velocyto.py
Velocyto.py a library for the analysis of RNA velocity.
Detailed information about velocyto.py can be found here: https://github.com/velocyto-team/velocyto.py.
Link to section 'Versions' of 'velocyto.py' Versions
- 0.17.17
Link to section 'Commands' of 'velocyto.py' Commands
- python
- python3
- velocyto
Link to section 'Module' of 'velocyto.py' Module
You can load the modules by:
module load biocontainers
module load velocyto.py/0.17.17-py39
Link to section 'Interactive job' of 'velocyto.py' Interactive job
To run Velocyto.py 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 3.9.10 | packaged by conda-forge | (main, Feb 1 2022, 21:24:11)
[GCC 9.4.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import velocyto as vcy
>>> vlm = vcy.VelocytoLoom("YourData.loom")
>>> vlm.normalize("S", size=True, log=True)
>>> vlm.S_norm # contains log normalized
Link to section 'Batch job' of 'velocyto.py' 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=Velocyto
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers velocyto.py/0.17.17-py39
velocyto run10x cellranger_count_1kpbmcs_out refdata-gex-GRCh38-2020-A/genes/genes.gtf