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.
- Install the tools on the cluster
- /share/apps/your_tool (email email@example.com to get the directory created)
- /lustre/project/your_project (email firstname.lastname@example.org to get the directory created)
- /share/apps/galaxy/galaxy-tools (only if this will ONLY be used in Galaxy)
- Create a personal galaxy for developement & testing
- See Shantanu's Create a personal galaxy page.
- Add the executable path to the galaxy environment
- $galaxyroot/modulefiles/galaxy*: edit the module definition file to add your tool location to the path
- 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
- Create a my_tool.xml wrapper to
- define tool ID and display name
- declare inputs
- declare outputs
- list test files
- user documentation
- Edit tool_conf.xml to add a line for the new XML file
- Restart galaxy