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EricScript on Biowulf

Description: EricScript is a computational framework for the discovery of gene fusions in paired end RNA-seq data. It is able to generate synthetic gene fusions by using the EricScript simulator and calculate a number of statistical measures for evaluating gene fusion detection methods' performance with EricScript CalcStats.

Citation

If you use EricScript to identify gene fusions in your RNA-seq data, please cite:
Documentation
Important Notes
Do NOT use the "-db", "--dbfolder" or "--downdb" arguments to access the databases.

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 EricScript
[user@cn3144 ~]$ ericscript.pl [arguments] <reads_1.fq(.gz)> <reads_2.fq(.gz)> 
[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. runericscript.sh) to submit the job. For example:

#!/bin/bash
module load EricScript
ericscript.pl [arguments] <reads_1.fq(.gz)> <reads_2.fq(.gz)> 

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] runericscript.sh
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. runericscript.swarm). For example:

ericscript.pl [arguments] <reads_1.fq(.gz)> <reads_2.fq(.gz)> 
ericscript.pl [arguments] <reads_3.fq(.gz)> <reads_4.fq(.gz)> 
ericscript.pl [arguments] <reads_5.fq(.gz)> <reads_6.fq(.gz)> 
ericscript.pl [arguments] <reads_7.fq(.gz)> <reads_8.fq(.gz)> 

Submit this job using the swarm command.

swarm -f runericscript.swarm [-g #] [-t #] --module EricScript
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 EricScript Loads the EricScript module for each subjob in the swarm