slamdunk.rst

Slamdunk

Introduction ~~~~~~~~ Slamdunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis.

For more information, please check:
Docker hub: https://hub.docker.com/r/tobneu/slamdunk
Home page: http://t-neumann.github.io/slamdunk/

Versions

• 0.4.3

Commands ~~~~~~~ - slamdunk - alleyoop

Module

You can load the modules by:

module load biocontainers
module load slamdunk

Example 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 run slamdunk on our clusters:

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

module --force purge
ml biocontainers slamdunk