Add docs

.env.dev

@@ -1,4 +1,9 @@
-DEBUG=1
-USE_CACHE=1
+# Disable debug mode per default
+DEBUG=0
+# Disable cache to avoid memory issues
+USE_CACHE=0
+# Use the REEV API. Change it if you have other instance of REEV.
 API_REEV_URL=https://reev.cubi.bihealth.org/internal/proxy
-SEQREPO_DATA_DIR=/home/username/seqrepo/master
+# Default path to seqrepo data for Docker. Change it to your local development path.
+# It can look like this: "/home/<username>/seqrepo/master"
+SEQREPO_DATA_DIR=

Dockerfile

@@ -34,18 +34,6 @@ RUN sed -i -e 's/if aliases_cur.fetchone() is not None/if next(aliases_cur, None
     .venv/lib/python3.12/site-packages/biocommons/seqrepo/cli.py
 
 # Set up seqrepo
-# RUN mkdir -p /usr/local/share/seqrepo \
-#     && chown -R root:root /usr/local/share/seqrepo
-# RUN pipenv run seqrepo init -i auto-acmg
-# RUN pipenv run seqrepo fetch-load -i auto-acmg -n RefSeq NC_000001.10 NC_000002.11 NC_000003.11 \
-#     NC_000004.11 NC_000005.9 NC_000006.11 NC_000007.13 NC_000008.10 NC_000009.11 NC_000010.10 \
-#     NC_000011.9 NC_000012.11 NC_000013.10 NC_000014.8 NC_000015.9 NC_000016.9 NC_000017.10 \
-#     NC_000018.9 NC_000019.9 NC_000020.10 NC_000021.8 NC_000022.10 NC_000023.10 NC_000024.9 \
-#     NC_012920.1 NC_000001.11 NC_000002.12 NC_000003.12 NC_000004.12 NC_000005.10 NC_000006.12 \
-#     NC_000007.14 NC_000008.11 NC_000009.12 NC_000010.11 NC_000011.10 NC_000012.12 NC_000013.11 \
-#     NC_000014.9 NC_000015.10 NC_000016.10 NC_000017.11 NC_000018.10 NC_000019.10 NC_000020.11 \
-#     NC_000021.9 NC_000022.11 NC_000023.11 NC_000024.10 NC_012920.1
-
 # The seqrepo data is too large to be included in the image
 VOLUME /usr/local/share/seqrepo/
 VOLUME /home/auto-acmg/seqrepo/master

docs/usage.rst

@@ -20,53 +20,103 @@ containing the Dockerfile. Use the following command to build the image:
 This command builds the Docker image with the tag ``auto-acmg``. You can replace ``auto-acmg`` with
 any other tag suitable for your deployment or versioning schema.
 
+Setting Up Volumes
+------------------
+
+The AutoACMG Docker container requires access to SeqRepo data directories for sequence information.
+You must set up volumes that the Docker container can use to access this data without needing to
+copy it into the container directly. Here's how you set up these volumes:
+
+1. **SeqRepo Data Volume:** This volume stores the SeqRepo datasets.
+2. **Custom Project Data Volume:** This volume stores the custom project seqrepo data.
+
+Ensure these directories exist on your host and are populated with the necessary data:
+
+.. code-block:: bash
+
+    mkdir -p /usr/local/share/seqrepo
+    chown -R root:root /usr/local/share/seqrepo
+
+.. code-block:: bash
+
+    pipenv run seqrepo init -i auto-acmg
+
+.. code-block:: bash
+
+    pipenv run seqrepo fetch-load -i auto-acmg -n RefSeq NC_000001.10 NC_000002.11 NC_000003.11 \
+        NC_000004.11 NC_000005.9 NC_000006.11 NC_000007.13 NC_000008.10 NC_000009.11 NC_000010.10 \
+        NC_000011.9 NC_000012.11 NC_000013.10 NC_000014.8 NC_000015.9 NC_000016.9 NC_000017.10 \
+        NC_000018.9 NC_000019.9 NC_000020.10 NC_000021.8 NC_000022.10 NC_000023.10 NC_000024.9 \
+        NC_012920.1 NC_000001.11 NC_000002.12 NC_000003.12 NC_000004.12 NC_000005.10 NC_000006.12 \
+        NC_000007.14 NC_000008.11 NC_000009.12 NC_000010.11 NC_000011.10 NC_000012.12 NC_000013.11 \
+        NC_000014.9 NC_000015.10 NC_000016.10 NC_000017.11 NC_000018.10 NC_000019.10 NC_000020.11 \
+        NC_000021.9 NC_000022.11 NC_000023.11 NC_000024.10 NC_012920.1
+
+.. note::
+
+    The paths used in this example are for demonstration purposes! You should adjust the paths
+    to match your actual directory structure and ensure that the directories have the correct
+    permissions for Docker to access them. The ``/usr/local/share/seqrepo`` directory is the default
+    location for Linux systems. The ``/home/auto-acmg/seqrepo/master`` directory is an example of
+    a custom project data directory.
+
 Running the Docker Image
 ------------------------
 
-Once the Docker image is built, you can run it using the following command:
+Once the Docker image is built, you can run it using the following command to include the volumes:
 
 .. code-block:: bash
 
-    docker run -d -p 8000:8000 --env-file .env.dev auto-acmg
+    docker run -d -p 8000:8000 --env-file .env \
+    -v /usr/local/share/seqrepo:/usr/local/share/seqrepo \
+    -v /home/auto-acmg/seqrepo/master:/home/auto-acmg/seqrepo/master \
+    auto-acmg
 
-Here, ``-d`` runs the container in detached mode (in the background), ``-p 8000:8000`` maps port
-8000 of the container to port 8000 on the host, making the application accessible via
-``localhost:8000``. The ``--env-file .env.dev`` option tells Docker to use the environment variables d
-efined in the ``.env.dev`` file. Replace ``.env.dev`` with the path to your actual environment
-file if different.
+This command runs the container in detached mode (in the background), maps port 8000 of the
+container to port 8000 on the host, making the application accessible via ``localhost:8000``.
+The ``--env-file .env`` option tells Docker to use the environment variables defined in the
+``.env`` file. Replace ``.env`` with the path to your actual environment file if different.
+The ``-v`` flags map the local directories to their respective directories within the container,
+ensuring that SeqRepo data is accessible.
 
 .. note::
 
-    You have to configure the environment file before running the Docker container. See the next
-    section for details.
+    You must configure the environment file before running the Docker container and ensure that
+    the directories used for volumes are properly set up and have the correct permissions for
+    Docker to access them. See the configuration details in the sections below.
 
 Configuring the Environment File
 --------------------------------
 
 The application can be configured using environment variables. An example configuration file named
 ``.env.dev`` might look like this:
 
-.. code-block:: none
-
-    API_V1_STR=/api/v1
-    DATABASE_URL=postgres://user:password@localhost/dbname
-    SECRET_KEY=your_secret_key
+Adjust the values according to your environment. Here are brief descriptions of the variables. Note
+that not all variables are required for the application to run. More info below.:
 
-Adjust the values according to your environment. Here are brief descriptions of the variables:
-
-- ``API_V1_STR``: Base path for API endpoints.
+- ``DEBUG``: Enable or disable debug mode.
 - ``USE_CACHE``: Enable or disable caching of API responses.
+- ``CACHE_DIR``: Path to the cache directory.
+- ``API_V1_STR``: Base path for API endpoints.
 - ``API_REEV_URL``: URL of the REEV API.
-- ``SEQREPO_DATA_DIR``: Path to the SeqRepo data directory.
+- ``SEQREPO_DATA_DIR``: Path to the project-specific SeqRepo data directory.
+- ``GENEBE_API_KEY``: API key for the GeneBE service. You'll need it for running the benchmarks.
+- ``GENEBE_USERNAME``: Username for the GeneBE service. You'll need it for running the benchmarks.
+
+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.
+- ``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.dev`` file is located where
 you run the ``docker run`` command or specify the correct path to the file using the ``--env-file``
 option.
 
 .. note::
 
-    The ``.env.dev`` file has example values for demonstration purposes. You will probably need to
-    adjust SEQREPO_DATA_DIR to point to the correct location on your system.
+    Ensure that the environment variables are correctly set up and that the paths are valid and
+    accessible by the Docker container.
 
 Accessing the OpenAPI Documentation
 ------------------------------------