scVelo

Introduction

scVelo is a scalable toolkit for RNA velocity analysis in single cells, based on https://doi.org/10.1038/s41587-020-0591-3. Its detailed usage can be found here: https://scvelo.readthedocs.io.

Versions

• 0.2.4

Commands

• python

• python3

Module

You can load the modules by:

module load biocontainers
module load scvelo/0.2.4

Interactive job

To run scVelo 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 scvelo/0.2.4
(base) UserID@bell-a008:~ $ python
Python 3.9.5 (default, Jun  4 2021, 12:28:51)
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import scvelo as scv
>>> scv.set_figure_params()

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=scvelo
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers scvelo/0.2.4

python script.py