3.1. Running a command line terminal

Starting the container

Start a command line terminal within the development-environment Docker container by executing the following commands (ensure that there are no trailing spaces following the end-of-line deliminators):

Important

Repeat the docker run command if you receive an error like: ‘docker: Error response from daemon’.

Linux and Mac

1. Open a new terminal on your host machine.

2. Check that you are using the bash shell:

echo $SHELL

3. If the command above does not print /bin/bash then start a bash shell:

bash

4. Run the following:

docker run \
    --rm \
    --name development-environment \
    -it \
    -v ~/development-environment/work:/home/jovyan/work \
    -v ~/development-environment/usr/local:/home/jovyan/.local \
    -v ~/development-environment/usr/cache:/home/jovyan/.cache \
    -v ~/development-environment/usr/etc/jupyter:/etc/jupyter \
    -v ~/development-environment/usr/bin/:/usr/local/bin \
    researchdevresources/development-environment:1.0-tensorflow-notebook start-terminal.sh

Important

Ensure that there are no trailing spaces following the end of line backslash deliminators.

Windows

1. Open a new PowerShell on your host machine (don’t use a standard terminal, as it does not support commands that span multiple lines).

2. Run the following:

docker run `

–rm ` –name development-environment ` -it ` -v c/Users/${env:UserName}/Documents/development-environment/work:/home/jovyan/work ` -v c/Users/${env:UserName}/Documents/development-environment/usr/local:/home/jovyan/.local ` -v c/Users/${env:UserName}/Documents/development-environment/usr/cache:/home/jovyan/.cache ` -v c/Users/${env:UserName}/Documents/development-environment/usr/etc/jupyter:/etc/jupyter ` -v c/Users/${env:UserName}/Documents/development-environment/usr/bin/:/usr/local/bin/ ` researchdevresources/development-environment:1.0-tensorflow-notebook start.sh

Important

Ensure that there are no trailing spaces following the end-of-line tilda deliminators.

Running python scripts

The command in the previous section will open a new bash terminal within the running development-environment Docker container as shown below:

A bash terminal running within the development-environment container.

In this terminal, either:

1. run python from the terminal:

python

2. or run a python script directly from the terminal:

python your_python_script.py

Note

As your work folder on your host operating system is mapped to /home/jovyan/work within the container, you can place python scripts in this folder and run them from within the container.

python /home/jovyan/work/your_python_script.py

or

cd /home/jovyan/work
python your_python_script.py

Docker run commandline arguments (optional information)

The commandline arguments associated with the docker run command are listed below:

• --name development-environment This argument specifies the name of the container that the docker run command will create.

• -it Run the docker container in an interactive mode. This will allow us to open a terminal within the development-environment container to perform some additional setup steps.

• -v [host-src]:[container-dest] Allows a folder, [host-src], on the host operating system (such as our environment folder described in the previous step, to be mounted within the container in the location specified by [container-dest]. For example, e.g. -v ~/development-environment/work:/home/jovyan/work will mount a folder located at ~/development-environment/work on the host operating system to /home/jovyan/work in the container).

• The final argument that the docker run command requires is the name of the script to run within the the container when it starts up. The OpenCMISS-Docker image has been automatically configured to access scripts located in the development-environment/usr/bin folder folder without needing to specify their full path.

• The second to last argument of the docker run command indicates the location of the Docker image that you want to run e.g. researchdevresources/development-environment:1.0 points to a image hosted on DockerHub.

More information on arguments for the docker run command can be found in Docker engine reference documentation.