GalaxyAddTool

From UABgrid Documentation
Revision as of 14:50, 2 November 2011 by Curtish@uab.edu (Talk | contribs)

Jump to: navigation, search

How-to for adding a new tool into UAB's Galaxy instance. This details adding a tool that has it's own executable(s), rather than a pure python script.

pre-requisits

  1. Install the tools on the cluster
    • /share/apps/your_tool (email mhanby@uab.edu to get the directory created)
    • /lustre/project/your_project (email mhanby@uab.edu to get the directory created)
    • /share/apps/galaxy/galaxy-tools (only if this will ONLY be used in Galaxy)
  2. Create a personal galaxy for developement & testing
  3. Add the executable path to the galaxy environment
    • $galaxyroot/modulefiles/galaxy*: edit the module definition file to add your tool location to the path
  4. Load the updated module and make sure the command works from the commandline!
    • module load galaxy
    • test, test, test...

Special Case: REST or SPARQL endpoints

There are already tools for integrating these through a wizard. See the Galaxy Toolshed and navigate to Tools Shed -> Data Source

creating a command-wrapper by hand

Personal tools
Namespaces

Variants
Actions
Navigation
Toolbox