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Miranda on Biowulf & Helix

miRanda is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL. MiRanda was developed at the Computational Biology Center of Memorial Sloan-Kettering Cancer Center.

Example files can be copied from /usr/local/apps/miranda/examples

Running on Helix

$ module load miranda
$ cd /data/$USER/Examples
$ miranda file1 file2 [options]

Running a single batch job on Biowulf

1. Create a script file similar to the lines below.

#!/bin/bash

module load miranda
cd /data/$USER/Examples
miranda file1 file2 [options]

2. Submit the script on biowulf:

$ sbatch jobscript

For more memory requirement (default 4gb), use --mem flag:

$ sbatch --mem=10g jobscript

Running a swarm of jobs on Biowulf

Setup a swarm command file:

  cd /data/$USER/dir1; miranda file1 file2 [options]
  cd /data/$USER/dir2; miranda file1 file2 [options]
  cd /data/$USER/dir3; miranda file1 file2 [options]
	[......]

Submit the swarm file:

  $ swarm -f swarmfile --module miranda

-f: specify the swarmfile name
--module: set environmental variables for each command line in the file

To allocate more memory, use -g flag:

  $ swarm -f swarmfile -g 10 --module miranda

-g: allocate more memory

For more information regarding running swarm, see swarm.html

Running an interactive job on Biowulf

It may be useful for debugging purposes to run jobs interactively. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.

biowulf$ sinteractive 
salloc.exe: Granted job allocation 16535

cn999$ module load miranda
cn999$ cd /data/$USER/Examples
cn999$ miranda file1 file2 [options]

cn999$ exit

biowulf$

Make sure to exit the job once finished.

If more memory is needed, use --mem flag. For example

biowulf$ sinteractive --mem=10g

Documentation

http://www.microrna.org/microrna/getDownloads.do