Streamlining SLAMseq analysis with ultra-high sensitivity: SlamDunk is a novel, fully automated software tool for automated, robust, scalable and reproducible SLAMseq data analysis.
Allocate an interactive session and run the program.
Sample session (user input in bold):
[user@biowulf]$ sinteractive --cpus-per-task=8 --mem=20g --gres=lscratch:20 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 slamdunk [user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID [user@cn3144 ~]$ cp /fdb/genome/hg19/chr_all.fa . [user@cn3144 ~]$ slamdunk all -r 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 ~]$
Create a batch input file (e.g. slamdunk.sh). For example:
#!/bin/bash set -e module load slamdunk cd /lscratch/$SLURM_JOB_ID cp /fdb/genome/hg19/chr_all.fa . slamdunk all -r 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=#] [--gres=lscratch:#] slamdunk.sh