Docker for Galaxy Pangeo notebook from official Pangeo image
University of Freiburg, Freiburg (Germany)
Docker for Galaxy Pangeo notebook from official Pangeo image.
It is based on Pangeo notebook docker image (https://github.com/pangeo-data/pangeo-docker-images) and contained a few additional packages required for Galaxy (to exchange data, etc.
Economy, business and finance/Economic sector/Computing and information technology/Wireless technology
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This Jupyter Docker container is used by the Galaxy Project.
This Jupyter Docker container is used by the Galaxy Project. It is based on Pangeo notebook docker image (https://github.com/pangeo-data/pangeo-docker-images) and contained a few additional packages required for Galaxy (to exchange data, etc.).
Docker for Galaxy Pangeo notebook from official Pangeo image - snapshot
Anne Foilloux, and Björn Grüning. "Docker for Galaxy Pangeo notebook from official Pangeo image." ROHub. Mar 26 ,2022. https://doi.org/10.24424/f0q9-8e35.
Nordic e-Infrastructure Collaboration (NeIC)
Copernicus Atmosphere Monitoring Service PM2.5, 2 day forecasts, 24th December 2021 at 12:00 UTC
CAMS PM2.5, 2 day forecasts, 24th December 2021 at 12:00 UTC
These docker images (different tags) correspond to the docker images built for Galaxy Pangeo JupyterLab. The docker images can be used within Galaxy and as standalone docker images. You can use the same images we use in Galaxy on your local computer or any other platform: 1. Pull an existing image locally docker pull quay.io/nordicesmhub/docker-pangeo-notebook 2. Run a pre-build image from docker registry 3. To start your JupyterLab: docker run -p 7777:8888 quay.io/nordicesmhub/docker-pangeo-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-pangeo-notebook:1c0f66b Then use the same tag when starting your JupyterLab application: docker run -p 7777:8888 quay.io/nordicesmhub/docker-pangeo-notebook:1c0f66b
Docker images for Galaxy Pangeo JupyterLab (Quay Container Registry)
Dataset used in the Galaxy Pangeo tutorials on Xarray. Data is in netCDF format and is from Copernicus Air Monitoring Service and more precisely PM2.5 (Particle Matter < 2.5 μm) 4 days forecast from December, 22 2021. This dataset is very small and there is no need to parallelize our data analysis. Parallel data analysis with Pangeo is not covered in this tutorial and will make use of another dataset.
netCDF input file PM2.5 4 days forecast from December, 22 2020
Default Jupyter Notebook used when starting Galaxy Climate JupyterLab if no other Jupyter Notebook is passed by the user.
Default Jupyter Notebook for Galaxy Climate JupyterLab
Training material (hands-on) where Pangeo Notebook is used to learn Xarray. This training is part of the Galaxy Training Network (GTN). In this tutorial, we will learn about Xarray, one of the most used Python library from the Pangeo ecosystem. We will be using data from Copernicus Atmosphere Monitoring Service and more precisely PM2.5 (Particle Matter < 2.5 μm) 4 days forecast from December, 22 2021. Parallel data analysis with Pangeo is not covered in this tutorial.
Pangeo Notebook in Galaxy - Introduction to Xarray (GTN)
This is a gif animated image showing how to start the Galaxy Pangeo JupyterLab in Galaxy Europe. In this video, we pass an input file (this file will be imported in the Jupyter Notebook /import folder).
How to start Galaxy Pangeo JupyterLab (gif animated)
Link to the online JupyterLab documentation.
This is a tarball for the Docker Galaxy pangeo-JupyterLab image - Version 1c0f66b. To use it: download the image file docker-pangeo-notebook-1c0f66b.tar load it with docker with the command: docker load --input docker-pangeo-notebook-1c0f66b.tar launch the Docker container binding of your data folder (on the local machine) with the /import folder i(inside the container) with the command: docker run -v my_data_folder:/import -p 7777:8888 quay.io/nordicesmhub/docker-pangeo-notebook:1c0f66b start your favorite web browser and go to: http://localhost:7777/ipython/ See https://github.com/NordicESMhub/docker-pangeo-notebook for more details
Docker Galaxy pangeo-JupyterLab image Version 1c0f66b
This is the Galaxy Pangeo JupyterLab tool wrapper used by Galaxy to start the Galaxy Pangeo JupyterLab on a Galaxy instance.
Galaxy Pangeo JupyterLab Tool wrapper (xml)
This github repository contains all the sources required for building the docker containers that are made available in Quay Container Registry.
Source code for building the docker container (github repository)