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Published 20 hours ago • verified publisher icon phac-nml

Upgrade SNVPhyl tools in Galaxy Docker

Open apetkau opened this issue 2 years ago • 3 comments

Describe the bug

The current version of Galaxy Docker used by IRIDA does not have the latest tools for SNVPhyl installed.

Steps to reproduce the problem

  1. Launch the latest IRIDA
  2. Launch the latest Galaxy Docker
  3. Launch SNVPhyl
  4. You will get an error.

Expected behaviour

I expected SNVPhyl to succeed.

Additional context

None

apetkau avatar Aug 25 '21 18:08 apetkau

Would it help to switch to my deployment implementation? https://github.com/brinkmanlab/irida-container

innovate-invent avatar Aug 26 '21 21:08 innovate-invent

So SNVPhyl is actually upgraded in Galaxy Docker and has been upgraded for a while. The issue is that we haven't updated our documentation to reference the newer Docker image. The up-to-date version of Galaxy/IRIDA Docker can be run with:

docker run -d -p 48888:80 -v /path/to/irida/data:/path/to/irida/data phacnml/galaxy-irida-20.09

(that is, we switched from phacnml/galaxy-irida-20.05 to phacnml/galaxy-irida-20.09).

apetkau avatar Sep 17 '21 21:09 apetkau

Thanks for the suggestion @innovate-invent. However we luckily don't need to re-build Docker at this stage. So maybe something we can look into later.

apetkau avatar Sep 17 '21 21:09 apetkau