Accessible and Reproducible Computational Analyses for Qualitative Biological Networks
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Project webpage: https://colomoto.github.io/colomoto-docker/
You need Docker. We support GNU/Linux, macOS, and Windows.
You need Python.
The script can be installed and upgraded by executing the following command
(you may have to use pip3 instead of pip depending on your configuration):
pip install -U colomoto-docker
The CoLoMoTo notebook can then be started by executing in a terminal (if using Docker Toolbox, in a Docker Terminal):
colomoto-docker
The container can be stopped by pressing Ctrl+C keys.
By default, the script uses the most recently fetched image; the first time, it fetches the most recent colomoto/colomoto-docker tag.
A specific tag can be specified using the -V option. For example:
colomoto-docker # uses the most recently fetched image
colomoto-docker -V latest # fetches the latest published image
colomoto-docker -V 2018-05-29 # fetches a specific image
Warning: by default, the files within the Docker container are isolated from the running host computer, therefore files are deleted after stopping the container, except the files within the persistent directory.
To have access to the files of your current directory you can use the --bind option:
colomoto-docker --bind .
If you want to have the tutorial notebooks alongside your local files, you can do the following:
mkdir notebooks
colomoto-docker -v notebooks:local-notebooks
in the Jupyter browser, you will see a local-notebooks directory which is
bound to your notebooks directory.
See
colomoto-docker --help
for other options.
First fetch the image with
docker pull colomoto/colomoto-docker:TAG
where TAG is the version of the image, among colomoto/colomoto-docker tags.
The image can be ran using
docker run -it --rm -p 8888:8888 colomoto/colomoto-docker:TAG
then, open your browser and go to http://localhost:8888 for the Jupyter notebook web interface
(note: when using Docker Toolbox, replace localhost with the result of
docker-machine ip default command).
See https://colomoto.github.io/colomoto-docker/#available-software-tools-with-python-api for the list of software shipped within the CoLoMoTo Docker image.
Docker images are timestamped with tags of the form YYYY-MM-DD after each tool addition or upgrade.
In order to guarantee the re-executability of your notebook, we recommend using these tagged images instead of the non-persistent next tag.
See CONTRIBUTING.md.
Content type
Image
Digest
sha256:05c2f5314…
Size
1.6 GB
Last updated
20 days ago
docker pull colomoto/colomoto-docker:next