Biowulf High Performance Computing at the NIH
tailseeker on Biowulf

Tailseeker is the official pipeline for TAIL-seq, which measures poly(A) tail lengths and 3′-end modifications with Illumina SBS sequencers.

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):

[user@biowulf]$ sinteractive --cpus-per-task 8 --mem 32g
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 tailseeker

[user@cn3144 ~]$ tseek -j $SLURM_CPUS_PER_TASK

[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. tailseeker.sh). For example:

#!/bin/bash
set -e
module load tailseeker
test -n "$SLURM_CPUS_PER_TASK" || SLURM_CPUS_PER_TASK=2
tseek -j $SLURM_CPUS_PER_TASK

Submit this job using the Slurm sbatch command.

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