Search for a command to run...
Why and how I set up a personal blog using GitHub Pages, Jekyll, and GitHub Actions
Passionate about computational biology, bioinformatics, software engineering, machine learning and data science.
Currently building data pipelines that can scale for the future of genetic medicine at GeneDx.
No comments yet. Be the first to comment.
I am excited to announce that starting next week I will be joining Seqera as a Senior Developer Advocate supporting the Nextflow, nf-core and Seqera Platform user communities. For this role, I'm going to be relocating to the San Francisco Bay area to...
I had the pleasure of attending the Nextflow Summit: Boston 2024 last week. It was a fantastic experience catching up with friends in the Boston bioinformatics community and finally meeting up in person with some of my collaborators from the nf-core ...
Why I've re-hosted my blog content to Hashnode
Getting to outputs quicker with lower configuration overhead
Based on the recommendation of multiple colleagues in the Flagship Pioneering informatics community, I recently listened to The Phoenix Project on audiobook. This novel focuses on a struggling IT department within the fictional company Parts Unlimited, and how the main character, Bill, turns things around by implementing the core principles of the DevOps movement. It is an engaging and educational read, and I highly recommend it to anyone interested in DevOps.
Although Bill's story is set in a medium-sized manufacturing company, I found many of the challenges he faced relatable as a computational biologist working in a small biotech startup. His frantic efforts to ensure integrity of critical data for his colleagues in HR and finance reminded me of the urgency I feel when delivering bioinformatic analyses to bench scientists who need them for their experiments. The novel inspired me to consider how I could apply DevOps principles to the specific problems I face at work.
As I started diving deeper into DevOps, I was somewhat surprised to discover that I already possessed all the core technical skills. I had simply lacked a framework to apply those technical skills in an integrated, synergistic way. That led to my decision to set up a blog focused on applying the principles of DevOps to specific problems faced by computational biologists, bioinformaticians, machine learning engineers and data scientists who work in the biotech and pharmaceutical industries.
If I wanted to write a blog that would in part be focused on DevOps, I wanted to set up the website using that same set of principles I wanted to write about. The DevOps principles I wanted to apply to the blog were:
I also had a few other criteria for the blog:
I decided to use Jekyll as the static site generator for the blog. Jekyll is a popular choice for static site generators, and is well supported by GitHub Pages. Because this was my first time using Jekyll and I don't believe in re-inventing the wheel, I decided to use a pre-built theme to get started. I chose Beautiful Jekyll because it is well documented, and has a clean, modern look.
I largely followed the instructions on the Beautiful Jekyll website to set up the blog, but I made a few modifications in-line with this blog's focus on DevOps and automation.
Earlier this year, I led an effort at ProFound to set up standardized development environments. I'll write more about that effort in a future post, but I wanted to use the same approach for this blog. VsCode makes it trivially easy to set up a DevContainer for a project even for a project that uses a framework/language that you are not familiar with. Using the "Add Development Container Configuration Files" command, I was able to quickly generate a `devcontainer.json` file that would launch a Docker container with all the necessary dependencies for Beautiful Jekyll.
{
"name": "Jekyll",
"image": "mcr.microsoft.com/devcontainers/jekyll:0-buster",
"features": { "ghcr.io/devcontainers/features/node:1": {} },
"forwardPorts": [4000],
"postCreateCommand": "bundle exec jekyll serve --watch"
}
As soon as this file was saved, VSCode automatically prompted me to re-open the project in the container.
One of the benefits of using a DevContainer is that you can use the same container to develop locally or in the cloud using Github Codespaces. Github Codespaces has a generous free tier, and is a great way to reduce the friction of setting up a new project. You can read more about how to set up a Github Codespace in the Github documentation.
The original repo for Beautiful Jekyll included a simple GitHub Actions workflow While enabling the Github Pages feature in the repo settings, I found a template Github Actions pipeline that can be used to build and deploy the site instead:
# Sample workflow for building and deploying a Jekyll site to GitHub Pages
name: Deploy Jekyll site to Pages
on:
push:
branches: ["main"]
workflow_dispatch:
# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
permissions:
contents: read
pages: write
id-token: write
# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
concurrency:
group: "pages"
cancel-in-progress: false
jobs:
# Build job
build:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v3
- name: Setup Ruby
uses: ruby/setup-ruby@ee2113536afb7f793eed4ce60e8d3b26db912da4 # v1.127.0
with:
ruby-version: '3.1' # Not needed with a .ruby-version file
bundler-cache: true # runs 'bundle install' and caches installed gems automatically
cache-version: 0 # Increment this number if you need to re-download cached gems
- name: Setup Pages
id: pages
uses: actions/configure-pages@v3
- name: Build with Jekyll
# Outputs to the './_site' directory by default
run: bundle exec jekyll build --baseurl "${{ steps.pages.outputs.base_path }}"
env:
JEKYLL_ENV: production
- name: Upload artifact
# Automatically uploads an artifact from the './_site' directory by default
uses: actions/upload-pages-artifact@v1
# Deployment job
deploy:
environment:
name: github-pages
url: ${{ steps.deployment.outputs.page_url }}
runs-on: ubuntu-latest
needs: build
steps:
- name: Deploy to GitHub Pages
id: deployment
uses: actions/deploy-pages@v2
I wanted to use a custom domain name for the blog, so I followed the instructions on the Github Pages documentation to set up a custom domain.
In order to use a custom domain, you need to create a CNAME record in your DNS settings that points to <username>.github.io.
I did this manually in the console for Cloudflare, but I plan to integrate these settings into a Terraform configuration file that I'll build into this repo in the future.
I could have waited until I had the Terraform setup ready to go too, but getting a minimum viable product up and running quickly is a key part of the DevOps philosophy.
I'm really happy with how with how simple it was to set up this blog using DevOps principles. It only took a few hours to set up the blog, and I have something simple and robust enough for me to write posts and iterate on with little-to-no overhead. I'm looking forward to writing more posts in the future, and I hope you'll join me on this journey!
Cover image credit by Nathan da Silva on Unsplash