While MEME is available via a web interface, it does not take advantage of the parallel processing capabilities when integrated with MPI.
To run MEME on the cluster, use the following as an example job script:
#Using the mpich2 MPI Library
#Requesting X number of slots
#$ -pe mpich2 X
#$ -N jobName
#$ -S /bin/bash
#Setup the mpich2 environment
#The following is an example of meme
#It looks for dna motifs in the input file using the OOPS model with the palindrome switch on
/share/apps/meme/bin/meme -p $NSLOTS crp0.s -dna -mod oops -pal
In the case you need to pass options to mpirun, use quotes after -p to include those options:
/share/apps/meme/bin/meme -p "$NSLOTS mpiOptions" .....