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Squid on Biowulf

SQUID is designed to detect transcriptomic structural variations from RNA-seq alignment.

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
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 squid
[user@cn3144 ~]$ squid commands

[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. squid.sh): For example:

#!/bin/bash
module load squid
squid commands

Submit this job using the Slurm sbatch command.

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

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

cd /data/$USER/dir1; squid command1; squid command2
cd /data/$USER/dir2; squid command1; squid command2
cd /data/$USER/dir3; squid command1; squid command2
cd /data/$USER/dir4; squid command1; squid command2

Submit this job using the swarm command.

swarm -f squid.swarm --module squid