GalaxyAddTool

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(Creating a command-wrapper by hand)
(pre-requisits)
 
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== pre-requisits ==
 
== pre-requisits ==
  
 +
# Check [http://toolshed.g2.bx.psu.edu/ Galaxy Toolshed] to make sure the wrapper doesn't already exist!
 
# Install the tools on the cluster
 
# Install the tools on the cluster
 
#* /share/apps/''your_tool'' (email mhanby@uab.edu to get the directory created)
 
#* /share/apps/''your_tool'' (email mhanby@uab.edu to get the directory created)

Latest revision as of 15:56, 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.

[edit] pre-requisits

  1. Check Galaxy Toolshed to make sure the wrapper doesn't already exist!
  2. 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)
  3. Create a personal galaxy for developement & testing
  4. Add the executable path to the galaxy environment
    • $galaxyroot/modulefiles/galaxy*: edit the module definition file to add your tool location to the path
  5. Load the updated module and make sure the command works from the commandline!
    • module load galaxy
    • test, test, test...

[edit] 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

[edit] Creating a command-wrapper by hand

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

Note: If you only need a simple wrapper for an exiting program, you'll only need to create an XML wrapper to describe it (my_tool.xml). However, if you need to create temporary directories or do any other pre- or post- processing, you'll also want to create some adapter code, and have my_tool.xml call that, rather than calling your tool directly. For example, sam_pileup.xml calls sam_pileup.py, which sets up a temp directory, indexes genomes on the fly, etc., then calls "samtools pileup ..."

  1. (optional) Create a my_tool.py/pl/etc adapter to do pre-/post- processing
  2. Create a my_tool.xml wrapper to
    • define tool ID and display name
    • declare inputs
    • declare outputs
    • list test files
    • user documentation
  3. Edit tool_conf.xml to add a line for the new XML file
  4. Restart galaxy
    • ./run.sh --stop-daemon; ./run.sh --daemon
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