toast VS Rust-Bio

This looks a lot like Toast [1], except that Toast runs your tasks in a (more) reproducible containerized environment to help eliminate the "works on my machine" problem.

[1] https://github.com/stepchowfun/toast

- A build system like Nix [1] but with a better user experience / more straightforward command-line tooling.

- A dependently typed programming language like Coq [2] (or Agda, Idris, Lean, etc.) that is sufficiently approachable to gain enough mindshare that companies start adopting it for mission-critical work.

- A version control system which scales to petabytes or more. Something that I could put large video files in without thinking twice about it. Something a large company could use for their monorepo—or even their data warehouse.

- A note-taking tool that allows me to organize notes in a graph with links between them (like a wiki), not as files and folders in a tree, which enforces the invariant that every note is transitively reachable from some "root" so I never lose a note.

- Something like Toast [3] but which is also designed for running services in production, not just local development and continuous integration. A unified way to run code in dev, test, and prod environments. A new k8s.

[1] https://nixos.org/

[2] https://coq.inria.fr/

[3] https://github.com/stepchowfun/toast (shameless plug)

I realize you are probably very busy, so feel free to say no...but could you glance at this Github listing and tell me if it is what I'm looking for...it seems correct, but I may be misunderstanding...

https://github.com/stepchowfun/toast

Thanks so much in advance...

If you're looking for an alternative way to reproduce your CI locally that isn't tied to a particular CI system (but which has a nice integration with GitHub Actions), there's also Toast: https://github.com/stepchowfun/toast

OP is using Docker + Make in a similar way to how I was a few years ago, before I started using Toast (https://github.com/stepchowfun/toast). Toast lets you define tasks like you would with Make (without all the hairy gotchas of Makefiles), but it runs them inside Docker containers for better portability/reproducibility.

toast: containerized workflow

Does anyone know of zig native libraries for bioinformatics (here is a Rust example https://rust-bio.github.io/ )? It seems as though one could pull in a lot of bioinformatics C libraries such as done with https://github.com/brentp/hts-zig.

e.g. Rust-Bio

I would start with the book and then rust-bio library. Rust is a pretty low level language compared to R/Python. It’s an especially good fit for writing efficient tools that make use of the kinds of algorithms / data structures that are implemented in rust-bio.

Absolutely! It already is, e.g., https://github.com/rust-bio/rust-bio. I'm moving from the academia/nonprofit world into industry bioinformatics, and I intend to use Rust as much as possible. I've already replaced as much of my Python as possible with Rust. I feel I'm able to create larger, more complex programs with Rust because I have the compiler to keep me from making common mistakes that are so easy to make in dynamically typed languages like Perl and Python. It might take longer to write a program initially, but I've started to create a library of functions I can paste together to do things like parse a positive integer, find a bunch of files with a certain file extension, search through data for a pattern, parse CSV files, etc. Writing my latest book has provided even more common patterns I keep finding I use over and over.

I think there is huge potential for Rust in bioinformatics, and there are already some great projects like https://rust-bio.github.io/. It seems industry is also hiring for these skills. This Nature article is a little old, but also covers why people in the field are looking for greater safety and performance. It's relatively easy to write a Python program to do bio stuff, but it's also very easy to get lots of things wrong or for the resulting program to be slow and/or impossible to extend and maintain. In the long run, I think it makes sense to write in Rust. Perl was king in biofx when I started, and I would not have predicted it being displaced by Python, so there's good reason to believe that Python may one day be eclipsed by Rust.

Well, someone mentioned https://rust-bio.github.io/

So generally stuff in this maths/numerical space. The term is a bit deceptive because it rarely means domain-specific science libraries like rust-bio even thought that might be what you think when you hear "scientific computing".