search

phac-nml / irida

Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology
https://irida.ca
Apache License 2.0
40 stars 31 forks source link

Upgrade SNVPhyl tools in Galaxy Docker #1077

Open apetkau opened 3 years ago

apetkau commented 3 years ago

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

innovate-invent commented 3 years ago

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

apetkau commented 3 years ago

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 commented 3 years ago

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.