GiN: Installation

Create conda env

conda create -n GiN python=3.10 jupyterlab=3.6 ipywidgets=8.0 nodejs=16  -y

Installing dependencies

yarn

npm install -g yarn

ipyuploads

pip install ipyuploads

nbtools

pip install nbtools

jupyter nbextension install --py nbtools --sys-prefix 
jupyter nbextension enable --py nbtools --sys-prefix

bioblend

pip install bioblend

GiN

Installation for a user

pip install galaxy-gin==0.1.0a8

jupyter nbextension install --py --symlink --overwrite --sys-prefix GiN
jupyter nbextension enable --py --sys-prefix GiN

For a development installation (requires Node.js and Yarn version 1),

$ cd GiN
$ npm install @g2nb/nbtools
$ pip install -e .
$ jupyter nbextension install --py --symlink --overwrite --sys-prefix GiN
$ jupyter nbextension enable --py --sys-prefix GiN
$ jupyter labextension develop --overwrite GiN

Then you need to rebuild the JS when you make a code change:

$ cd js
$ yarn run build

You then need to refresh the JupyterLab page when your javascript changes.

Docker

A Docker image with GiN and the full JupyterLab stack is available through DockerHub.

docker pull jayadevjoshi12/gin:latest
docker run --rm -p 8888:8888 jayadevjoshi12/gin:latest

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Screenshots..

Login tool

Galaxy tool form

Job status

History Data

Data sharing widget

Restores form state from the saved parameters from the shared notebook for the current user to reproduce the workflow.