Cytomine Dockerfiles

This repository provides a set of Dockerfile used to build some Cytomine Docker images which are not related to other Cytomine projects. These images are used in the Cytomine-bootstrap procedure.

Overview

Every Cytomine component is encapsulated inside a Docker container. The recipes to build these containers are Dockerfiles.

The Dockerfiles of Cytomine components with their own Github repository are directly stored in such repositories. You will find here Dockerfiles for components not associated to a dedicated Github repository.

Dockerfiles inside this repository

Base Dockerfiles:

• base (inherits official ubuntu)
• java8 (inherits base)
• tomcat7 (intherits java8)

Database Dockerfiles:

• backup (inherits base)
• mongodb (inherits base)
• postgres (inherits base)
• postgis (inherits postgres)

Cytomine component Dockerfiles:

• slurm (inherits official centos)
• rabbitmq (inherits base)
• memcached (inherits base)
• nginx (inherits base)
• iip-jp2000 (inherits base)
• retrieval (inherits java8)
• iris (inherits tomcat7)

Dockerfiles outside this repository

Cytomine component Dockerfiles:

• core (inherits tomcat7) - See Cytomine-core repository
• ims (inherits tomcat7) - See Cytomine-IMS repository
• software_router (inherits java8) - See Cytomine-software-router repository
• bioformat (inherits java8) - See Cytomine-BioFormats repository
• iip-cyto (inherits base) - See Cytomine iipsrv repository

Base Dockerfiles for Cytomine software:

• software-python2-base (inherits official python) - See Cytomine-python-client repository
• software-python3-base (inherits official python) - See Cytomine-python-client repository
• software-java8-base (inherits official openjdk) - See Cytomine-java-client repository
• software-groovy-base (inherits official groovy) - See Cytomine-java-client repository

Install

To install official release of Cytomine, see @cytomine. Follow this guide to install forked version by ULiege.

It is automatically installed with the Cytomine-bootstrap procedure using Docker. See Cytomine installation documentation for more details.

Develop

1. Set versions in versions.sh
2. Build images with sh build_images.sh
3. Push built images onto a Docker registry such as DockerHub with sh push_images.sh

References

When using our software, we kindly ask you to cite our website url and related publications in all your work (publications, studies, oral presentations,...). In particular, we recommend to cite (Marée et al., Bioinformatics 2016) paper, and to use our logo when appropriate. See our license files for additional details.

• URL: http://www.cytomine.org/
• Logo: Available here
• Scientific paper: Raphaël Marée, Loïc Rollus, Benjamin Stévens, Renaud Hoyoux, Gilles Louppe, Rémy Vandaele, Jean-Michel Begon, Philipp Kainz, Pierre Geurts and Louis Wehenkel. Collaborative analysis of multi-gigapixel imaging data using Cytomine, Bioinformatics, DOI: 10.1093/bioinformatics/btw013, 2016.

License

Apache 2.0