Proxy Web Apps#

You can host many web applications by running them on the command line and then accessing them through the jupyter-proxy plugin.

Underneath the hood we are using the Jupyterhub Proxy Plugin in order to access web applications through jupyterhub.

Before we start you’ll need your:

Jupyterhub URL - copy and paste this from the browser
The service prefix, if any
Your username

env |grep JUPYTERHUB_SERVICE_PREFIX
env |grep JUPYTERHUB_BASE_URL

Proxy URLs#

The official docs. Many docs are embedded directly from the source docs.

Starting and Proxying Processes#

Starting and Proxying Processes

Accessing Arbitrary Ports#

Accessing Arbitrary Ports

More Examples#

Typically, you can grab the url from your browser.

For example, the URL for this browser is:

https://jhub1.bioanalyzedev.io/user/jillian/lab/tree/bioanalyze-hpc/docs/web-apps/proxy-web-apps.md

The base jupyterhub url is:

https://jhub1.bioanalyzedev.io/user/jillian/

The proxy path is:

https://jhub1.bioanalyzedev.io/user/jillian/proxy/${PORT}/

Gotchas#

You always want to make sure that you’re serving your application from 0.0.0.0, not localhost. Usually this option is available through the CLI to run the program either as --host or --ip.

Example - ExCellxGene#

Let’s proxy the ExCellxGene in Jupyterhub.

Excellxgene needs to be installed to it’s own conda environment because it doesn’t play nice with the existing conda env.

Grab the excellxgene-environment.yaml from this repo.
Create the excellxgene environment
Register the excellxgene environment as a Python Kernel.

git clone https://github.com/dabble-of-devops-bioanalyze/single-cell-saturn-cloud
git clone https://github.com/scverse/scanpy-tutorials

cd single-cell-saturn-cloud
mamba env create -f ./excellxgene-environment.yaml -p ~/.conda/envs/excellxgene
source activate conda activate excellxgene

If you are running on a local system or BioAnalyze HPC I recommend using these settings.

Now that we have some data let’s visualize some clusters!

git clone https://github.com/czbiohub/excellxgene
cd excellxgene
cd example-dataset
wget https://raw.githubusercontent.com/dabble-of-devops-bioanalyze/single-cell-saturn-cloud/main/prepare.py
source activate excellxgene
python ./prepare.py pbmc3k.h5ad --output ./pbmc3k-preprocessed.h5ad --overwrite

Launch the ExCellxGene Web App#

excellxgene launch --host 0.0.0.0 --port 8000 ./pbmc3k-preprocessed.h5ad