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Implement container_register for tool repositories. #675

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jmchilton commented May 22, 2017

xref - last bullet of #646

@jmchilton jmchilton added this to the GCC 2017 milestone May 22, 2017

@peterjc peterjc changed the title [WIP] Implement container_regsiter for tool repositories. [WIP] Implement container_register for tool repositories. May 22, 2017

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peterjc commented May 22, 2017

Is it worth fixing the typo in the commit message?

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peterjc commented May 22, 2017

The documentation is somewhat cryptic without being familiar with the area, but that also means I can't suggest how to improve this:

   """Register multi-requirement containers as needed.

    BioContainers publishes all Bioconda packages automatically as individual
    container images. These however are not enough for tools with multiple
    best-practice requirements. Such requirements should be recorded and published
    so that a container can be created and registered for these tools.
    """

@jmchilton jmchilton force-pushed the jmchilton:mulled_register branch from 2bb46c3 to 49df20e May 22, 2017

@jmchilton jmchilton force-pushed the jmchilton:mulled_register branch 5 times, most recently from 49b03d3 to 8de4bb8 May 30, 2017

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jmchilton commented May 31, 2017

@peterjc Agreed this is not documented well and I'm still trying to figure out how to describe what is going on. There was a bit of a conversation about this in the tools-iuc Gitter just now and there is some discussion on the README of this repo if you want to dig a little deeper. At a high level, the goal is that all tools that have Conda-ified requirement tags will automatically have containers registered and published quay.io/biocontainers for each unique combination of requirements. This new command opens a PR against a registry of such combinations that when merged will result in a container being published. I want to just monitor repositories though and take care of these details without intervention on a per tool basis - so to leverage this tool developers will just need to add their repository to the list in this file (https://github.com/jmchilton/mulled-monitor/blob/master/monitor.sh#L3). I'm going to present this as the GCC - so hopefully I figure out how to talk about this before then.

@jmchilton jmchilton force-pushed the jmchilton:mulled_register branch 2 times, most recently from f9dd933 to 653ab43 Jun 1, 2017

Implement ``container_regsiter`` command.
Along with associated enhancements to Github, Conda, and mulled utilities.

@jmchilton jmchilton force-pushed the jmchilton:mulled_register branch from e07aa3d to 44a0a7c Jun 5, 2017

@jmchilton jmchilton changed the title [WIP] Implement container_register for tool repositories. Implement container_register for tool repositories. Jun 5, 2017

@jmchilton jmchilton merged commit 1e72bd8 into galaxyproject:master Jun 5, 2017

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bgruening commented Jun 5, 2017

Wuhu!!!!

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jmchilton commented Jun 5, 2017

Thanks @bgruening - I've updated #646 with your v2 mulled idea.

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