How Do I …

This section contains a number of smaller topics with links and examples meant to provide relatively concrete answers for specific Galaxy development scenarios.

… interact with the Galaxy database interactively?

This can be done with either IPython or a plain Python console, depending on your preferences:

python -i scripts/db_shell.py

… build Galaxy Javascript frontend client?

We have added a Makefile which will let you do this. You can simply run:

make client

Please see the Makefile itself for details and other options. There is also a readme at client/README.md.

… rebuild the Galaxy configuration schema?

Galaxy and the Tool Shed each have a schema that is used to validate their configuration files. These schemas are defined in lib/galaxy/config/schemas/config_schema.yml (for galaxy.yml) and lib/galaxy/config/schemas/tool_shed_config_schema.yml (for tool_shed.yml). If you need to add or modify a configuration option, edit the relevant schema file directly instead of the corresponding lib/galaxy/config/sample/*.yml.sample file, then run the following command from Galaxy’s root directory to regenerate the sample YAML files (and, for Galaxy, the RST documentation and type stubs):

make config-rebuild

Then add the regenerated files to your commit.

… add or update a Galaxy Python dependency?

Galaxy’s Python dependencies are declared in the root pyproject.toml file. Each subdirectory of packages/ also corresponds to a package published on PyPI (e.g. packages/util/ is galaxy-util) and has its own pyproject.toml. If a dependency is needed by the code of one or more of these packages, also add it to the dependencies list of the relevant packages/<package>/pyproject.toml file(s).

After editing the root pyproject.toml, run the following command from Galaxy’s root directory to update the pinned requirements files under lib/galaxy/dependencies/ (this also updates uv.lock, which is not tracked in the repository):

make update-dependencies

Then add the updated pyproject.toml and pinned requirements files to your commit.