Galaxy-docker-rnaseq

About

Dockerize a Galaxy container for RNA-Seq analysis (in the context of a deployment for the Universidad Nacional de Colombia).

The Galaxy contains tools for metagenomics + tools for RNASeq (HiSat2, RNA STAR, featurecounts, DESeq2, heatmap2...)

This was helped by this Tutorial

Run the Galaxy docker container

sudo docker run -p 8080:80 dereeper/galaxy-unal:latest

Test it locally and modify the container with additional flavors

1- Clone this repository

git clone https://github.com/SouthGreenPlatform/Galaxy-docker-rnaseq.git
cd Galaxy-docker-rnaseq

2- Modify the list of tools and adapt to your need

Edit the tools_rnaseq.yml file and the homepage welcome.html.

3- Build the docker image from the Dockerfile

sudo docker build --no-cache -t galaxy-unal:latest .

4- Run the container

sudo docker run -p 8080:80 galaxy-unal

The Galaxy instance is then accessible to this URL: http://localhost:8080

5- Once you are satisfied, stop the local container and publish it into Docker Hub

sudo docker ps -a
sudo docker stop <container_id>

Create a new repository in Docker Hub with a new name <repository_name>.

Build the image and push it into Docker Hub

sudo docker build -t <login>/<repository_name>:latest .
sudo docker push <login>/<repository_name>:latest

6- Test the published Docker image

sudo docker run -p 8080:80 <login>/<repository_name>:latest

Authors

• Alexis Dereeper (IRD)