#bioconda — Public Fediverse posts

My #BioConda PR was merged overnight (thank you @bgruening), another two submitted for review - also rebuilding packages for Python 3.13. I should then be able to easily install the assembly tool I wanted to run...

I did some more triage while waiting for builds - the automated version bumps are easiest - but need to scan the change logs or commits for any dependency changes.

My #BioConda PR was merged overnight (thank you @bgruening), another two submitted for review - also rebuilding packages for Python 3.13. I should then be able to easily install the assembly tool I wanted to run...

I did some more triage while waiting for builds - the automated version bumps are easiest - but need to scan the change logs or commits for any dependency changes.

My #BioConda PR was merged overnight (thank you @bgruening), another two submitted for review - also rebuilding packages for Python 3.13. I should then be able to easily install the assembly tool I wanted to run...

I did some more triage while waiting for builds - the automated version bumps are easiest - but need to scan the change logs or commits for any dependency changes.

My #BioConda PR was merged overnight (thank you @bgruening), another two submitted for review - also rebuilding packages for Python 3.13. I should then be able to easily install the assembly tool I wanted to run...

I did some more triage while waiting for builds - the automated version bumps are easiest - but need to scan the change logs or commits for any dependency changes.

My #BioConda PR was merged overnight (thank you @bgruening), another two submitted for review - also rebuilding packages for Python 3.13. I should then be able to easily install the assembly tool I wanted to run...

I did some more triage while waiting for builds - the automated version bumps are easiest - but need to scan the change logs or commits for any dependency changes.

I was feeling pretty optimistic about getting https://github.com/bioconda/bioconda-recipes/pull/66326 merged overnight to rebuild pybedtools for #BioConda with current Python (not my ultimate goal but a step towards it) until I saw over 100 pending with "please review & merge": https://github.com/bioconda/bioconda-recipes/pulls?q=is%3Aopen+is%3Apr+label%3A%22please+review+%26+merge%22

I did my bit with some general triage of older issues... but that's quite a backlog?

I was feeling pretty optimistic about getting https://github.com/bioconda/bioconda-recipes/pull/66326 merged overnight to rebuild pybedtools for #BioConda with current Python (not my ultimate goal but a step towards it) until I saw over 100 pending with "please review & merge": https://github.com/bioconda/bioconda-recipes/pulls?q=is%3Aopen+is%3Apr+label%3A%22please+review+%26+merge%22

I did my bit with some general triage of older issues... but that's quite a backlog?

I was feeling pretty optimistic about getting https://github.com/bioconda/bioconda-recipes/pull/66326 merged overnight to rebuild pybedtools for #BioConda with current Python (not my ultimate goal but a step towards it) until I saw over 100 pending with "please review & merge": https://github.com/bioconda/bioconda-recipes/pulls?q=is%3Aopen+is%3Apr+label%3A%22please+review+%26+merge%22

I did my bit with some general triage of older issues... but that's quite a backlog?

I was feeling pretty optimistic about getting https://github.com/bioconda/bioconda-recipes/pull/66326 merged overnight to rebuild pybedtools for #BioConda with current Python (not my ultimate goal but a step towards it) until I saw over 100 pending with "please review & merge": https://github.com/bioconda/bioconda-recipes/pulls?q=is%3Aopen+is%3Apr+label%3A%22please+review+%26+merge%22

I did my bit with some general triage of older issues... but that's quite a backlog?

I was feeling pretty optimistic about getting https://github.com/bioconda/bioconda-recipes/pull/66326 merged overnight to rebuild pybedtools for #BioConda with current Python (not my ultimate goal but a step towards it) until I saw over 100 pending with "please review & merge": https://github.com/bioconda/bioconda-recipes/pulls?q=is%3Aopen+is%3Apr+label%3A%22please+review+%26+merge%22

I did my bit with some general triage of older issues... but that's quite a backlog?

Over last few days I wrote about publishing #Python packages to #PyPI and #bioconda. Enjoy!
#bionformatics
https://wasi.ovh/yachay/posts/2026/publish_python/

Over last few days I wrote about publishing #Python packages to #PyPI and #bioconda. Enjoy!
#bionformatics
https://wasi.ovh/yachay/posts/2026/publish_python/

Over last few days I wrote about publishing #Python packages to #PyPI and #bioconda. Enjoy!
#bionformatics
https://wasi.ovh/yachay/posts/2026/publish_python/

Over last few days I wrote about publishing #Python packages to #PyPI and #bioconda. Enjoy!
#bionformatics
https://wasi.ovh/yachay/posts/2026/publish_python/

Over last few days I wrote about publishing #Python packages to #PyPI and #bioconda. Enjoy!
#bionformatics
https://wasi.ovh/yachay/posts/2026/publish_python/

X-post from Bluesky:

🧑‍💻Satellite Hackathon at #ViBioM2026!

Join the #Virus #Bioinformatics + @nf_core Hybrid Collaborative #Hackathon & collaborate on bioinformatic tools and ideas & contribute to reproducible workflows & research infrastructure.

Want to write nf-core modules for virus tools? Convert viral analysis workflows to #Nextflow? Add tools to #bioconda ? Contribute VirJenDB? Or your own project?

(supported by @NFDI4Microbiota )

Register your interest 👇

https://evbc.uni-jena.de/events/vibiom2026/hackathon-satellite-event/

X-post from Bluesky:

🧑‍💻Satellite Hackathon at #ViBioM2026!

Join the #Virus #Bioinformatics + @nf_core Hybrid Collaborative #Hackathon & collaborate on bioinformatic tools and ideas & contribute to reproducible workflows & research infrastructure.

Want to write nf-core modules for virus tools? Convert viral analysis workflows to #Nextflow? Add tools to #bioconda ? Contribute VirJenDB? Or your own project?

(supported by @NFDI4Microbiota )

Register your interest 👇

https://evbc.uni-jena.de/events/vibiom2026/hackathon-satellite-event/

X-post from Bluesky:

🧑‍💻Satellite Hackathon at #ViBioM2026!

Join the #Virus #Bioinformatics + @nf_core Hybrid Collaborative #Hackathon & collaborate on bioinformatic tools and ideas & contribute to reproducible workflows & research infrastructure.

Want to write nf-core modules for virus tools? Convert viral analysis workflows to #Nextflow? Add tools to #bioconda ? Contribute VirJenDB? Or your own project?

(supported by @NFDI4Microbiota )

Register your interest 👇

https://evbc.uni-jena.de/events/vibiom2026/hackathon-satellite-event/

X-post from Bluesky:

🧑‍💻Satellite Hackathon at #ViBioM2026!

Join the #Virus #Bioinformatics + @nf_core Hybrid Collaborative #Hackathon & collaborate on bioinformatic tools and ideas & contribute to reproducible workflows & research infrastructure.

Want to write nf-core modules for virus tools? Convert viral analysis workflows to #Nextflow? Add tools to #bioconda ? Contribute VirJenDB? Or your own project?

(supported by @NFDI4Microbiota )

Register your interest 👇

https://evbc.uni-jena.de/events/vibiom2026/hackathon-satellite-event/

X-post from Bluesky:

🧑‍💻Satellite Hackathon at #ViBioM2026!

Join the #Virus #Bioinformatics + @nf_core Hybrid Collaborative #Hackathon & collaborate on bioinformatic tools and ideas & contribute to reproducible workflows & research infrastructure.

Want to write nf-core modules for virus tools? Convert viral analysis workflows to #Nextflow? Add tools to #bioconda ? Contribute VirJenDB? Or your own project?

(supported by @NFDI4Microbiota )

Register your interest 👇

https://evbc.uni-jena.de/events/vibiom2026/hackathon-satellite-event/

This cannot be:

I am trying to compile a few stats for the #Snakemake executor plugin for #SLURM on #HPC systems. Preparing for a lighting talk at the #SnakemakeHackathon2026

PyPi: 20,000 downloads last month
BioConda: > 60,000 total (aggregated over all versions)

Impressive as it might be, this is contradictory. PyPi would exceed BioConda by a huge margin.

Does anyone know how to get all-time statistics from either platform? #BioConda or #PyPi?

This cannot be:

I am trying to compile a few stats for the #Snakemake executor plugin for #SLURM on #HPC systems. Preparing for a lighting talk at the #SnakemakeHackathon2026

PyPi: 20,000 downloads last month
BioConda: > 60,000 total (aggregated over all versions)

Impressive as it might be, this is contradictory. PyPi would exceed BioConda by a huge margin.

Does anyone know how to get all-time statistics from either platform? #BioConda or #PyPi?

This cannot be:

I am trying to compile a few stats for the #Snakemake executor plugin for #SLURM on #HPC systems. Preparing for a lighting talk at the #SnakemakeHackathon2026

PyPi: 20,000 downloads last month
BioConda: > 60,000 total (aggregated over all versions)

Impressive as it might be, this is contradictory. PyPi would exceed BioConda by a huge margin.

Does anyone know how to get all-time statistics from either platform? #BioConda or #PyPi?

This cannot be:

I am trying to compile a few stats for the #Snakemake executor plugin for #SLURM on #HPC systems. Preparing for a lighting talk at the #SnakemakeHackathon2026

PyPi: 20,000 downloads last month
BioConda: > 60,000 total (aggregated over all versions)

Impressive as it might be, this is contradictory. PyPi would exceed BioConda by a huge margin.

Does anyone know how to get all-time statistics from either platform? #BioConda or #PyPi?

This cannot be:

I am trying to compile a few stats for the #Snakemake executor plugin for #SLURM on #HPC systems. Preparing for a lighting talk at the #SnakemakeHackathon2026

PyPi: 20,000 downloads last month
BioConda: > 60,000 total (aggregated over all versions)

Impressive as it might be, this is contradictory. PyPi would exceed BioConda by a huge margin.

Does anyone know how to get all-time statistics from either platform? #BioConda or #PyPi?

CondaNest – GUI quản lý môi trường Conda trên Linux, phù hợp cho xử lý đa môi trường Bioconda. Giao diện nhẹ, trực quan, không cần activate để xem gói. Tạo, xóa, dọn dẹp môi trường dễ dàng. Viết bằng Python & GTK4, hiệu năng cao. Đang ở giai đoạn beta – góp ý để cải thiện! #Conda #Bioconda #Linux #Python #GTK4 #OpenSource #conda #bioconda #linux #opensource

https://www.reddit.com/r/opensource/comments/1qi9ewg/i_built_a_native_linux_gui_to_organize_conda/

@pjacock @maartenk

Just _now_ in #bioconda . Please give it a try, Peter. The execution is skipped in a CI environment. The fact that it passed the Bioconda test makes me optimistic.

As for the documentation page: I have to wait, as I cannot trigger an update. But I will pay attention.

AS for the change: It was a crude hack. See:

https://fediscience.org/@snakemake/115701873440242545

@pjacock @maartenk

Just _now_ in #bioconda . Please give it a try, Peter. The execution is skipped in a CI environment. The fact that it passed the Bioconda test makes me optimistic.

As for the documentation page: I have to wait, as I cannot trigger an update. But I will pay attention.

AS for the change: It was a crude hack. See:

https://fediscience.org/@snakemake/115701873440242545

@pjacock @maartenk

Just _now_ in #bioconda . Please give it a try, Peter. The execution is skipped in a CI environment. The fact that it passed the Bioconda test makes me optimistic.

As for the documentation page: I have to wait, as I cannot trigger an update. But I will pay attention.

AS for the change: It was a crude hack. See:

https://fediscience.org/@snakemake/115701873440242545

@pjacock @maartenk

Just _now_ in #bioconda . Please give it a try, Peter. The execution is skipped in a CI environment. The fact that it passed the Bioconda test makes me optimistic.

As for the documentation page: I have to wait, as I cannot trigger an update. But I will pay attention.

AS for the change: It was a crude hack. See:

https://fediscience.org/@snakemake/115701873440242545

@pjacock @maartenk

Just _now_ in #bioconda . Please give it a try, Peter. The execution is skipped in a CI environment. The fact that it passed the Bioconda test makes me optimistic.

As for the documentation page: I have to wait, as I cannot trigger an update. But I will pay attention.

AS for the change: It was a crude hack. See:

https://fediscience.org/@snakemake/115701873440242545

@egonw a few days ago, I bumped the #Bioconda package of r-wikipathways to v1.30 . Thank you for this wonderful package!

Today, after quite some tinkering, I managed to overlay differential expression results. This is not stable code, yet. The enrichment is a bit fiddly and the overlay relies on finding the right offsets in a downloaded path figure. But perhaps, I am naive and there is a better way?

@egonw a few days ago, I bumped the #Bioconda package of r-wikipathways to v1.30 . Thank you for this wonderful package!

Today, after quite some tinkering, I managed to overlay differential expression results. This is not stable code, yet. The enrichment is a bit fiddly and the overlay relies on finding the right offsets in a downloaded path figure. But perhaps, I am naive and there is a better way?

@egonw a few days ago, I bumped the #Bioconda package of r-wikipathways to v1.30 . Thank you for this wonderful package!

Today, after quite some tinkering, I managed to overlay differential expression results. This is not stable code, yet. The enrichment is a bit fiddly and the overlay relies on finding the right offsets in a downloaded path figure. But perhaps, I am naive and there is a better way?

@egonw a few days ago, I bumped the #Bioconda package of r-wikipathways to v1.30 . Thank you for this wonderful package!

Today, after quite some tinkering, I managed to overlay differential expression results. This is not stable code, yet. The enrichment is a bit fiddly and the overlay relies on finding the right offsets in a downloaded path figure. But perhaps, I am naive and there is a better way?

My first contribution to #Bioconda - not much, a rather old software. Took a while ...

the last version is already in #bioconda

But the issue with the reference might be more severe. I just LOVE it, if things break in a course, which are supposed to work. For now:
- WiFi led to several outages on student laptops. Lost connection also means lost connection of a Live Linux system on these laptops. Worst case: Need to reboot.
- need to have a reservation, which despite a "MAGNETIC" flag needs the `--reservation` flag. Luckily, I already implemented to provide `--slurm-reservation` to #snakemake
- the thing with the QoS flag. It is the first time, during a course, I was required to use this. In > 10 years! Of course, this was unanticipated and unannounced.
- disk quota issues, because I cannot use a shared conda repo, even though I tested this.

Whish me luck. I might just end my interrupted Python intro - this at least is working.

8/n

Benchmarking and rebuilding bwa-mem2 with LLVM vs. GCC.

https://github.com/bioconda/bioconda-recipes/pull/56242

#bioconda

There is quite a backlog of open pull requests for #BioConda, with a lot of new recipes judging from the little bit of triage I just did https://github.com/bioconda/bioconda-recipes/pulls

Due to maintenance of the cluster I usually work on, only minor updates to the #SLURM plugin for #HPC compatible workflows could be made.

However, it now has better GPU support by generic resources. Already on #PyPi, soon on #Bioconda, too.

By default, the #Seqera #Containers web interface searches the #bioconda and #condaforge channels 📦

But did you know that you can prepend your search with *any* conda channel?

Try it out: https://seqera.io/containers/

#bioconda has reached 11.111 packages. Great end of the year 2024. Thanks a lot for all contributors and the Bioconda Core team to keep the infrastructure up and running.

New release for the #Snakemake #SLURM plugin to use on #HPC clusters.

A bug fix release to reliably submit and cancel jobs, where admins overwrote `sbatch` behaviour with additional output on `stderr`. See https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v0.11.2 (will automatically be released on #bioconda and #pypi)

Finally resuming work on the plugin. It has been a stressful time, lately.

#ReproducibleResearch #bioinformatics #OpenScience

And if anyone from #bioconda sees this and likes it, I would be happy to chat about maybe porting it to proper docs if of interest :)

[🧵 2/2]

Do you work in #bioinformatics, love #conda & #bioconda, but didn't know how to start adding (or debugging) your/someone else's software to it?

Here's a three-part (opinionated) guide for the #microbifinie blog on just that, based on my own experiences!

Adding: https://ubinfie.github.io/2024/08/16/adding-to-bioconda-quickguide.html
Updating: https://ubinfie.github.io/2024/08/16/updating-bioconda-recipe-quickguide
Debugging: https://ubinfie.github.io/2024/08/16/debugging-bioconda-build-quickguide

Many thanks to George Bouras for nudging me to formalise my notes, and @shl , Wytamma Wirth, and @pmenzel for the testing/review!

[🧵1/2]

Lately, we’ve seen some concern and confusion among our users, so we want to clear things up. In this blog post, we’re breaking down the #conda ecosystem: the tools, the channels (like #conda-forge, #bioconda), how to get started, and how multi-stakeholder governance ensures the ecosystem remains reliable and accessible for everyone. 👉 https://conda.org/blog/2024-08-14-conda-ecosystem-explained
This was a collaborative effort from across conda ecosystem, and we hope it’s helpful for the whole community. 🤗

#bioconda #usegalaxy @elixir_europe all my favourites in one slide :-)
59 new tools in Galaxy for Exposome research!

CompareM2 is published on Bioconda! Enjoy!

For all of your prokaryotic genomes-to-report needs.

https://comparem2.readthedocs.io/en/latest/

#bioinformatics #genomics #microbiology #bioconda #foss

Nice - my tool's test suite passed first time on Apple M3 ARM silicon 🎉

The only catch is no #BioConda support, meaning I've skipped a few soft dependencies. And I had to locally compile a key dependency not yet ready via conda-forge.

@stackprotector @vaurora I needed to add to a #bioconda contributor's PR today, so tried this out with the gh cli.

Turns out that checking out the PR with `gh pr checkout PRNUM` does indeed set up the branch's pushRemote etc config so that pushing the branch pushes to the right fork without needing it set up as a remote. (And later deleting the branch tidies up .git/config.)

Very handy, and I may start using this instead of my home-grown equivalent.

@johnm their bus factor does worry me - how many people truly understand the internals of #BioConda, and are they gaining any newcomers or missing out on potential people like you? (I've personally only stuck to adding or updating recipes)

@pjacock I assumed “they're busy” was going to be a reply to my other rant, about #bioconda being unresponsive. 🤣

I saw that biopython accidental report. Sure, they're busy, but by doing no analysis on the incoming report and just spraying it upstream in various directions, the result is more work for everyone — including themselves. Which makes everyone busier…