'which' is missing in recent seqera containers

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1

A simple r-base container currently does not work:

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image634×455 66 KB

This is because which is missing from the container. When comparing current build URLs with older ones, I saw that the base image changed. So I compared the base images:

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image587×620 43.2 KB

The new base image does not contain which. This leads to r-base not working as expected. This probably means that currently no R image built with seqera containers works. Workarounds could be adding which as a conda package to the image, or overriding the base image via wave CLI.

Long-term solution would be either reverting the default base image to the old one, or installing which like currently procps is handled.

2

For people looking for a temporary base image solution with the wave cli until a fix/update:
--conda-base-image mambaorg/micromamba:2.0.5
This one works for r/which. Example nf-core module env file: modules/modules/nf-core/fungtion/fungtion/environment.yml at b0423b7c1b5d45c42ab163efd17fe87975c2a5e4 · nf-core/modules · GitHub

And then the wave cli command to build the containers should look like this:
wave --conda-file /path/to/environment.yml --singularity --freeze --await 60m --conda-base-image mambaorg/micromamba:2.0.5

(and without --singularity for the docker link)

3

Thanks for reporting this issue. A long term is going to be provided by this fix fix: make `which` available for R (bioconda) post-links in conda v2 builds by pditommaso · Pull Request #1070 · seqeralabs/wave · GitHub