Biowulf High Performance Computing at the NIH
exceRpt on Biowulf

The extra-cellular RNA processing toolkit (exceRpt) was designed to handle the variable contamination and often poor quality data obtained from low input smallRNA-seq samples such as those obtained from extra-cellular preparations. However the tool is perfectly capable of processing data from more standard cellular preparations and, with minor modifications to the command-line call, is also capable of processing WGS/exome and long RNA-seq data.

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
[user@cn0000]$ module load exceRpt
[user@cn0000]$ cp -Rp $EXCERPT_EXAMPLES/input .
[user@cn0000]$ mkdir output
[user@cn0000]$ make -f $EXCERPT_HOME/exceRpt_smallRNA INPUT_FILE_PATH=input/SRR026761.sra OUTPUT_DIR=output N_THREADS=${SLURM_CPUS_PER_TASK} JAVA_RAM=${SLURM_MEM_PER_NODE}M
[user@cn0000]$ exit
[user@biowulf]$

Batch job
Most jobs should be run as batch jobs.

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

#!/bin/bash
module load exceRpt
cp -Rp ${EXCERPT_EXAMPLES}/input .
mkdir output
make -f ${EXCERPT_HOME}/exceRpt_smallRNA \
  INPUT_FILE_PATH=input/SRR026761.sra \
  OUTPUT_DIR=output \
  N_THREADS=${SLURM_CPUS_PER_TASK} \
  JAVA_RAM=${SLURM_MEM_PER_NODE}M \
  REMOVE_LARGE_INTERMEDIATE_FILES="true"
Rscript ${EXCERPT_HOME}/mergePipelineRuns.R output

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=16 --mem=24g exceRpt.sh