Automated cell type annotation

The script requires GPUs on your host system.

Run script using container environment

We provide a container environment with all required software dependencies. Pre-build Docker images are available here.

Note: If you encounter any GPU related issues with the commands below, make sure that GPU support for container applications is set up correctly on your host system.

Singularity

singularity run --nv --pwd /mnt --bind /path/on/host:/mnt docker://matmu/cell_type_annotation:latest

Docker

docker run --rm -it --gpus=all -v /path/on/host:/mnt -w /mnt matmu/cell_type_annotation:latest