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:
#!/bin/bash # Using the mpich2 MPI library # Requesting N number of slots #$ -pe mpich2 N #$ -N jobName #$ -cwd #$ -S /bin/bash # Setup the mpich2 environment export MPICH2_ROOT="/opt/mpich2/gnu" export PATH="$MPICH2_ROOT/bin:$PATH" export MPD_CON_EXT="sge_$JOB_ID.$SGE_TASK_ID" # 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 $NSLOTS crp0.s -dna -mod oops -pal exit 0
In the case you need to pass options to mpirun, use quots after the '-p' option to include those options:
/share/apps/meme/bin/meme -p "$NSLOTS mpiOptions" ...