I am happy to announce that I am seeking for a #postdoctoral bioinformatician or computer scientist for a full, #permanent_position as a research fellow in my lab! Co-maintain popular #opensource projects like #Bioconda, #Snakemake, and #Varlociraptor!
Develop exciting, versatile, and sustainably maintained solutions that will shape the future of precision medicine and bioinformatics in general.

https://koesterlab.github.io/#research-fellow-permanent

I've spent the last weeks to conduct a major rebuild of #bioconda packages, using newer compilers and e.g. openssl 3. There are quite some packages that need further fixes. You find a nightly updated list here: https://github.com/bioconda/bioconda-recipes/wiki/build-failures. Fixes are very welcome!

RT @tallphil
Had a lot of fun doing this - a nice beginner friendly tutorial 😊 Take your #Python analysis script and build it into a command-line tool, ready for release via @pypi / #bioconda / @BioContainers 🐍🐳🎉

Watch now on YouTube: https://www.youtube.com/watch?v=hOuS6mXCwhk https://twitter.com/nf_core/status/1653351656686333953

Had a lot of fun doing this - a nice beginner friendly tutorial 😊 Take your #Python analysis script and build it into a command-line tool, ready for release via @pypi / #bioconda / @BioContainers 🐍🐳🎉

Watch now on YouTube: https://www.youtube.com/watch?v=hOuS6mXCwhk
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RT @nf_core
Hej, todays @nf_core #bytesize talk about python script packaging with Phil Ewels will start in 8 minutes, 1pm CEST. Find the zoom link here: https://nf-co.re/…
https://twitter.com/nf_core/status/1653351656686333953

After some annoying #Bioconda package build failures, I've raised a feature request with the #conda mainline. However the other issues I've previously reported there have been ignored for 8 months, two years, and two years respectively, so this is more of a quixotic gesture than anything else… https://github.com/conda/conda-build/issues/4869

Companies like to keep their source code hidden. If you look at the PacificBiosciences github repo (e.g. https://github.com/PacificBiosciences/ccs ) you will find a "release" containing exactly this "repo": only the docs and License and a "readme" file. Also a link to a compressed tar file, containing a static binary. Unversioned. And there is no issue tracking. Issues can't be.

But, hey! It is in #bioconda !1!11!!

#reproducibility

RT @nomad421
Ok, who's been following my "why doesn't this build/work properly when built" drama regarding #bioconda. Well, the problem, as ever, was C++! TLDR: static variables at namespace scope are evil, bad and unpredictable, because the language is not fit for purpose.

RT @nomad421@twitter.com

Ok .... #bioconda drama. I think maybe the reason that certain headers are not being found is because the $PREFIX path is ... tooo long?!?! The penultimate path is just `_h_env_placeholder_....` for 209 characters. Anyone seen this? Ideas to overcome it?

🐦🔗: https://twitter.com/nomad421/status/1619888458230808577

Ok .... #bioconda drama. I think maybe the reason that certain headers are not being found is because the $PREFIX path is ... tooo long?!?! The penultimate path is just `_h_env_placeholder_....` for 209 characters. Anyone seen this? Ideas to overcome it?

One of the things that keep breaking my #python packages in #pypi or a #conda repositories like #condaforge or #bioconda is the fuzziness about dependency management.

Let's say my package depends on X, but I don't specify a particular version. All working today, but in a couple of weeks there is a X release which is not compatible.

Even if you set your dependency versions carefully, you cannot control the dependencies of your dependencies...

How do you define your dependencies? Any advice?

Just released @PacBio@twitter.com lima v2.7.1 on #bioconda #bioinformatics.
The 96-plex "SMRTbell Barcoded Adapter Plate 3.0" achieves 99.5% demux yield (97.0% before) on #HiFi with an average barcode precision of 99.993%.

Also pbmm2 v1.10.0 is ready for Revio with many fixes.

Did you know you can retrieve annotation and gene expression data from #Bgee and perform #TopAnat analyses in #BioContainers? It's the fashionable way to access curated #GeneExpression 😎
https://biocontainers.pro/tools/bioconductor-bgeedb
#BioConda #Singularity #Docker #bioinformatics #biocuration #RNAseq #microarrays #UberAnat #SIB

My latest article on Medium walks you through how to publish Python packages of bioinformatics software on Bioconda. 🐍👩🏻‍💻
#Bioinformatics #bioconda #Python #Software
https://towardsdatascience.com/all-you-need-to-know-about-publishing-software-on-bioconda-680d48e52868?sk=bcd00f3bedb4638239e6f35779c6638b

Has anyone had trouble (or success) using std::filesystem from c++17 under OSX when building in #bioconda (https://dev.azure.com/bioconda/bioconda-recipes/_build/results?buildId=24636&view=logs&jobId=3e927886-88a5-5ae4-09f7-f53fa1a22322&j=3e927886-88a5-5ae4-09f7-f53fa1a22322&t=577c9198-bb4c-5a92-f06b-21e420caadce)?

Do any #bioconda folks know if it's possible to use this trick (https://conda-forge.org/docs/maintainer/knowledge_base.html#requiring-newer-macos-sdks) with bioconda recipes to require newer OS X SDKs? I tried it, but it doesn't seem to be working. Am I missing something? (relevant PR: https://github.com/bioconda/bioconda-recipes/pull/38087)

Don‘t miss the 5th de.NBI #denbi Cloud User Meeting from Dec. 6th-7th at Forschungszentrum Jülich @fzj Registration closes on November 20th. More information here: https://events.denbi.de/e/clum2022 Topics include: cloud computing, such as container orchestration using #Kubernetes, the application of infrastructure as code technologies #Ansible and #OpenStack, SimpleVM as well as bioinformatics related workshops such as an introduction to #Bioconda and #BioContainers and #cwl

@drjulie_b @multimeric I haven’t looked at the statistics, but my guess would be the majority of #bioconda packages are made by conda regulars or others who want to use the tools themselves or make them more available, rather than by the upstream authors themselves.

Sometimes upstream then incorporates a bioconda link into their documentation. Sometimes not.

Hi all. I am Johannes Köster, a computer scientist and bioinformatician working at the @unidue. I am developer of the widely used workflow management system #Snakemake and the genomic variant caller #Varlociraptor. Further I am the founder of the #Bioconda project which offers the largest collection of #Conda packages for bioinformatics software. #introduction

#introductions

Hi, I'm a Senior Bioinformatician at SAGA Diagnostics working on #cancer diagnostics, #genomics, #ctDNA, and #liquidbiopsy. I did my PhD at Lund University working on large-scale #breastcancer #transcriptomics, and I’m still affiliated with LU working on cancer-related projects.

Before #bioinformatics I worked a lot on the #FreeBSD operating system. Nowadays I mostly contribute to #Bioconda (core team), #condaforge (R stack co-maintainer), and other bioinf / #datasci projects.

Referenced link: https://orcid.org/0000-0002-0173-3009
Originally posted by backofenlab / @BackofenLab@twitter.com: https://twitter.com/BackofenLab/status/1341360978810814464#m

Heartfelt congratulations to @MiladMiladi_ for successfully defending his PhD thesis last friday. He published an amazing number of papers, 12 of them with a major contribution! Check out his work here: https://orcid.org/0000-0002-0173-3009 #bioinformatics #COVID19 #bioconda #RNA #usegalaxy