clarified docker docs

README.md

@@ -45,14 +45,24 @@ conda install -c bioconda -c conda-forge metagraph
 If docker is available on the system, immediately get started with
 
 ```
-docker run -v ${HOME}:/mnt ghcr.io/ratschlab/metagraph:master build -v -k 10 \
-                            -o /mnt/transcripts_1000 \
-                            /mnt/transcripts_1000.fa
+docker pull ghcr.io/ratschlab/metagraph:master
+docker run -v ${HOME}:/mnt ghcr.io/ratschlab/metagraph:master \
+    build -v -k 10 -o /mnt/transcripts_1000 /mnt/transcripts_1000.fa
 ```
+and replace `${HOME}` with a directory on the host system to map it under `/mnt` in the container.
 
-(Replace `${HOME}` with a directory on the host system to map it under `/mnt` in the container.)
+To run the binary compiled for the `Protein` alphabet, just add `--entrypoint metagraph_Protein`:
+```
+docker run -v ${HOME}:/mnt --entrypoint metagraph_Protein ghcr.io/ratschlab/metagraph:master \
+    build -v -k 10 -o /mnt/graph /mnt/protein.fa
+```
+
+As you see, running MetaGraph from docker containers is very easy. Also, the following command (or similar) may be handy to see what directory is mounted in the container or other sort of debugging of the command:
+```
+docker run -v ${HOME}:/mnt --entrypoint ls ghcr.io/ratschlab/metagraph:master /mnt
+```
 
-All different versions of the container are listed [here](https://github.com/ratschlab/metagraph/pkgs/container/metagraph).
+All different versions of the container image are listed [here](https://github.com/ratschlab/metagraph/pkgs/container/metagraph).
 
 ### Install From Sources
 

metagraph/docs/source/installation.rst

@@ -23,15 +23,28 @@ Docker container
 
 If docker is available on your system, you can immediately get started with::
 
-    docker run -v ${DATA_DIR_HOST}:/mnt ghcr.io/ratschlab/metagraph:latest \
+    docker run -v ${DATA_DIR_HOST}:/mnt ghcr.io/ratschlab/metagraph:master \
         build -v -k 10 -o /mnt/transcripts_1000 /mnt/transcripts_1000.fa
 
 
-where you'd need to replace ``${DATA_DIR_HOST}`` with a directory on the host system to map it
+where ``${DATA_DIR_HOST}`` should be replaced with a directory on the host system to map it
 under ``/mnt`` in the container. This docker container uses the latest version of MetaGraph from
 the source `GitHub repository <https://github.com/ratschlab/metagraph>`_ (branch ``master``).
 See also the `image overview <https://github.com/ratschlab/metagraph/pkgs/container/metagraph>`_ for
-other versions of the metagraph image.
+other versions of the image.
+
+By default, it executes the binary compiled for the DNA alphabet.
+To run the binary compiled for the `Protein` alphabet, just add ``--entrypoint metagraph_Protein``::
+
+    docker run --entrypoint metagraph_Protein \
+               -v ${DATA_DIR_HOST}:/mnt ghcr.io/ratschlab/metagraph:master \
+        build -v -k 10 -o /mnt/graph /mnt/protein.fa
+
+As you see, running MetaGraph from docker containers is very easy.
+Also, the following command (or similar) may be handy to see what directory is mounted in the
+container or other sort of debugging of the command::
+
+    docker run -v ${DATA_DIR_HOST}:/mnt --entrypoint ls ghcr.io/ratschlab/metagraph:master /mnt
 
 
 Install from source