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GATC Logo galaxy logo

GAT - 2016 - Salt Lake City

Tool Management Exercise

by @martenson

#usegalaxy #GAT2016 @galaxyproject

Task 1

Your users want to use freebayes software on the instance you administer.

  • Find what Tool Shed repository has freebayes tools in it.

Hint: You can use search in https://toolshed.g2.bx.psu.edu/ or http://toolshed.tools.

Task 2

  • Install devteam/freebayes from MTS in revision 22:99684adf84de into new section 'Freebayes' using TS dependencies.

Hint: Note the revision, it is NOT the latest.

Task 3

New freebayes revision has been uploaded to the MTS.

  • Install devteam/freebayes from MTS in revision 24:da6e10dee68b into section 'New Freebayes'.

Task 4

Now you have two sections with two versions of freebayes. Confusing. You could uninstall it but you want users to be able to re-run jobs with old freebayes though.

  • Hide the Freebayes section (with the older tool) from the tool panel without uninstalling it.

Hint: You need to modify shed_tool_conf.xml in order to do this.

Task 5

You want to show both versions of freebayes and allow users to switch versions on the tool form

  • Move freebayes revision 24:da6e10dee68b into 'New Freebayes' section and display it.

Hint: tools with the same ID and different version in the same section will 'collapse' into one and offer the switch button.

Task 6

Now there is only one section we might not want to call it 'New'.

  • Rename the 'New Freebayes' section to just 'Freebayes'.

Hints:

  • You can rename sections using configuration file(s).
  • When renaming you need to be consistent across the configs.

Task 7

The old freebayes version is no longer useful

  • Uninstall the revision 22:99684adf84de of freebayes.

Task 8

We want to use Conda package manager for our HPC sw deployment.

  • Enable Conda in your Galaxy instance.

Hint: One way is to enable conda_auto_init in config and restart Galaxy.

Task 9

  • Install latest seqtk and install only Conda dependencies for it.

Hint: By default Galaxy installs packages from both TS and Conda if available.

Task 10

  • Find where the dependencies are present on the filesystem.

Hint: The information is in the config.