Biowulf High Performance Computing at the NIH
cellxgene on Biowulf

cellxgene (pronounced "cell-by-gene") is an interactive data explorer for single-cell transcriptomics datasets, such as those coming from the Human Cell Atlas.

Documentation
Important Notes

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 input in bold):

[user@biowulf]$ sinteractive --tunnel
salloc.exe: Pending job allocation 53558687
salloc.exe: job 53558687 queued and waiting for resources
salloc.exe: job 53558687 has been allocated resources
salloc.exe: Granted job allocation 53558687
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn0959 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 40567:localhost:40567 user@biowulf.nih.gov

For Windows instructions, see https://hpc.nih.gov/docs/tunneling
At this point, users should create the SSH tunnel from their workstation as specified in the instructions above. Note the port number: this will be needed for the cellxgene command.
[user@cn3144 ~]$ module load cellxgene
[+] Loading cellxgene 0.15.0  ...

[user@cn3144 ~]$  cellxgene launch --port 40567 https://cellxgene-example-data.czi.technology/pbmc3k.h5ad
[cellxgene] Starting the CLI...
/usr/local/Anaconda/envs_app/cellxgene/0.15.0/lib/python3.6/site-packages/anndata/_core/anndata.py:21: FutureWarning: pandas.core.index is deprecated and will be removed in a future version.  The public classes are available in the top-level namespace.
  from pandas.core.index import RangeIndex
[cellxgene] Loading data from pbmc3k.h5ad.
[cellxgene] Warning: Annotation log1p_n_genes_by_counts will be converted to 32 bit float and may lose precision.
[cellxgene] Warning: Annotation pct_counts_in_top_50_genes will be converted to 32 bit float and may lose precision.
[cellxgene] Warning: Annotation pct_counts_in_top_100_genes will be converted to 32 bit float and may lose precision.
[cellxgene] Warning: Annotation pct_counts_in_top_200_genes will be converted to 32 bit float and may lose precision.
[cellxgene] Warning: Annotation pct_counts_in_top_500_genes will be converted to 32 bit float and may lose precision.
[cellxgene] Warning: Annotation pct_dropout_by_counts will be converted to 32 bit float and may lose precision.
[cellxgene] Launching! Please go to http://127.0.0.1:40567 in your browser.
[cellxgene] Type CTRL-C at any time to exit.
Point a web browser on your desktop to the URL specified by cellxgene, in this case http://127.0.0.1:40567:

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$