Debugging Galaxy

Debugging Galaxy in VS Code

The following instructions assume that you have cloned your Galaxy fork into the ~/galaxy directory and have created a VS Code workspace per instructions here. Additionally, we assume you have configured Galaxy and are using ~/galaxy/config/galaxy.yml as your galaxy configuration file (so, not the default .sample). If you are still using the default configuration, simply cp config/galaxy.yml.sample config/galaxy.yml and it should work fine.

1. Add the following code snippet to ~/galaxy/.vscode/launch.json (create the file if it does not already exist):

   {
       "version": "0.2.0",
       "configurations": [
           {
               "name": "Python: Current File (Integrated Terminal)",
               "type": "python",
               "request": "launch",
               "program": "${file}",
               "console": "integratedTerminal"
           },
           {
               "name": "GalaxyFastAPI uvicorn",
               "type": "python",
               "request": "launch",
               "module": "uvicorn",
               "args": ["--app-dir", "lib",  "--factory", "galaxy.webapps.galaxy.fast_factory:factory"],
               "env": {
                   "GALAXY_CONFIG_FILE": "${workspaceFolder}/config/galaxy.yml"
               }
           },
       ]
   }
   

2. Re-start VS Code

3. Add a breakpoint somewhere in your code

4. Select Run and Debug on Activity Bar, on the far left hand side. In the RUN AND DEBUG drop down, select GalaxyFastAPI uvicorn, and click the Start Debugging button (green arrow)

5. Galaxy should stop right on the break point you added.

6. Enjoy your debugging session :-)