cell2location on Biowulf

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Cell2location: Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)

References:

Cell2location maps fine-grained cell types in spatial transcriptomics. Nat Biotechnol. 2022 May;40(5):661-671. doi: 10.1038/s41587-021-01139-4. Epub 2022 Jan 13

Documentation

Important Notes

Module Name: cell2location (see the modules page for more information)
/usr/local/apps/cell2location/test.ipynb is available for demonstration which is from https://cell2location.readthedocs.io/en/latest/notebooks/cell2location_tutorial.html.
This installation of cell2location is able to make use of gpu.

Interactive job

Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ module load tmux
[user@biowulf]$ tmux
[user@biowulf]$ sinteractive --time=8:00:00 --gres=lscratch:5,gpu:p100:1 --mem=5g --tunnel
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job
                                                                           
Created 1 generic SSH tunnel(s) from this compute node to                  
biowulf for your use at port numbers defined                               
in the $PORTn ($PORT1, ...) environment variables.                         
                                                                           
                                                                           
Please create a SSH tunnel from your workstation to these ports on biowulf.
On Linux/MacOS, open a terminal and run:                                   
                                                                           
    ssh  -L 33327:localhost:33327 biowulf.nih.gov                          
                                                                           
For Windows instructions, see https://hpc.nih.gov/docs/tunneling       


[user@cn4224 ~]$ cd /lscratch/$SLURM_JOBID
[user@cn4224 46116226]$ cp /usr/local/apps/cell2location/test.ipynb

Now open a local terminal from your desktop (powershell for windows or terminal for Mac/Linux) and run the command below. Replace 33327 with the port number you see above.

ssh  -L 33327:localhost:33327 biowulf.nih.gov

Back to the interactive session,

[user@cn4224 46116226]$ module load cell2location
[+] Loading cell2location 0.1.3 
[user@cn4224 46116226]$ jupyter notebook --ip localhost --port $PORT1 --no-browser

Copy and paste the URL from the output to your choice of internet browser and start jupyter notebook.
Open the test.ipynb file and start the test.

[user@cn4224 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226

[user@biowulf ~]$