Biowulf High Performance Computing at the NIH
Slamdunk on Biowulf

SLAMseq is a novel sequencing protocol that directly uncovers 4-thiouridine incorporation events in RNA by high-throughput sequencing. When combined with metabolic labeling protocols, SLAM-seq allows to study the intracellular RNA dynamics, from transcription, RNA processing to RNA stability. SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis.

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold). In this example, the input files are in the user's /data area, and the reference genome file is in /fdb, so SINGULARITY_BINDPATH is set to "/data/$USER,/fdb"

[user@biowulf]$ sinteractive --cpus-per-task=8 --mem=20g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load singularity

[user@cn3144 ~]$ export SINGULARITY_BINDPATH="/data/$USER,/fdb"

[user@cn3144 ~]$ singularity run docker://tobneu/slamdunk

[user@cn3144 ~]$ slamdunk all -r /fdb/genome/hg19/chr_all.fa -b ./exampleBAM.bed \
      -o out -t $SLURM_CPUS_PER_TASK ./exampleBAM.bam
slamdunk all
Running slamDunk map for 1 files (8 threads)
.
Running slamDunk sam2bam for 1 files (8 threads)
.
Creating output directory: out/filter
Running slamDunk filter for 1 files (8 threads)
.
[...]

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. slamdunk.sh). For example:

#!/bin/bash
set -e
module load singularity
export SINGULARITY_BINDPATH="/data/$USER,/fdb,/lscratch"
singularity exec docker://tobneu/slamdunk \
      slamdunk all -r /fdb/genome/hg19/chr_all.fa -b ./exampleBAM.bed \
      -o out -t $SLURM_CPUS_PER_TASK ./exampleBAM.bam

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] slamdunk.sh