Debugging Galaxyļ
Debugging Galaxy in VS Codeļ
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.
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" } }, ] }
Re-start VS Code
Add a breakpoint somewhere in your code
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)Galaxy should stop right on the break point you added.
Enjoy your debugging session :-)