run the server on a different port than 3306.
        # - MYSQL_TCP_PORT=3306

    volumes:
        # this is where you will keep the database persistently
        # for Windows users it might look like this
        # - D:\Users\Nico\elab-data\mysql:/var/lib/mysql
        # host:container
        - /var/elabftw/mysql:/var/lib/mysql
     # The mysql container exposes 3306/33060. Though it does not make an operational difference,
     # make sure to document your usage here.
    expose:
      - '3306'
    networks:
      - elabftw-net

  #chem-plugin:
  #  image: elabftw/chem-plugin
  #  container_name: chem-plugin
  #  restart: always
  #  networks:
  #    - elabftw-net

  #opencloning-plugin:
  #  image: manulera/opencloning:prod-baseurl-opencloning
  #  container_name: opencloning-plugin
  #  restart: always
  #  networks:
  #    - elabftw-net
  #  environment:
  #    - ALLOWED_ORIGINS=*
  #    - ROOT_PATH=/opencloning
  #    - BACKEND_URL=/opencloning/
  #    - SHOW_APP_BAR=false
  #    - DATABASE=elabftw
  # Optional environment variable used to restrict access to external repositories (e.g., WekWikGene).
  # References:
  #    https://github.com/manulera/OpenCloning_backend/blob/master/src/opencloning/app_settings.py
  #    https://github.com/manulera/OpenCloning/blob/master/docker-compose.yml
  # By default (i.e., if this environment variable is unset or empty), all external repositories are enabled.
  # To restrict which external repositories users can access, set this variable to a comma-separated list of allowed base URLs.
  #    - ALLOWED_EXTERNAL_URLS=https://www.addgene.org/,https://media.addgene.org/,https://seva-plasmids.com/,https://api.ncbi.nlm.nih.gov/datasets/v2alpha/,https://eutils.ncbi.nlm.nih.gov/entrez/eutils/,https://www.snapgene.com/local/fetch.php,https://benchling.com/,https://assets.opencloning.org/annotated-igem-distribution,http://www.euroscarf.de/


  # example of a redis container
  # uncomment if you want to spawn a redis container to manage sessions
  #redis:
  #  image: redis:7-alpine
  #  restart: always
  #  container_name: redis
  #  networks:
  #    - elabftw-net

  # example of a keeex container (experimental!)
  #keeex:
  #  image: repo.keeex.me/fkeeex_daemon:latest
  #  container_name: keeex
  #  restart: always
  #  environment:
  #    - FKEEEX_CONFIG_USER=user@example.org
  #    - FKEEEX_CONFIG_PASSWORD=
  #    # Set a random passphrase here. You can generate one with "openssl rand -base64 32".
  #    - FKEEEX_CONFIG_PASSPHRASE=
  #  expose:
  #    - 8080
  #  networks:
  #    - elabftw-net

  ###############################################################
  # EVERYTHING BELOW THIS LINE IS FOR DEVELOPMENT PURPOSES ONLY #
  # You can safely delete everything below                      #
  ###############################################################

  # PHPMYADMIN
  # uncomment this part if you want to have phpmyadmin running too
  #phpmyadmin:
  #    image: phpmyadmin/phpmyadmin
  #    container_name: phpmyadmin
  #    environment:
  #        - PMA_PORT=3307
  #    links:
  #        - mysql:db
  #    ports:
  #        - "8080:80"
  #    networks:
  #        - elabftw-net

  # SWAGGER UI
  # swagger allows you to consult the documentation generated by apidoc/v2/openapi.yaml
  # running a local container is perfect to see the changes right after a change
  #
  #swagger:
  #  image: swaggerapi/swagger-ui:v5.0.0
  #  restart: always
  #  container_name: swagger-elab-local
  #  ports:
  #    - "8085:8080"
  #  volumes:
  #    - /path/to/local/elabftw/apidoc/v2:/usr/share/nginx/html/swagger:ro
  #  environment:
  #    - API_URL=swagger/openapi.yaml
  #  networks:
  #      - elabftw-net


  # LDAP
  # example for ldap server + admin interface
  # uncomment if you want to work on LDAP authentication
  #ldap:
  #    image: osixia/openldap:1.4.0
  #    container_name: ldap
  #    restart: always
  #    hostname: example.org
  #    environment:
  #      - LDAP_TLS_VERIFY_CLIENT=try
  #      - LDAP_OPENLDAP_UID=1000
  #      - LDAP_OPENLDAP_GID=1000
  #    ports:
  #      - "389:389"
  #      - "636:636"
  #    volumes:
  #      - /var/elabftw/ldap-data/ldap:/var/lib/ldap
  #      - /var/elabftw/ldap-data/slapd.d:/etc/ldap/slapd.d
  #    networks:
  #        - elabftw-net
  #ldapadmin:
  #    image: osixia/phpldapadmin:0.9.0
  #    container_name: ldapadmin
  #    environment:
  #      - PHPLDAPADMIN_LDAP_HOSTS=ldap
  #    restart: always
  #    ports:
  #      - "6443:443"
  #    networks:
  #        - elabftw-net