MemeSuite
Overview
Meme Suite is a suite of programs to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses.
Version 5.1.1 is installed on the CSF.
Restrictions on use
There are no restrictions on accessing this software on the CSF. It cannot be used for commercial work. Please ensure your usage adheres to the notice at:
Please cite your usage of the software using:
Timothy L. Bailey, Mikael Bodén, Fabian A. Buske, Martin Frith, Charles E. Grant, Luca Clementi, Jingyuan Ren, Wilfred W. Li, William S. Noble, “MEME SUITE: tools for motif discovery and searching”, Nucleic Acids Research, 37:W202-W208, 2009.
Set up procedure
We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.
Load one of the following modulefiles:
module load apps/intel-18.0/memesuite/5.1.1
Running the application
Please do not run Meme Suite tools on the login node. Jobs should be submitted to the compute nodes via batch.
Serial batch job submission
Create a batch submission script (which will load the modulefile in the jobscript), for example:
#!/bin/bash --login #$ -cwd # Job will run from the current directory # NO -V line - we load modulefiles in the jobscript # We now recommend loading the modulefile in the jobscript module load apps/intel-18.0/memesuite/5.1.1 meme args...
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Parallel batch job submission
Create a batch submission script (which will load the modulefile in the jobscript), for example:
#!/bin/bash --login #$ -cwd # Job will run from the current directory ### Choose ONE of the following parallel environments #$ -pe smp.pe 16 # Small MPI job (between 2 and 32 cores permitted) ### OR #$ -pe mpi-24-ib.pe 48 # Large MPI (multinode) job. Cores must be 48 or more # in multiples of 24. # We now recommend loading the modulefile in the jobscript module load apps/intel-18.0/memesuite/5.1.1 # NSLOTS is automatically set to one in a serial job meme -p $NSLOTS args...
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.