This looks useful, but can it submit jobs to cloud compute clusters or HPC systems and operate locally? Maybe I’m missing the point in terms of the purpose.
This looks useful, but can it submit jobs to cloud compute clusters or HPC systems and operate locally? Maybe I’m missing the point in terms of the purpose.
I'm very excited that this is based on Scheme -- I've long wanted a lispy workflow language!
I'm a little concerned about the coverage of the Guix package manager though. I guess instead of writing Dockerfiles the user would have to learn to write Guix packages.
The "Getting Started" example uses samtools so I guess this is oriented towards a similar bioinformatics audience. However without HPC/Cloud support it's probably not too practical, yet.
Addendum: Listened to the FOSDEM 2019 talk, seems like it does support Docker and HPC. However I need AWS Batch support for it to be really useful to me, hopefully that will be implemented at some point.
Edit: adding gnu guix manual link
It's actually very cool since you can drop in any Java library you like, which is particularly nice in the bioinformatics space where HTSJDK, Picard and co. give you enormous power in that space.
My efforts with BioNix (https://github.com/PapenfussLab/bionix) achieve reproducible pipelines by using Nix to capture the software, workflow, and handle execution either locally, on a compute cluster, or HPC.
Guixwl looks similar to BioNix, though BioNix is a thin layer of Nix expressions and Guixwl seems to be more then that and could be more general. BioNix is targeted at bioinformatics and just builds on nixpkgs.