Convenience Scripts for Deploying Galaxy on Kubernetes

Prerequisites

• A working Kubernetes cluster
• Setting /.kube/config
• kubectl installed (See Kubernetes docs)
• helm installed (SEe Helm docs)

Placeholder variables

In the examples below, I will be using a number of placeholder variables

export GXYDOMAIN=kubedev.usegalaxy.org # Domain at which to deploy galaxies
export MYBRANCH=my_branch # Branch on which I want to develop
export BASEBRANCH=upstream/dev # Base branch
export IMAGEREPO=galaxy/galaxy-min # Base image
export IMAGETAG=latest # latest == dev ;; 21.01 == release_21.01, etc... 

Note: In order for the code injection to work, the code on the image used needs to correspond to the base branch, in order for the list of changes generated by git diff to be accurate.

Quick Start

One-time setup

1. Clone the scripts repository:

git clone https://github.com/CloudVE/galaxy-k8s-dev-env
cd galaxy-k8s-dev-env

2. a) Using existing clones of galaxy and galaxy-helm

bash symlink_branch.sh $MYBRANCH /path/to/galaxy /path/to/galaxy-helm

NOTE: This will run git checkout -b $MYBRANCH in both repositories

2. b) Start with fresh clones of galaxy and galaxy-helm

bash setup_branch.sh $MYBRANCH

Repeatable

3. Make changes to code in galaxy and galaxy-helm repositories. If you used setuo_branch.sh, you will find your clones under galaxy-k8s-dev-env/branches/$MYBRANCH/galaxy[-helm]. If you symlinked existing repositories, you can continue to use them and make commits or keep changes uncommitted until you're ready to preview. You must have $MYBRANCH checked out before the next step.

4. Detect updates from the base branch.

bash update_links.sh $MYBRANCH $GXYDOMAIN /my-desired-path $BASEBRANCH

Note: This will detect changed files (currently supporting added and modified files), then will symlink them into galaxy-helm/galaxy/extrafiles. This enables deploying the newest code without rebuilding the image from scratch. It also creates a specific values.yaml and extra-values.yaml for this branch, the first deploying Galaxy at the desired domain and path, and the latter injecting the symlinked code as configmaps.

6. Deploy Galaxy

bash helm_update.sh $MYBRANCH desired-namespace --set image.repository=$IMAGEREPO --set image.tag=$IMAGETAG