expectation: spend 4 hours on deep work to do some bioinformatics analysis... reality: spend 4 hours troubleshooting issues with our HPC environment and trying to figure out why my conda environment is not letting me do what i want... 🖥🧬 🧪 - ThreadSky

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bioinformer.bsky.social • 30 days ago

expectation: spend 4 hours on deep work to do some bioinformatics analysis...

reality: spend 4 hours troubleshooting issues with our HPC environment and trying to figure out why my conda environment is not letting me do what i want...

🖥🧬 🧪

Comments

typemat12.bsky.social•30 days ago

At least you still have conda access. The institutional licence changes were so high that our access has been blocked to default channels completely to stop us getting charged, which then effectively blocks most prebuilt package recipes.

bioinformer.bsky.social•30 days ago

Doh! 😖

arcane-mahesh.bsky.social•30 days ago

What do you need from the default channels? I thought most researcher tools and packages were now on bioconda and conda-forge. I also switched from conda to Pixi (https://Pixi.sh) which gives better error messages. I can explore what I need with Pixi and then make a container using Seqera Containers after.

typemat12.bsky.social•30 days ago

Basically nothing, but recipes built by the community (inc on bioconda) can include them anyway.

traversaro.bsky.social•27 days ago

This is interesting, which bioconda packages use defaults dependencies? As far as I know bioconda stopped using defaults a long time ago, see https://github.com/bioconda/bioconda-docs/pull/30 .

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