Celltypist

Introduction

Celltypist is a tool for semi-automatic cell type annotation.

For more information, please check its website: https://biocontainers.pro/tools/celltypist and its home page on Github.

Versions

• 0.2.0

• 1.1.0

Commands

• celltypist

• python

• python3

Module

You can load the modules by:

module load biocontainers
module load celltypist

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Celltypist on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 8
#SBATCH --job-name=celltypist
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers celltypist

celltypist --indata demo_2000_cells.h5ad --model Immune_All_Low.pkl --outdir output