Running Hinxton Single Cell Interactive Analysis Environment¶
Hinxton Single Cell is a Galaxy setup with tools for tertiary analysis of single cell data. 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¶
- Helm installed: Please follow official instructions for installing Helm.
- Access to a Kubernetes cluster (with shared file system accessible through a Persistent Volume or equivalent). - For development purposes or local tests, the local Minikube environment can be used. Install minikube following official instructions for minikube.
- kubectl cli: The command line argument for connection to a Kubernetes instance (remote cluster or local minikube). If not installed as part of Minikube steps, follow ONLY the installation steps (not the configuration ones) from here.
Minikube¶
If using minikube, you need to make sure that it is running. If you just
installed it, you need to execute minikube start. In general you can check
the status of minikube through minikube status. For a smoother run, you might want to assign more RAM to Minikube.
First time installation¶
If using helm for the first time, you will need to initialise helm on the cluster and add the helm repo to the local helm directories:
helm init --wait
helm repo add galaxy-helm-repo https://pcm32.github.io/galaxy-helm-charts
if you have done this once in the past, you might need, from time to time, to update the local repo, by doing:
helm repo update
Retrieve and customise configuration file¶
The galaxy-stable Helm chart that we will use allows the configuration of most Galaxy settings. For that, get the sample config file.
Edit or make a copy of this file based on your needs and the galaxy-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 hinxton-singlecell-1.0.0_g18.05-minikube.yaml \
--version 2.0.2 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/.
If you are not using minikube, the Galaxy instance will be on port 30700 of any of the node’s IPs of the k8s cluster (unless that you had setup the ingress).