colomoto/colomoto-docker

By colomoto

Updated 20 days ago

Accessible and Reproducible Computational Analyses for Qualitative Biological Networks

Image
Languages & frameworks
Machine learning & AI
Data science
1

10K+

colomoto/colomoto-docker repository overview

Binder Gitter

Project webpage: https://colomoto.github.io/colomoto-docker/

Quick usage guide

You need Docker. We support GNU/Linux, macOS, and Windows.

Using the colomoto-docker script

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.

Manual invocation

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).

Embedded software

See https://colomoto.github.io/colomoto-docker/#available-software-tools-with-python-api for the list of software shipped within the CoLoMoTo Docker image.

Tagging policy and re-executability considerations

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.

Contribute

See CONTRIBUTING.md.

Tag summary

Content type

Image

Digest

sha256:05c2f5314

Size

1.6 GB

Last updated

20 days ago

docker pull colomoto/colomoto-docker:next