Comparison of singlecell-rapids and scanpy for single-cell RNA-seq data analysis.
This repository contains the following notebooks:
scanpy-clustering.ipynb: Clustering of single-cell data usingscanpy.rapids-clustering.ipynb: Clustering of single-cell data usingsinglecell-rapidscompare.ipynb: Comparison of the clustering results fromscanpyandsinglecell-rapids
| URL/repo | https://github.com/scverse/rapids_singlecell |
| URL/docerfile | https://github.com/cellgeni/dockage/blob/master/rapids-singlecell/Dockerfile_0.14.1 |
| URL/container | https://quay.io/repository/cellgeni/rapids-singlecell |
| Version | 0.14.1 |
Create an interactive job with GPU access
bsub -Is \
-G cellgeni \
-q gpu-interactive \
-n 8 -M "16GB" \
-R "select[mem>16GB] rusage[mem=16GB]" \
-gpu "mode=shared:j_exclusive=no:gmem=16000:num=1" \
/bin/bashRun jupyter
singularity exec \
--bind /lustre,/nfs \
--nv \
/nfs/cellgeni/singularity/images/rapids-singlecell-0.14.1.sif \
jupyter server \
--no-browser \
--ServerApp.ip=0.0.0.0 \
--ServerApp.port=7878 \
--ServerApp.allow_remote_access=True \
--ServerApp.allow_origin='*' \
--IdentityProvider.token='password'Open ssh connection in separate terminal
ssh -L 7878:localhost:7878 <node-name>