Running Galaxy SC Tertiary locally

Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research.

Within this project, we have created a Galaxy flavour (a Galaxy setup with defined tools and workflows) for the tertiary analysis of single cell RNA-Seq data.

This guide shows you how to run the Galaxy Single Cell Tertiary analysis setup on your own machine using Minikube. The setup relies on the Kubernetes container orchestrator.

Requirements

Please follow the “Requirements”, “Minikube” and “First time installation” sections from the Galaxy helm chart site at https://github.com/galaxyproject/galaxy-kubernetes/blob/develop/README.md

Retrieve and costumize configuration file

The galaxy-stable Helm chart that we will use allows to configure most Galaxy settings. For that, get the sample config file.

Edit or make a copy of this file based on your needs and the galax-stable chart documentation. However, if you only need to run on Minikube, the sample config file should do fine. You might want to set a user and password there.

Normal run

Now the only step needed is to initialize Galaxy through the helm chart just added. For this execute:

helm install -f tertiary-portals-galaxy-18.05-minikube.yaml \
  --version 2.0.1 galaxy-helm-repo/galaxy-stable

Access Galaxy

To access your local Galaxy setup you need to find out the ip from minikube:

minikube ip

Usually the ip number will be 192.168.99.100 (but confirm with the above call). Then access on that ip port 30700 with the galaxy prefix http://192.168.99.100:30700/.