User’s Guide

Understanding the GTG workspace

After launching the GTG application, you should see the the folder gtg_dev_dir in your current directory and three subdirectories within it:

gtg_dev_dir/
├── database
├── galaxy_tool_repository
└── shed_tools

The galaxy_tool_repository subdirectory stores all files that form a Galaxy Tool Repository and can be published to Galaxy ToolShed with GTG. The subdirectory is mounted to the GTG container so that a developer can easily add non-XML files from the host machine to the GTG container. The XML files should be generated via GTG.

The shed_tools subdirectory is mounted to both the GTG container and the Galaxy container so that the galaxy tool repository being developed in GTG can be synced to the Galaxy instance for interactive testing.

The database subdirectory is mounted to the Galaxy container and displays the job working status of Galaxy. When the tool is being tested in Galaxy, the job running process can be monitored. This is useful for debugging your tools.

Creating the Tool XML

GTG provides three ways to build a Galaxy XML file:

• From scratch: builds XML from scratch using GTG.
• Uploaded XML: starts with an uploaded XML.
• Aurora Galaxy Tool: this option starts with an template file for developing an Aurora Galaxy Tool.

Select the appropriate method and click the Save button.

Creating The XML:

• From Scratch
  • Initialize an XML
  • Build The Tool Components
    • 1. Create the root tool component
    • 2. Define the tool’s requirements
    • 3. Create tool->command component
    • 4. Create tool->inputs component
    • 5. Create tool->outputs component
    • 6. Create tool->tests component
    • 7. Create tool->help component
    • 8. Create tool->citations component
  • View the complete XML file
• Uploaded XML
  • Upload XML
  • Correct Tool ID attribute
  • Add more components
    • The tool->tests component
    • The content in the tool->help component
    • The tool->citations component
  • View the complete XML file
• Aurora Galaxy Tool

Final Steps and Publishing

Building Your Tool

• Building the Finished Galaxy Tool
  • Add Files
  • Connect to ToolShed
  • Publish to Tool Repository
  • Install and test Tool in Galaxy