Specify command for pulled Docker image

Author: niklases

README.md

@@ -79,20 +79,22 @@ Pull from Docker Hub or build the image using the stored [Dockerfile](./Dockerfi
   # docker pull niklases/pypef:VERSION_TAG, e.g.
   docker pull niklases/pypef:0.4.2
   ```
-
+  a chained container command using the built Docker image can be run with e.g.:
+  ```bash
+  docker run --gpus=all -v ./datasets/:/datasets --workdir /datasets/AVGFP niklases/pypef:0.4.2 /bin/bash -c \
+      "python /app/run.py mklsts --wt P42212_F64L.fasta --input avGFP.csv --ls_proportion 0.01 && \
+       python /app/run.py hybrid --ls LS.fasl --ts TS.fasl --params GREMLIN --llm prosst --wt P42212_F64L.fasta --pdb GFP_AEQVI.pdb"
+  ```
 - building image from Dockerfile
   ```bash
   docker build -t pypef . # --progress=plain --no-cache
   ```
-
-
-A chained container command using the built Docker image can be run with e.g.:
-```bash
-docker run --gpus=all -v ./datasets/:/datasets --workdir /datasets/AVGFP pypef /bin/bash -c \
-    "python /app/run.py mklsts --wt P42212_F64L.fasta --input avGFP.csv --ls_proportion 0.01 && \
-     python /app/run.py hybrid --ls LS.fasl --ts TS.fasl --params GREMLIN --llm prosst --wt P42212_F64L.fasta --pdb GFP_AEQVI.pdb"
-
-```
+  a chained container command using the built Docker image can be run with e.g.:
+  ```bash
+  docker run --gpus=all -v ./datasets/:/datasets --workdir /datasets/AVGFP pypef /bin/bash -c \
+      "python /app/run.py mklsts --wt P42212_F64L.fasta --input avGFP.csv --ls_proportion 0.01 && \
+       python /app/run.py hybrid --ls LS.fasl --ts TS.fasl --params GREMLIN --llm prosst --wt P42212_F64L.fasta --pdb GFP_AEQVI.pdb"
+  ```
 
 
 <a name="gui-installation"></a>