agilebio/labcollector repository overview

⁠Version

• v6.34

⁠Quick reference

• Maintained by
  Pierre Rodrigues - AgileBio⁠
• Where to get help:
  Open a ticket for LabCollector⁠

⁠Supported tags

• v6-latest⁠

⁠What is LabCollector?

LabCollector is a unique LIMS and ELN. It is an Intranet based software, allowing centralized management of all your lab data. By using LabCollector, your teams can benefit from efficient information sharing and access via a local network or the Internet.

⁠How to use this image

$ docker run --name some-labcollector --network some-network -d agilebio/labcollector:v6-latest

If you'd like to be able to access the instance from the host without the container's IP, standard port mappings can be used:

$ docker run --name some-labcollector -p 8080:80 -d agilebio/labcollector:v6-latest

Then, access it via http://localhost:8080 or http://host-ip:8080 in a browser.

⁠... via docker-compose⁠ or docker stack deploy⁠

If you wish to use Docker Compose (recommended), actions are required.

Example docker-compose.yml for labcollector:

services:
  labcollector:
    ports:
      - "8080:80"
    image: agilebio/labcollector:v6-latest
    volumes:
      - documents:/var/www/html/documents
      - maps:/var/www/html/maps
      - files:/var/www/html/files
      - extra_modules:/var/www/html/extra_modules
      - backup:/var/www/html/backup
      - images:/var/www/html/netplasmid/images
      - UserFiles:/var/www/html/UserFiles
      - cron:/var/spool/cron
###################################################################################
      # Uncomment the following line for any subsequent install/upgrade to keep database connection configuration:
      #- /path/to/backup/config.php:/var/www/html/config.php
##################################################################################
    networks:
      - labcollector-backend

  mariadb:
    image: mariadb:10.6.10
    ports:
      - "3308:3306"
    restart: always
    environment:
      MARIADB_ROOT_PASSWORD: A_SECURE_PASSWORD
    volumes:
      - mysql:/var/lib/mysql
    networks:
      - labcollector-backend
networks:
  labcollector-backend: {}
volumes:
  documents:
  maps:
  files:
  extra_modules:
  backup:
  images:
  UserFiles:
  mysql:
  cron:

After copy pasting the docker-compose.yml, you can run for the first installation.

$ docker compose pull    # Update with the latest version of the LC image
$ docker compose up -d   # Launch the containers (LabCollector + MariaDB)

After Choose the folder on the host machine that will store the config.php container backup.

Retrieve LabCollector container ID :

docker ps

Copy the container's config.php file to the desired folder: (example: /home/user/backup/)

docker cp <ID_CONTAINER>:/var/www/html/config.php /home/user/backup/

Once you've finished installing labcollector (login page) and copied config.php, stop the containers

docker compose down

Edit and uncomment in the docker-compose.yaml :

 #- /<path to backup config.php>/config.php:/var/www/html/config.php

Run docker compose up -d

or

Run docker stack deploy -c stack.yml labcollector (or docker-compose -f stack.yml up), wait for it to initialize completely, and visit http://swarm-ip:9080, http://localhost:9080, or http://host-ip:9080 (as appropriate).

⁠Adding additional libraries / extensions

This image comes with pre-installed PHP extensions for working with LabCollector. If you need additional PHP extensions, you'll need to create your own image FROM this one. The documentation of the php image explains how to compile additional extensions.

⁠Image Variants

The labcollector images will come in many flavors, each designed for a specific use case. For now, the v6-latest comes with PHP and Apache

⁠Disclaimer

The image contains libraries (python3-autocommand, python3-jaraco.context, python3-jaraco.functools) under GNU GPL2 and GPL3