March 3, 2017

Chef and DevOPs at Eagle

In my day to day work at Eagle, all of the projects I work on need tools installed. Bioinformatics tools infrequently come in one simple bundle and sometimes the dependencies can be vast and platform dependant. Here at Eagle we embrace the culture of DevOps to retain our sanity!


We use Chef to manage our tools deployment, whether it be onto an AWS instance, a VM or a Docker container. If we are going to use a tool on a project then it’s pretty likely we’ve used it before. This week however I needed to install REAPR to evaluate a genome assembly I’ve been playing around with. Normally I like to email the author and let them now that we’ve written a cookbook that deploys their hard work but this week I decided to tell the world via our blog ;-).   I’ll tell the author when I see them around the Genome Campus now we have moved (apparently one or two bioinformatics tools have been developed here over the years, not to mention formats, compression algorithms, assemblies, the list goes on!)

There are a LOT of bioinformatics tools out there and we only support a couple of flavours of linux at the moment but it’s a work in progress; currently we have 35 publicly available NGS tools cookbooks at our github repository:

All of the code is tested using Rspec, ServerSpec and more recently: InSpec. The projects are continuously integrated using Jenkins, KitchenCI, Foodcritic and Rubocop.


It’s good to be able to give something back to the community by open sourcing our Chef cookbooks!


Topics: AWS, Blog, DevOPs, Eagle, EagleGenomics-cookbooks, Foodcritic, github, Jenkins, KitchenCi, Rubocop, ruby