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Cytomine BigPicture Edition

Cytomine BigPicture Edition is an assemblage of modules from the Cytomine ULiège Community Edition and additional modules specific to BigPicture (including libraries coming from https://github.com/imi-bigpicture).

This repository provides a way to install Cytomine based on Docker compose.

Requirements

The requirements to install Cytomine BigPicture edition are:

  • Docker Engine
  • Git
  • Have the root permissions on the machine where you want to install Cytomine

Install

To install Cytomine BigPicture edition, follow the steps below:

  1. Clone the repository on your machine:
git clone https://github.com/Cytomine-ULiege/Cytomine-bigpicture-edition.git
  1. Enter the cloned repository:
cd Cytomine-bigpicture-edition/

  1. Add your configurations in the cytomine.template file if you want to change default values (like URLs and/or SMTP setup).

  2. Launch the Cytomine installer:

sudo docker pull cytomine/installer
sudo docker run -v $(pwd):/install --user "$(id -u):$(id -g)" --rm -it cytomine/installer:latest deploy -s /install

This will create all the folders and files necessary to launch Cytomine with Docker Compose

  1. Launch cytomine:
sudo docker compose up -d

As a side effect, this command will write in your local /etc/hosts file.

Cytomine is now ready to be used!

If you have kept the default values in cytomine.template, Cytomine is available at http://cytomine.local.

By default, an admin account has been created. To connect to Cytomine in your browser, retrieve the admin password by opening the generated cytomine.yml file and looking for the ADMIN_PASSWORD key, as shown in the snippet below:

services:
  default:
    bioformat:
      constant:
        BIOFORMAT_PORT: 4321
    core:
      constant:
        ADMIN_PASSWORD: <generated-password>

or by running the following command:

cat cytomine.yml | grep ADMIN_PASSWORD:

To follow the community edition installation procedure, the documentation is available at https://doc.uliege.cytomine.org/admin-guide/ce/ce-install

Import BigPicture datasets

See the procedure to import datasets.