SHRiMP is a software package for aligning genomic reads against a target genome. It was primarily developed with the multitudinous short reads of next generation sequencing machines in mind, as well as Applied Biosystem's colourspace genomic representation.

References:

• SHRiMP was originally designed and written by Michael Brudno and Stephen M. Rumble, with considerable input and testing by the SidowLab. Since then, Adrian Dalca, Marc Fiume and Vladimir Yanovsky have made considerable contributions to probability calculations and 2-pass SMS mapping algorithms. The original SHRiMP publication can be found here.

• Shrimp documentation

• Module Name: shrimp (see the modules page for more information)
• Multithreaded/singlethreaded/MPI...
• Environment variables set
  • shrimp_HOME
• Example files in $SHRIMP_DATA
• Reference data in /fdb/shrimp/

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
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 shrimp

[user@cn3144 ~]$ cd /data/$USER

[user@cn3144 ~]$ cp $SHRIMP_DATA/example/* . 

[user@cn3144 ~]$ gmapper-cs test_S1_F3.csfasta ch11_12_validated.fasta -N 8 -o 5 -h 80% >map.out 2>map.log

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

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

#!/bin/bash
set -e
module load shrimp
cd /data/$USER/example
gmapper-cs test_S1_F3.csfasta ch11_12_validated.fasta -N 8 -o 5 -h 80% >map.out 2>map.log

Submit this job using the Slurm sbatch command.

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

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

gmapper-cs  file1.csfasta ch11_12_validated.fasta -N 8 -o 5 -h 80% >file1.out 2>&1
gmapper-cs  file2.csfasta ch11_12_validated.fasta -N 8 -o 5 -h 80% >file2.out 2>&1
gmapper-cs  file3.csfasta ch11_12_validated.fasta -N 8 -o 5 -h 80% >file3.out 2>&1
[...]

Submit this job using the swarm command.

swarm -f shrimp.swarm [-g #] [-t #] --module shrimp