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README.md

Cloudgene Docker Image 🐳

Docker Build Status Docker Pulls Travis

This repository provides a ready-to-use Docker image for Cloudgene and installs all requirements, especially Apache Hadoop (CDH5). Cloudgene is a workflow system for managing Hadoop jobs graphically. Cloudgene applications can be installed graphicaly or using application repositories.

Requirements

Docker must be installed on your local computer. Please checkout the step by step guide to install the latest version.

Getting Started

After the successful installation of Docker, all you need to do is:

 docker run -d -p 8080:80 genepi/cloudgene

After about 1 minute you are able to access your Cloudgene instance on http://localhost:8080.

Login as admin with the default admin password admin1978. You can now install applications and run jobs. More about installing applications ca be found in our Documentation.

Persistent Cloudgene Container

Docker images are not persistent, all jobs submitted inside one session will be lost after restart. To keep your jobs, results and installed applications between sessions, you need to mount a folder from your host to the container:

docker run -d -p 8080:80  -v /home/lukas/cloudgene_data/:/data/ genepi/cloudgene

This folder contains all results of your jobs, all installed applications and all configuration files. If you mount an empty folder, then a fresh installation of Cloudgene is performed. To restart a session, you have to use the same folder. It is also possible to use different folders for different projects or tests.

Start Cloudgene without Hadoop cluster

If you need a Cloudgene instance without Hadoop, then you can use the environment variable START_HADOOP to disable the Hadoop service:

 docker run -d -p 8080:80 -e START_HADOOP="false" genepi/cloudgene

Interactive Session

For an interactive session, you can execute:

 docker run -it -p 8080:80 genepi/cloudgene

You well see all log messages from Hadoop and from Cloudgene itself.

To get access to Hadoop specific web-applications you can map additional ports to your host:

 docker run -d -p 8080:80 -p 50030:50030 genepi/cloudgene

Hadoop's web-interface is now accessible on http://localhost:50030.

Install Applications from a Repository

A repository is a collection of applications that can be installed when you start a new Cloudgene Docker instance. For example, we can use the repository provided by the Michigan Imputationserver to clone it in our Docker instance:

docker run -d -p 8080:80 -e CLOUDGENE_REPOSITORY="https://imputationserver.sph.umich.edu/static/downloads/apps.yaml" -v /home/lukas/cloudgene_data/:/data/ genepi/cloudgene

Credits

Thanks to the people behind this Galaxy image for inspiration.

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