cellrank
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/.
Link to section 'Versions' of 'cellrank' Versions
- 1.5.1
Link to section 'Commands' of 'cellrank' Commands
- python
- python3
Link to section 'Module' of 'cellrank' Module
You can load the modules by:
module load biocontainers
module load cellrank/1.5.1
The CellRank container also contained scVelo and scanpy. When you want to use CellRank, do not load scVelo or scanpy.
Link to section 'Interactive job' of 'cellrank' 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
Link to section 'Batch job' of 'cellrank' 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=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