.. _configuration:

Configuration
=============

.. figure:: ../../assets/protflow_config_v2.drawio.png
    :alt: The ProtFlow configuration file
    :align: center
    :width: 420px

    Where ProtFlow looks for its config and runners find tool environments.


Set up
------

ProtFlow uses a configuration file to locate the Python environments of your installed design tools. If you followed the :ref:`installation` page, you already created ``config.py`` using ``protflow-init-config``.

You need to link ProtFlow’s runners to the Python environments you have on your system. By default, ProtFlow looks for paths in the file ``config.py`` that was created during installation. If you try to initialize a runner without defining its paths in ``config.py``, ProtFlow raises an error telling you which path is missing and where to set it.

By default, ``protflow-init-config`` writes ``config.py`` to ``~/.config/protflow/config.py``. If you want to point your ProtFlow installation to a different ``config.py`` elsewhere (useful on shared clusters), use the CLI tool ``protflow-set-config``:

Simply provide the path to the target config.py to the tool:

.. code-block:: bash

    protflow-set-config /path/to/your/config.py

To remove this override, use ``--unset``:

.. code-block:: bash

    protflow-set-config --unset

To check which ``config.py`` ProtFlow is using:

.. code-block:: bash

    protflow-check-config

Adding tools
------------

With ``config.py`` in place, add paths for your design tools. Open the file and fill in the placeholders as shown below. If you run a tool without setting its path here, ProtFlow will raise a clear error pointing to the missing key.

.. code-block:: python
   :caption: ~/.config/protflow/config.py (excerpt)
   :name: config-excerpt

   # Path to the ProtFlow repository root (optional but recommended for tooling)
   PROTFLOW_DIR = ""  # e.g. "/path/to/ProtFlow"

   # Python interpreter inside the environment where ProtFlow itself is installed
   PROTFLOW_ENV = ""  # e.g. "/path/to/conda/envs/protflow/bin/python3"