UROPA is a command line based tool intended for genomic region annotation.

References:

• Kondili M, Fust A, Preussner J, Kuenne C, Braun T, Looso M. UROPA: a tool for Universal RObust Peak Annotation. Scientific Reports. 2017;7:2593. doi:10.1038/s41598-017-02464-y

• UROPA Main Site

• Module Name: UROPA (see the modules page for more information)

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@cn1234 ~]$ module load uropa

[user@cn1234 ~]$ uropa -h
[+] Loading singularity  on cn3397 
[+] Loading uropa 2.0.3  ... 
[user@cn1234 ~]$ uropa -i test.json -p output/test -s
[user@cn1234 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load uropa
uropa -i test.json -p output/test_gem -s

Submit this job using the Slurm sbatch command.

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

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

uropa -i test1.json -p output/test1_gem -s
uropa -i test2.json -p output/test2_gem -s
uropa -i test3.json -p output/test3_gem -s

Submit this job using the swarm command.

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