GalaxyAddTool

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(Creating a command-wrapper by hand)
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Galaxy's public instructions for adding tools: http://wiki.g2.bx.psu.edu/Admin/Tools
 
Galaxy's public instructions for adding tools: http://wiki.g2.bx.psu.edu/Admin/Tools
 +
# Create a my_tool.xml wrapper to
 +
#* define tool ID and display name
 +
#* declare inputs
 +
#* declare outputs
 +
#* list test files
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#* user documentation
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# Edit tool_conf.xml to add a line for the new XML file
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# Restart galaxy

Revision as of 14:51, 4 November 2011

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

Galaxy's public instructions for adding tools: http://wiki.g2.bx.psu.edu/Admin/Tools

  1. Create a my_tool.xml wrapper to
    • define tool ID and display name
    • declare inputs
    • declare outputs
    • list test files
    • user documentation
  2. Edit tool_conf.xml to add a line for the new XML file
  3. Restart galaxy
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