Last week, Anthropic released a new feature for Claude: skills. In our lab, we have been using Claude Code fora a while and striving to document our workflows so that new students and postdocs can quickly get up to speed (for example, in this public repository. However, adapting code from others is still a daunting task for newcomers.
I am working on a paper currently and right now have the problem of adapting a workflow provided by a collaborator. Basically, this is a workflow for inferring phylogenies from genomes by using BUSCOs, and there are several little things we need to think about: how to make an environment in my particular system, what are the resources available, what is the best BUSCO dataset for my target organisms, how to combine NCBI data with locally available genomes.
As I was in the process of adapting the scripts, it occurred to me this would be a great use case for a Claude Code skill: what if I could teach Claude how to implement what I wanted, and then have it ask questions and generate functional scripts that I could run as a pipeline?
So instead of spending a few hours doing the actual programming work, I spent a few hours on this sort of metaprogramming. In a first pass, it is working decently. I still needed to check individual files, and in almost all cases the scripts generated by Claude needed a few small fixes. I am now feeding these back into the skill to hopefully improve it for a next use. But it seems that both (1) bioinformaticians are still not out of jobs and (2) this is a huge time saver, even if not yet perfect.
But one might ask: creating skills seems too complicated, how can I do that quickly? Well, Claude has a skill for that! For now I am keeping all my skills in this repository, including the phylogenetics one and another to make Claude less agreeable and more useful to me. Check it out and reuse if interested: https://github.com/brunoasm/my_claude_skills
