CellRank

Introduction

CellRank a toolkit to uncover cellular dynamics based on Markov state modeling of single-cell data. Detailed information about CellRank can be found here: https://cellrank.readthedocs.io/en/stable/.

Versions

• 1.5.1

Commands

• python

• python3

Module

You can load the modules by:

module load biocontainers
module load cellrank/1.5.1

Note

The CellRank container also contained scVelo and scanpy. When you want to use CellRank, do not load scVelo or scanpy.

Interactive job

To run CellRank interactively on our clusters:

(base) UserID@bell-fe00:~ $ sinteractive -N1 -n12 -t4:00:00 -A myallocation
salloc: Granted job allocation 12345869
salloc: Waiting for resource configuration
salloc: Nodes bell-a008 are ready for job
(base) UserID@bell-a008:~ $ module load biocontainers cellrank/1.5.1
(base) UserID@bell-a008:~ $ python
Python 3.9.9 |  packaged by conda-forge |  (main, Dec 20 2021, 02:41:03)
[GCC 9.4.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scanpy as sc
>>> import scvelo as scv
>>> import cellrank as cr
>>> import numpy as np
>>> scv.settings.verbosity = 3
>>> scv.settings.set_figure_params("scvelo")
>>> cr.settings.verbosity = 2

Batch 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 submit a sbatch job on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=cellrank
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers cellrank/1.5.1

python script.py