miRanda is an algorithm for the detection of potential microRNA target sites in genomic sequences. MiRanda was developed at the Computational Biology Center of Memorial Sloan-Kettering Cancer Center.
The easiest way to set up your environment for miRanda is to use the modules commands, as in the example below:
biowulf% module avail miranda --------------- /usr/local/Modules/3.2.9/modulefiles -------------------- miranda/3.3a biowulf% module load miranda biowulf% module list Currently Loaded Modulefiles: 1) miranda/3.3a
1. Create a script file similar to the one below:
#!/bin/bash # This file is YourOwnFileName # #PBS -N yourownfilename #PBS -m be #PBS -k oe module load miranda cd /data/user/somewhereWithInputFile miranda file1 file2 -strict
2. Submit the script using the 'qsub' command on Biowulf.
This command will submit your job to a node with at least 1 GB of memory, and 2 cores. If your miranda run requires more than 1 GB of memory, you can specify this in the memory required. For example
Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.
Set up a swarm command file (eg /data/username/cmdfile). Here is a sample file:
miranda file1a file1b --out 1.out miranda file2a file2b --out 2.out miranda file3a file3b --out 3.out
Submit this swarm with:
swarm -f cmdfile --module miranda
By default, each line of the commands above will be executed on '1' processor core of a node and uses 1GB of memory. If each miranda command needs more than 1 GB of memory, you can specify the memory required by using the '-g #' flag to swarm, where # is the number of Gigabytes of memory required for a single miranda command.
Say if each line of the commands above also will need to use 10gb of memory instead of the default 1gb of memory, make sure swarm understands this by including '-g 10' flag:
[user@biowulf]$ swarm -g 10 -f cmdfile
For more information regarding running swarm, see swarm.html
Users may need to run jobs interactively sometimes. 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.
qsub: waiting for job 2236960.biobos to start
qsub: job 2236960.biobos ready
[user@p4]$ cd /data/user/myruns
[user@p4]$ module load miranda
[user@p4]$ cd /data/userID/miranda/run1
[user@p4]$ miranda file1 file2 --strict --out fileout
[user@p4] exit
qsub: job 2236960.biobos completed
[user@biowulf]$
Users may add a node property in the qsub command to request specific interactive node. For example, if you need a node with 24gb of memory to run job interactively, do this:
