Open OnDemand Apps
clone into ~/ondemand/dev/ , ie:
git clone https://github.com/amcpherson/openondemandapps.git ~/ondemand/dev/
and then enable through the 'develop' button on the ondemand webapp.
The Jupyter app requires an installation of jupyter in a conda environment. Enter the name of the conda environment in which jupyter is installed in the Conda Environment Name config option. Use the Jupyter Binary field to specify either jupyter-lab or jupyter-notebook. Jupyter will launch in the Notebooks directory directory.
The RStudio app runs from an rocker based rstudio singularity image.
To build the singularity image first build a docker image on your local machine using:
cd $REPODIR/docker
docker build -t $DOCKERUSER/rocker-custom:4.2.2 .
docker push $DOCKERUSER/rocker-custom:4.2.2
Then build the singularity image with:
cd /data1/soldatr/singularity/
singularity pull docker://$DOCKERUSER/rocker-custom:4.2.2
To run the app, enter $SINGIMAGEDIR/rocker-custom_4.2.2.sif into the RStudio Singularity Image field. Also enter an existing directory into the R packages into which newly installed R packages will be stored.