Software: scVelo
Description
scVelo is a scalable toolkit for RNA velocity analysis in single cells
Available Versions
Unspecified: | 0.2.4 |
---|
Based on https://doi.org/10.1038/s41587-020-0591-3. Its detailed usage can be found here: https://scvelo.readthedocs.io.
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
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