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bgruening / docker-galaxy

:whale::bar_chart::books: Docker Images tracking the stable Galaxy releases.
http://bgruening.github.io/docker-galaxy
MIT License
226 stars 134 forks source link

Duplicate tools within the tools panel #203

Closed lecorguille closed 2 weeks ago

lecorguille commented 8 years ago

Hi all, In our Galaxy instance, we need to duplicate tools in the tools panel.

Indeed, we order tools by area and tasks:

LC-MS

  • Format Conversion
  • Preprocessing
  • Normalisation
  • Quality Control
  • Statistical Analysis
  • Annotation

GC-MS

  • Format Conversion
  • Preprocessing
  • Normalisation
  • Quality Control
  • Statistical Analysis
  • Annotation

NMR

  • Format Conversion
  • Preprocessing
  • Normalisation
  • Quality Control
  • Statistical Analysis
  • Annotation

But some tools can be share by both LS-MS and GC-MS (Normalisation) and some by the three thematics (Statistical Analysis).

But when you use the ansible-galaxy-tools solution with RUN install-tools $GALAXY_ROOT/my_tool_list.yml, it seems that you can't do that without modify manually the shed_tool_conf.xml (as you can do on your standard Galaxy instance at home)

So if someone have the same need, I have just write a little script to do that: https://github.com/lecorguille/galaxy_utils/blob/master/galaxy_duplicate_tools.py It's not as elegan as an ansible role but it works! 👍

In the Dockerfile, you have that:

# Duplicate tools in the tools panel
ADD galaxy_utils/galaxy_duplicate_tools.py $GALAXY_ROOT/galaxy_duplicate_tools.py
RUN $GALAXY_ROOT/galaxy_duplicate_tools.py $GALAXY_ROOT/tools.yaml $GALAXY_ROOT/config/shed_tool_conf.xml -i

OR mayby I just waste my time and you have a more elegan solution?

bgruening commented 8 years ago

Oh this is fantastic! Thanks for sharing. I think the proper solution would be to extend the playrole to allow a list of categories and extend the Galaxy API to consume this list. Do you have time to work on this?

lecorguille commented 8 years ago

Heu ... currently, actually, any exceed time nor knowledge in ansible. But never say never!

bgruening commented 2 weeks ago

The new 24.1 image contains a lot of changes and reflects the latest developments in Galaxy. I would like to close this PR, but please feel free to reopen and rebase against the latest version.

Please give it a try:

docker run -p 8080:80 -p 8021:21 -p 4002:4002 --privileged=true -e "GALAXY_DESTINATIONS_DEFAULT=slurm_cluster_docker"   -v /tmp/galaxy-data/:/export/ quay.io/bgruening/galaxy:24.1

... or any other combination. The readme has been updated. Please add any useful tip to it.

For a list of changes, see the Changelog.