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. …

When the package manager - in it’s current state was released, with it’s features for maintaining multiple registries and the like there came talk of having organisation and topic specific registries. I thought it was really cool and jumped to be an early adopter as I could - but at the same time, s…

I am a fan of this proposal. I’ll be honest, I’ve always been sceptical of the BioJulia registry, and never saw enough benefit to move BioStructures.jl to it. Not that I think it’s bad, I just never saw the big advantage. I think putting more on biojulia.net is essential, e.g. a list of packages a…

Ok then, I’ll begin the transition. Yeah it might be good to come up with notebooks and tutorials showing how you can piece together the ecosystem. We should also perhaps have clear instructions on how to avoid the more common julia pitfalls, if we can stop new users from getting that holding the …

For what it’s worth, it was never the intention for there to be multiple public registries of open source projects. The purpose of supporting multiple registries was to allow fully private (not available to the public) and semi-private registries (available but meant for use within an organization/g…

Ok, the process has begun with BioGenerics, BioSymbols, and FormatSpecimens but it’s 3am so I’m gonna crash. In the comming days, if anyone observing General, with the power to merge anything, notices that CI has lit green something that I’m migrating, that is sat waiting for the 3 day wait for new …

Maybe I’m dense or there are complications related to registry CI but wouldn’t it be easier and better to do a wholesale merge of the BioJulia registry into General in a single PR? Assuming there are no name clashes, the package directories (with Package.toml, Versions.toml, Deps.toml, and Compat.to…

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.

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

Specific Domains Biology, Health, and Medicine

dilumaluthge May 24, 2020, 2:13am 35

I’ll keep an eye on the registry.

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

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