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Use the spam docker image

Use the spam docker image#

With this method you don’t need to install spam to run it. You only need to install docker.

We’ve created a docker image based on debian 10 bullseye and python 3.10 with spam and all its dependencies already installed on it. This way you won’t have to install anything to run your programs.

1. Pull the image#

You can pull the image and rename it to spam for conveniency:

$ docker pull registry.gitlab.com/spam-project/docker/spam
$ docker image tag registry.gitlab.com/spam-project/docker/spam spam
$ docker rmi registry.gitlab.com/spam-project/docker/spam

2. Input/output folder on the host#

On your computer (hearafter refered to as the host), have a folder with all your input data and scripts. The output files will be written in this folder too, as if you were running your script directly on the host.

WARNING: avoid reading and writing outside of this directory.

For example your folder can look like this:

/home/me/mydata
    im1.tif
    im2.tif
    myscript.py

In the following docker commands you will see the option

-v /home/me/mydata:/work

that binds your host folder /home/me/mydata with the container. It means that all inputs and outputs will be read and written by the container in /home/me/mydata. Keep in mind to change /home/me/mydata with the actual path of your working directory on your computer.

3. Execute your script or a spam command#

You can now execute your script with the following command:

$ docker run --rm -v /home/me/mydata:/work spam python myscript.py

You can also directly use spam commands

$ docker run --rm -v /home/me/mydata:/work spam spam-ldic --help

4. Jupyter notebooks#

The image embeds a jupyter lab server accessible at http://127.0.0.1:8888 with the command

$ docker run --rm -p 8888:8888 -v /home/me/mydata:/work spam
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