docs

docs/dev_quickstart.rst

@@ -116,8 +116,9 @@ Then you can initialize the SeqRepo instance:
 .. note::
 
     The ``-i auto-acmg`` flag is used to set the SeqRepo instance name to ``auto-acmg``.
-    If you want to use a different default seqrepo directory, you can set the ``SEQREPO_DIR``
-    environment variable or provide the ``-r`` flag to the ``seqrepo`` command.
+    If you want to use a different default seqrepo directory, you can set the
+    ``AUTO_ACMG_SEQREPO_DATA_DIR`` environment variable or provide the ``-r`` flag to the
+    ``seqrepo`` command.
 
 
 2. Download the reference genomes:
@@ -156,12 +157,12 @@ can be found in the `.env.dev` file. Copy the contents with the following comman
 
     cp .env.dev .env
 
-**Important**: You need to set the `SEQREPO_DIR` variable in the `.env` file to the path of the
-SeqRepo instance you created in the previous step. It should look similar to this:
+**Important**: You need to set the `AUTO_ACMG_SEQREPO_DATA_DIR` variable in the `.env` file to the
+path of the SeqRepo instance you created in the previous step. It should look similar to this:
 
 .. code-block:: bash
 
-    SEQREPO_DIR=/usr/local/share/seqrepo/auto-acmg
+    AUTO_ACMG_SEQREPO_DATA_DIR=/usr/local/share/seqrepo/auto-acmg
 
 ---------------
 Running the CLI

docs/usage.rst

@@ -139,8 +139,8 @@ Adjust the values according to your environment. Here are brief descriptions of
 that not all variables are required for the application to run. More info below.:
 
 - ``DEBUG``: Enable or disable debug mode.
-- ``USE_CACHE``: Enable or disable caching of API responses.
-- ``CACHE_DIR``: Path to the cache directory.
+- ``AUTO_ACMG_USE_CACHE``: Enable or disable caching of API responses.
+- ``AUTO_ACMG_CACHE_DIR``: Path to the cache directory.
 - ``API_V1_STR``: Base path for API endpoints.
 - ``API_REEV_URL``: URL of the REEV API.
 - ``AUTO_ACMG_API_ANNONARS_URL``: URL of the Annonars API.
@@ -153,7 +153,7 @@ that not all variables are required for the application to run. More info below.
 You will most likely need to set the following variables:
 
 - ``DEBUG``: Set to ``1`` to enable debug mode.
-- ``USE_CACHE``: Set to ``1`` to enable caching. This is recommended only for development.
+- ``AUTO_ACMG_USE_CACHE``: Set to ``1`` to enable caching. This is recommended only for development.
 - ``AUTO_ACMG_SEQREPO_DATA_DIR``: Set to the path of the custom project SeqRepo data directory.
 
 To pass this configuration to the Docker container, ensure the ``.env`` file is located where