Running Seurat v5 via Jupyter
Creation date: 3/12/2024 9:43 AM
Updated: 3/12/2024 9:47 AM
To run Seurat version 5 via Jupyter, open a jupyter session as described in: https://www.hoffman2.idre.ucla.edu/Using-H2/Connecting/Connecting.html#connecting-via-jupyter-notebook-lab, to load the needed dependencies please use:
python h2jupyb -u joebruin -b glpk/5.0 -m 10 #add any other needed request
where you will replace `joebruin` with your actual Hoffman2 Cluster user name.
When the jupyter session starts on your browser open an R session selecting the kernel:
R 4.3.0 gcc 10.2.0a sample jupyter notebook is available at:
/u/local/apps/R/R_TUTORIALS/SEURAT5_GUIDED_CLUSTERING_TUTORIAL/Seurat\ -\ Guided\ Clustering\ Tutorial.ipynb
you will need to open a terminal and:
mkdir $HOME/R_SEURAT5_GUIDED_CLUSTERING_TUTORIAL; cd $HOME/R_SEURAT5_GUIDED_CLUSTERING_TUTORIAL
cp /u/local/apps/R/R_TUTORIALS/SEURAT5_GUIDED_CLUSTERING_TUTORIAL/pbmc3k_filtered_gene_bc_matrices.tar.gz ./
cp /u/local/apps/R/R_TUTORIALS/SEURAT5_GUIDED_CLUSTERING_TUTORIAL/Seurat\ -\ Guided\ Clustering\ Tutorial.ipynb ./
from the Jupyter interface you can then navigate to the newly created
R_SEURAT5_GUIDED_CLUSTERING_TUTORIAL directory and start the jupyter notebook.Should you have any issues please open a support ticket at: https://support.idre.ucla.edu/helpdesk/Tickets/New
---
RD, 2024/03/12
DataImage77.png