fix: update docker compose for uta + update docs for manual dl (#78)

see uta issue: biocommons/uta#274

also fixes indentation for note about seqrepo_vol

Author: korikuzma

compose.anyvar.yaml

@@ -24,11 +24,20 @@ services:
       - seqrepo_vol:/usr/local/share/seqrepo
 
   uta:
+    # Test:
+    # psql -XAt postgres://anonymous@localhost:5433/uta -c 'select count(*) from uta_20241220.transcript'
+    # 329090
     image: biocommons/uta:uta_20241220
     environment:
       - POSTGRES_PASSWORD=some-password-that-you-make-up
     volumes:
       - uta_vol:/var/lib/postgresql/data
+      - type: bind
+        source: ./uta_20241220.pgd.gz
+        target: /tmp/uta_20241220.pgd.gz
+        read_only: true
+        bind:
+          create_host_path: false
     ports:
       - 127.0.0.1:5433:5432
 

docs/source/configuration/docker_compose.rst

@@ -69,32 +69,36 @@ The following volumes may be required, depending on which services you run:
 
 * ``seqrepo_vol``: Storage for sequence repository data. Required when running ``compose.anyvar.yaml`` or ``compose.test.yaml``.
 
-.. note::
+   .. note::
 
-   If you already have a SeqRepo database on your local filesystem, you can use it directly instead of the Docker volume. Both ``compose.anyvar.yaml`` and ``compose.test.yaml`` can be updated to bind-mount your local SeqRepo directory in place of ``seqrepo_vol``.
+      If you already have a SeqRepo database on your local filesystem, you can use it directly instead of the Docker volume. Both ``compose.anyvar.yaml`` and ``compose.test.yaml`` can be updated to bind-mount your local SeqRepo directory in place of ``seqrepo_vol``.
 
-   For example, if your SeqRepo lives at ``/usr/local/share/seqrepo/2024-12-20``, replace:
+      For example, if your SeqRepo lives at ``/usr/local/share/seqrepo/2024-12-20``, replace:
 
-   .. code-block:: yaml
+      .. code-block:: yaml
 
-      volumes:
-        - seqrepo_vol:/usr/local/share/seqrepo
+         volumes:
+         - seqrepo_vol:/usr/local/share/seqrepo
 
-   with:
+      with:
 
-   .. code-block:: yaml
+      .. code-block:: yaml
 
-      volumes:
-        - $SEQREPO_ROOT_DIR:$SEQREPO_ROOT_DIR
+         volumes:
+         - $SEQREPO_ROOT_DIR:$SEQREPO_ROOT_DIR
 
-   Then export the path before starting the stack:
+      Then export the path before starting the stack:
 
-   .. code-block:: bash
+      .. code-block:: bash
 
-      export SEQREPO_ROOT_DIR=/usr/local/share/seqrepo/2024-12-20
+         export SEQREPO_ROOT_DIR=/usr/local/share/seqrepo/2024-12-20
 
 * ``uta_vol``: Storage for UTA database data. Required when running ``compose.anyvar.yaml``.
 
+   .. important::
+
+      You must download ``uta_20241220.pgd.gz`` from https://dl.biocommons.org/uta/ using a web browser and move it to the root of the repository.
+
 * ``anyvar_vol``: Storage for AnyVar application data. Required when running ``compose.anyvar.yaml``.
 
 Before starting a stack that relies on external volumes, ensure the required volumes exist. For example:

docs/source/getting_started/docker_compose.rst

@@ -24,6 +24,8 @@ Create all required volumes:
 
    % make volumes
 
+Download ``uta_20241220.pgd.gz`` from https://dl.biocommons.org/uta/ using a web browser and move it to the root of the repository.
+
 Then, launch the application:
 
 .. code-block:: bash