TRUP on Biowulf
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Documentation
Notes
Interactive job
Batch job
Swarm of jobs

Cancer cells express many rearranged transcripts posing increased complexity to transcriptome analysis. As an unified pipeline, TRUP is designed to sensitively and accurately dissect the complexity of the cancer transcriptome by analyzing RNA-seq data obtained from tumour tissues. The current functionalities of TRUP include: 1) identification of fusion transcripts; 3) RNA-seq quality assesment; 2) Gene-read counting. The fusion detection module in TRUP combines split-read/read-pair mapping with regional de-novo assembly to achieve a balance between sensitivity and precision.

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@biowulf]$ sinteractive --cpus-per-task=4
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 ~]$ perl $TRUPPATH/RTrace.pl -h

[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. trup.sh). For example:

#!/bin/bash
set -e
module load trup
perl $RTrace.pl --runlevel 1 --sampleName SAMPLE --seqType p --readpool RP --root PD --threads $SLURM_CPUS_PER_TASK --anno AD 2>>run.log

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --mem=10g trup.sh

Note that $SLURM_CPUS_PER_TASK in the script will be automatically replaced by '4' in the sbatch command.

Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

Create a swarmfile (e.g. trup.swarm). For example:

cd dir1; perl $RTrace.pl --threads $SLURM_CPUS_PER_TASK...
cd dir2; perl $RTrace.pl --threads $SLURM_CPUS_PER_TASK...
cd dir3; perl $RTrace.pl --threads $SLURM_CPUS_PER_TASK...
cd dir4; perl $RTrace.pl --threads $SLURM_CPUS_PER_TASK...

Submit this job using the swarm command.

swarm -f trup.swarm -g 10 -t 4 --module trup
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module Loads the module for each subjob in the swarm