from the community news: " Biofast is a small benchmark for evaluating the performance of programming languages and implementations on a few common tasks in the field of Bioinformatics. It currently includes two benchmarks: FASTQ parsing and interval query ." Please help to improve the Julia part. …

There are packages that have different versions that span both registries, and I don’t trust myself to manually sort that out in a PR without human error creeping in. But for the packages with no previous entries in General it would be easier.

Manually sounds barbaric but let there be tools. Try this and see if you like the result in /tmp/General (adjust the paths as necessary if you’re not running Linux): using Pkg pkg"add LocalRegistry#merge" using LocalRegistry run(`git clone https://github.com/JuliaRegistries/General.git /tmp/General…

I tried this this morning - I totally did not clock the merge_packages option facepalm.

It probably didn’t exist at the time. :slight_smile:

OMG that merge function has saved my sanity. Thank you!

Ok, everything in the BioJuliaRegistry has been merged into General. I’m going to update the website, but there may be references to the registry in READMEs and old doc builds whilst we get around to hunting them out and correcting them. In the meantime it would help if any users could remove the Bi…

New Getting Started instructions are available on the website, as is a new post explaining Bio.jl is deprecated, and which packages should be used instead.

What should I do to migrate from BioJuliaRegistry to General ?

Assuming it worked as expected, I think just delete the BioJulia registry (~/.julia/registries/BioJuliaRegistry/), then resolve? I did that (well, I moved the registry instead of deleting, just in case), and that seems to have worked.

I just did pkg> registry rm BioJuliaRegistry and then for my few active projects on my desktop deleted any manifests and instantiated them again. Resolve seems to work as @kevbonham says. Any packages - mostly BioJulia ones that still get the BioJuliaRegistry in their CI in order to work, should wor…

lhe/Biofast benchmark | FASTQ parsing [Julia,Nim,Crystal,Python,...]

Specific Domains Biology, Health, and Medicine

dilumaluthge May 25, 2020, 8:17pm 56

Okay, here is one of @StefanKarpinski’s good comments on the matter. If you search the Julia Discourse, you can also find many other good comments by Stefan on this matter.

Topic		Replies	Views
[ANN] BioToolkit.jl: A high-performance biocomputing package Package Announcements package , announcement , bioinformatics	8	520	March 27, 2026
Julia motivation: why weren't Numpy, Scipy, Numba, good enough? Community history	123	84270	September 21, 2018
Thoughts on eventual Julia 2.0 transition Internals & Design upgrades	47	9401	October 15, 2018
How I learned to stop worrying about being fastest and love microbenchmarks Community	22	3246	November 3, 2023
What do you work on? Why is it important? Community	29	4520	June 7, 2021

lhe/Biofast benchmark | FASTQ parsing [Julia,Nim,Crystal,Python,...]

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