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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 bedtools on the instance you administer.

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

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

Task 2

  • Install iuc/bedtools from MTS in revision 10:c78cf6fe3018 (2016-10-03) into new section 'BEDtools' using TS dependencies.

Hints:

  • Note the revision, it is NOT the latest.
  • If you did not set tool_config_file and tool_dependency_dir in the production basics session, you'll need to do it now.

Task 3

New bedtools revision has been uploaded to the MTS.

  • Install iuc/bedtools from MTS in revision 13:fadebae7e69b into section 'New BEDtools'.

Task 4

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

  • Hide the BEDtools 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 bedtools and allow users to switch versions on the tool form

  • Move bedtools revision 10:c78cf6fe3018 into 'New BEDtools' 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 BEDtools' section to just 'BEDtools'.

Hints:

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

Task 7

The old bedtools version is no longer useful

  • Uninstall the revision 10:c78cf6fe3018 of bedtools.

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.
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