Replace vanilla Linux Biocontainer with Ubuntu #1557
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Is there an option to use a base alpine container for these utilities? That would limit the network traffic needed to pull the images? |
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We could do but like with all other modules it makes sense to use a container that has both Docker and Singularity images that we can pull directly, and this particular container does. |
You could override the container with your Also, 22.04 got released yesterday https://discourse.ubuntu.com/t/jammy-jellyfish-release-notes/24668 just in case you weren't aware that was an option. |
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22.04 doesn't have a Singularity container 😏 But no reason we can't update in the future. At this point, I think we just need access to basic Linux utilities so I think it's fine. As you mentioned, you can always override the configuration with your own container definitions. |
| @@ -2,10 +2,10 @@ process UNTAR { | |||
| tag "$archive" | |||
| label 'process_low' | |||
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| conda (params.enable_conda ? "conda-forge::tar=1.34" : null) | |||
| conda (params.enable_conda ? "conda-forge::sed=4.7" : null) | |||
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That's the only change that I don't get. Isn't it much more explicit to install tar in the untar module rather than sed which happens to include tar?
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Good spot! Missed that in the copy/paste. Wondering whether we need to care about this specifically because these tools should all be installed in the base Conda env anyway right? So do we go for standardisation here where we always define sed for modules using the ubuntu image or do we define the specific tools we are using? The latter could also be a pain in general because in most instances you will want to use multiple utilities like cat, awk, sed in the same module etc
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Fair point. If there's a way to pull in multiple standard tools that are also available in the container images, then that's probably preferable. Would that make available ps btw? I think that's needed for resource tracing, right?
x-ref: nf-core/rnaseq#764