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Fix containerized merqury #5945

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merged 7 commits into from
Apr 13, 2024

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mvdbeek
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@mvdbeek mvdbeek commented Apr 12, 2024

Might be faster than bioconda/bioconda-recipes#47201

FOR CONTRIBUTOR:

  • I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
  • License permits unrestricted use (educational + commercial)
  • This PR adds a new tool or tool collection
  • This PR updates an existing tool or tool collection
  • This PR does something else (explain below)

@natefoo
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natefoo commented Apr 12, 2024

I'm +1 on not bumping the version since the previous version is broken with containers.

Also just for reference the coreutils bump is necessary since 8.32 was from defaults, does not exist in conda-forge, and no longer exists in defaults.

@bgruening
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I take care of the bioconda one

@natefoo
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natefoo commented Apr 12, 2024

In this case we can drop the addition of awk and sed requirements but will still need the coreutils change to build a new mulled container?

@bgruening
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Yes. Will do ... do you need it today or can we wait for the bot until tm?

@natefoo
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natefoo commented Apr 12, 2024

I think we can wait for the bot, thanks!

@mvdbeek
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mvdbeek commented Apr 13, 2024

I'm +1 on not bumping the version since the previous version is broken with containers.

This makes it much harder to tell what version of a tool was run if users run into this on other servers. We should really always bump the version.

@@ -1 +1 @@
assembly 0 1037953
assembly 0 1037953 +inf 0
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It's normal that this changes, it just means that the bug is fixed. The problem is that the test data was wrong initially.

@mvdbeek mvdbeek merged commit 9aec17d into galaxyproject:main Apr 13, 2024
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3 participants