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Running Seurat version 5 on the Hoffman2 Cluster

Creation date: 3/11/2024 4:20 PM    Updated: 3/12/2024 9:39 AM    r seurat tutorial
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Seurat version 5 (https://satijalab.org/seurat/) is available on the Hoffman2 Cluster under these environmental modules combination:

module load gcc/10.2.0; module load R/4.3.0; module load glpk/5.0

NOTE: in case your R library contains some packages that interfere with this installation of Seurat you should consider removing the directory $HOME/R/x86_64-pc-linux-gnu-library-RH7/4.2.2/gcc10.2.0_intel2022.1.1 and start afresh. Make sure also that your $HOME/.Rprofile is not hardcoding any specific version of R.

You can test this version of R with the following tutorial (adapted from https://satijalab.org/seurat/articles/pbmc3k_tutorial):

qrsh -l h_data=10G
module load gcc/10.2.0; module load R/4.3.0; module load glpk/5.0
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/test_seurat_clustering.R ./
tar xvr pbmc3k_filtered_gene_bc_matrices.tar.gz
R

and at the R prompt issue:

source("test_seurat_clustering.R")

Should you have any issues please open a support ticket at: https://support.idre.ucla.edu/helpdesk/Tickets/New

Running Seurat v5 via Jupyter

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 10.2.0

a 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


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RD, 2024/03/12
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