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🐳 🔬 📚 Jupyter running in a docker container. This image can be used to integrate Jupyter into Galaxy

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Docker Climate Analysis Jupyter Container

This Jupyter Docker container is used by the Galaxy Project and can be installed from the quay.io index.

Usage of pre-built images

You can use the same images we use in Galaxy on your local computer or any other platform:

  • Pull an existing image locally
docker pull quay.io/nordicesmhub/docker-climate-notebook
  • Run a pre-build image from docker registry

To start your JupyterLab:

docker run -p 7777:8888 quay.io/nordicesmhub/docker-climate-notebook

and you will top open a new terminal and start your favorite web browser: your running Jupyter Notebook instance on http://localhost:7777/ipython/.

Remark: for reproducibility purpose, we suggest you use a specific tag e.g.

docker pull quay.io/nordicesmhub/docker-climate-notebook:2021-11-30

Then use the same tag when starting yoru JupyterLab application:

docker run -p 7777:8888 quay.io/nordicesmhub/docker-climate-notebook:2021-11-30 

Build your own docker image

  • Build your own image and run it

Docker is a pre-requirement for this project. You can build the container with:

 docker build -t climate-notebook . 

The build process can take some time, but if finished you can run your container with:

 docker run -p 7777:8888 -i -t climate-notebook

and you will have a running Jupyter Notebook instance on http://localhost:7777/ipython/.

Environment Variables

Some environment variables are made available to the user which will allow for configuring the behaviour of individual instances.

Variable Use
API_KEY Galaxy API Key with which to interface with Galaxy
CORS_ORIGIN If the notebook is proxied, this is the URL the end-user will see when trying to access a notebook
DEBUG Enable debugging mode, mostly for developers
GALAXY_URL URL at which Galaxy is accessible
GALAXY_WEB_PORT Port on which Galaxy is running, if applicable
HISTORY_ID ID of current Galaxy History, used in easing the dataset upload/download process
NOTEBOOK_PASSWORD Password with which to secure the notebook
PROXY_PREFIX Prefix to URL which allows Galaxy proxy to share cookies with Galaxy itself.

Authors

  • Bjoern Gruening
  • Eric Rasche
  • Anne Fouilloux

History

  • v1.0: Initial public release with pangeo notebook sotware stack and a few more additional packages.

  • v1.1: Public release with the same set of packages than version v1.0 but it produces a slightly smaller docker container.

Licence (MIT)

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

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🐳 🔬 📚 Jupyter running in a docker container. This image can be used to integrate Jupyter into Galaxy

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