Update index.md

Author: loftytopping

docs/index.md

@@ -80,55 +80,54 @@ Other dependecies include:
 
 If you would like to run PyBox within a Docker container, I have provided a Dockerfile that will automatically build all dependencies within a new container based on the Ubuntu:16.04 image. To build the new image, assuming you have Docker installed, run the following command in the directory of the supplied Dockerfile:
 
-> docker build -t pybox .
+    docker build -t pybox .
 
 After this has completed [which may take some time], type the following to see your new image listed:
 
-> docker images
+    docker images
 
 To create and run a new container based on this image, with a name 'project_pybox', type:
 
-> docker run --name=project_pybox -it pybox
+    docker run --name=project_pybox -it pybox
 
 This will take you in to the container. So, lets run the gas phase model in PyBox whilst you are there. Change directory to where PyBox is located:
 
-> cd /Code/Git_repos/PyBox/
+    cd /Code/Git_repos/PyBox/
 
 Lets run the default simulation:
 
-> python Gas_simulation.py 
+    python Gas_simulation.py 
 
 Dont worry about the error message regarding the Matplotlib plots. This is a result of working in a Docker container. For those of you not familiar with Docker commands, lets leave the container. Type:
 
-> exit
+    exit
 
 You are now back in your original 'host' operating system. To list all available containers, type:
 
-> docker ps -a
+    docker ps -a
 
 You should see how long ago you exited our 'project_pybox' container. Lets restart this container. To do this type the following:
 
-> docker start project_pybox
-> docker exec -it project_pybox bash
+    docker start project_pybox
+    docker exec -it project_pybox bash
 
 We are back in! Lets exit again:
 
-> exit
+    exit
 
 To remove the container, you can type:
 
-> docker rm project_pybox
-
+    docker rm project_pybox
+    
 To remove the image on which the container is based, which was built from our Dockerfile, type:
 
-> docker rmi pybox
-
+    docker rmi pybox
 
 ## Folder structure and running the model <a name="Folder-Structure"></a>
 
 If you are happy all dependencies are installed and working, to run PyBox 'out of the box', type the following in the root directory:
 
-> python Gas_simulation.py
+    python Gas_simulation.py
 
 If you are not in a Docker container, you will see a plot displaying the concentration of two compounds over time. To understand what this simulation has actually done, let us now discuss the repository structure.