Creating More Complex Container Images

Overview
  • Teaching: 30
  • Exercises: 30
  • Questions:
    • How can I add local files (e.g. data files) into container images at build time?
    • How can I access files stored on the host system from within a running Docker container?
  • Objectives:
    • Explain how you can include files within Docker container images when you build them.
    • Explain how you can access files on the Docker host from your Docker containers.

In order to create and use your own container images, you may need more information than our previous example. You may want to use files from outside the container, that are not included within the container image, either by copying the files into the container image, or by making them visible within a running container from their existing location on your host system. You may also want to learn a little bit about how to install software within a running container or a container image. This episode will look at these advanced aspects of running a container or building a container image. Note that the examples will get gradually more and more complex – most day-to-day use of containers and container images can be accomplished using the first 1–2 sections on this page.

Using scripts and files from outside the container

In your shell, change to the sum folder in the docker-intro folder and look at the files inside.

cd ~/Desktop/docker-intro/sum
ls

This folder has both a Dockerfile and a Python script called sum.py. Let’s say we wanted to try running the script using a container based on our recently created alpine-python container image.

Running containers

Question: What command would we use to run Python from the alpine-python container?

We can run a container from the alpine-python container image using:

docker container run alice/alpine-python

What happens? Since the Dockerfile that we built this container image from had a CMD entry that specified ["python3", "--version"], running the above command simply starts a container from the image, runs the python3 --version command and exits. You should have seen the installed version of Python printed to the terminal.

Instead, if we want to run an interactive Python terminal, we can use docker container run to override the default run command embedded within the container image. So we could run:

docker container run -it alice/alpine-python python3

The -it tells Docker to set up and interactive terminal connection to the running container, and then we’re telling Docker to run the python3 command inside the container which gives us an interactive Python interpreter prompt. (type exit() to exit!)

If we try running the container and Python script, what happens?

docker container run alice/alpine-python python3 sum.py
python3: can't open file '//sum.py': [Errno 2] No such file or directory
No such file or directory

Question: What does the error message mean? Why might the Python inside the container not be able to find or open our script?

This question is here for you to think about - we explore the answer to this question in the content below.

The problem here is that the container and its filesystem is separate from our host computer’s filesystem. When the container runs, it can’t see anything outside itself, including any of the files on our computer. In order to use Python (inside the container) and our script (outside the container, on our host computer), we need to create a link between the directory on our computer and the container.

This link is called a “mount” and is what happens automatically when a USB drive or other external hard drive gets connected to a computer – you can see the contents appear as if they were on your computer.

We can create a mount between our computer and the running container by using an additional option to docker container run. We’ll also use the variable ${PWD} which will substitute in our current working directory. The option will look like this

--mount type=bind,source=${PWD},target=/temp

What this means is: make my current working directory (on the host computer) – the source – visible within the container that is about to be started, and inside this container, name the directory /temp – the target.

Types of mounts

You will notice that we set the mount type=bind, there are other types of mount that can be used in Docker (e.g. volume and tmpfs). We do not cover other types of mounts or the differences between these mount types in the course as it is more of an advanced topic. You can find more information on the different mount types in the Docker documentation.

Let’s try running the command now:

docker container run --mount type=bind,source=${PWD},target=/temp alice/alpine-python python3 sum.py

But we get the same error!

python3: can't open file '//sum.py': [Errno 2] No such file or directory

This final piece is a bit tricky – we really have to remember to put ourselves inside the container. Where is the sum.py file? It’s in the directory that’s been mapped to /temp – so we need to include that in the path to the script. This command should give us what we need:

docker container run --mount type=bind,source=${PWD},target=/temp alice/alpine-python python3 /temp/sum.py

Note that if we create any files in the /temp directory while the container is running, these files will appear on our host filesystem in the original directory and will stay there even when the container stops.

Other Commonly Used Docker Run Flags

Docker run has many other useful flags to alter its function. A couple that are commonly used include -w and -u.

The --workdir/-w flag sets the working directory a.k.a. runs the command being executed inside the directory specified. For example, the following code would run the pwd command in a container started from the latest ubuntu image in the /home/alice directory and print /home/alice. If the directory doesn’t exist in the image it will create it.

docker container run -w /home/alice/ ubuntu pwd

The --user/-u flag lets you specify the username you would like to run the container as. This is helpful if you’d like to write files to a mounted folder and not write them as root but rather your own user identity and group. A common example of the -u flag is --user $(id -u):$(id -g) which will fetch the current user’s ID and group and run the container as that user.

Exercise: Explore the script

What happens if you use the docker container run command above and put numbers after the script name?

This script comes from the Python Wiki and is set to add all numbers that are passed to it as arguments.

Exercise: Checking the options

Our Docker command has gotten much longer! Can you go through each piece of the Docker command above and explain what it does? How would you characterize the key components of a Docker command?

Here’s a breakdown of each piece of the command above

  • docker container run: use Docker to run a container
  • --mount type=bind,source=${PWD},target=/temp: connect my current working directory (${PWD}) as a folder inside the container called /temp
  • alice/alpine-python: name of the container image to use to run the container
  • python3 /temp/sum.py: what commands to run in the container

More generally, every Docker command will have the form: docker [action] [docker options] [docker container image] [command to run inside]

Exercise: Interactive jobs

Try using the directory mount option but run the container interactively. Can you find the folder that’s connected to your host computer? What’s inside?

The docker command to run the container interactively is:

docker container run --mount type=bind,source=${PWD},target=/temp -it alice/alpine-python sh

Once inside, you should be able to navigate to the /temp folder and see that’s contents are the same as the files on your host computer:

/# cd /temp
/# ls

Mounting a directory can be very useful when you want to run the software inside your container on many different input files. In other situations, you may want to save or archive an authoritative version of your data by adding it to the container image permanently. That’s what we will cover next.

Including your scripts and data within a container image

Our next project will be to add our own files to a container image – something you might want to do if you’re sharing a finished analysis or just want to have an archived copy of your entire analysis including the data. Let’s assume that we’ve finished with our sum.py script and want to add it to the container image itself.

In your shell, you should still be in the sum folder in the docker-intro folder.

pwd
/Users/yourname/Desktop/docker-intro/sum

Let’s add a new line to the Dockerfile we’ve been using so far to create a copy of sum.py. We can do so by using the COPY keyword.

COPY sum.py /home

This line will cause Docker to copy the file from your computer into the container’s filesystem. Let’s build the container image like before, but give it a different name:

docker image build -t alice/alpine-sum .
The Importance of Command Order in a Dockerfile

When you run docker image build it executes the build in the order specified in the Dockerfile. This order is important for rebuilding and you typically will want to put your RUN commands before your COPY commands.

Docker builds the layers of commands in order. This becomes important when you need to rebuild container images. If you change layers later in the Dockerfile and rebuild the container image, Docker doesn’t need to rebuild the earlier layers but will instead used a stored (called “cached”) version of those layers.

For example, in an instance where you wanted to copy multiply.py into the container image instead of sum.py. If the COPY line came before the RUN line, it would need to rebuild the whole image. If the COPY line came second then it would use the cached RUN layer from the previous build and then only rebuild the COPY layer.

Exercise: Did it work?

Can you remember how to run a container interactively? Try that with this one. Once inside, try running the Python script.

You can start the container interactively like so:

docker container run -it alice/alpine-sum sh

You should be able to run the python command inside the container like this:

/# python3 /home/sum.py

This COPY keyword can be used to place your own scripts or own data into a container image that you want to publish or use as a record. Note that it’s not necessarily a good idea to put your scripts inside the container image if you’re constantly changing or editing them. Then, referencing the scripts from outside the container is a good idea, as we did in the previous section. You also want to think carefully about size – if you run docker image ls you’ll see the size of each container image all the way on the right of the screen. The bigger your container image becomes, the harder it will be to easily download.

Security Warning

Login credentials including passwords, tokens, secure access tokens or other secrets must never be stored in a container. If secrets are stored, they are at high risk to be found and exploited when made public.

Copying alternatives

Another trick for getting your own files into a container image is by using the RUN keyword and downloading the files from the internet. For example, if your code is in a GitHub repository, you could include this statement in your Dockerfile to download the latest version every time you build the container image:

RUN git clone https://github.com/alice/mycode

Similarly, the wget command can be used to download any file publicly available on the internet:

RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.0/ncbi-blast-2.10.0+-x64-linux.tar.gz

Note that the above RUN examples depend on commands (git and wget respectively) that must be available within your container: Linux distributions such as Alpine may require you to install such commands before using them within RUN statements.

More fancy Dockerfile options (optional, for presentation or as exercises)

We can expand on the example above to make our container image even more “automatic”. Here are some ideas:

Make the sum.py script run automatically

FROM alpine
RUN apk add --update python3 py3-pip python3-dev
COPY sum.py /home

# Run the sum.py script as the default command
CMD ["python3", "/home/sum.py"]

Build and test it:

docker image build -t alpine-sum:v1 .
docker container run alpine-sum:v1

You’ll notice that you can run the container without arguments just fine, resulting in sum = 0, but this is boring. Supplying arguments however doesn’t work:

docker container run alpine-sum:v1 10 11 12

results in

docker: Error response from daemon: OCI runtime create failed:
container_linux.go:349: starting container process caused "exec:
\"10\": executable file not found in $PATH": unknown.

This is because the arguments 10 11 12 are interpreted as a command that replaces the default command given by CMD ["python3", "/home/sum.py"] in the image.

To achieve the goal of having a command that always runs when a container is run from the container image and can be passed the arguments given on the command line, use the keyword ENTRYPOINT in the Dockerfile.

FROM alpine

RUN apk add --update python3 py3-pip python3-dev
COPY sum.py /home

# Run the sum.py script as the default command and
# allow people to enter arguments for it
ENTRYPOINT ["python3", "/home/sum.py"]

# Give default arguments, in case none are supplied on
# the command-line
CMD ["10", "11"]

Build and test it:

docker image build -t alpine-sum:v2 .
# Most of the time you are interested in the sum of 10 and 11:
docker container run alpine-sum:v2
# Sometimes you have more challenging calculations to do:
docker container run alpine-sum:v2 12 13 14
Overriding the ENTRYPOINT

Sometimes you don’t want to run the image’s ENTRYPOINT. For example if you have a specialized container image that does only sums, but you need an interactive shell to examine the container:

docker container run -it alpine-sum:v2 /bin/sh

will yield

Please supply integer arguments

You need to override the ENTRYPOINT statement in the container image like so:

docker container run -it --entrypoint /bin/sh alpine-sum:v2

Add the sum.py script to the PATH so you can run it directly:

FROM alpine

RUN apk add --update python3 py3-pip python3-dev

COPY sum.py /home
# set script permissions
RUN chmod +x /home/sum.py
# add /home folder to the PATH
ENV PATH /home:$PATH

Build and test it:

docker image build -t alpine-sum:v3 .
docker container run alpine-sum:v3 sum.py 1 2 3 4
Best practices for writing Dockerfiles

Take a look at Nüst et al.’s “Ten simple rules for writing Dockerfiles for reproducible data science” [1] for some great examples of best practices to use when writing Dockerfiles. The GitHub repository associated with the paper also has a set of example Dockerfiles demonstrating how the rules highlighted by the paper can be applied.

[1] Nüst D, Sochat V, Marwick B, Eglen SJ, Head T, et al. (2020) Ten simple rules for writing Dockerfiles for reproducible data science. PLOS Computational Biology 16(11): e1008316. https://doi.org/10.1371/journal.pcbi.1008316

Key Points
  • Docker allows containers to read and write files from the Docker host.
  • You can include files from your Docker host into your Docker container images by using the COPY instruction in your Dockerfile.
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