Difference between revisions of "Meme"
(Created page with "== Description == MEME allows discovery of motifs (highly conserved regions) in groups of related DNA or protein sequences. == Version == *3.5.7 == Authorized Users == *<...") |
(No difference)
|
Revision as of 16:22, 28 June 2016
Description
MEME allows discovery of motifs (highly conserved regions) in groups of related DNA or protein sequences.
Version
- 3.5.7
Authorized Users
CIRCE
account holders
Platforms
CIRCE
cluster
Running MEME jobs on CIRCE
Modules
Meme requires the following module file and some prerequisites to run:
apps/meme/3.5.7
- Prerequisites:
compilers/pgi/7.0-7.x86_64
openmpi/1.2.6-x86_64-pgi-7.0-7
See Modules for more information.
Submitting a Job
If, for example, you have an MEME input file named meme.in, you would set up a submit script like this:
- The script below (for testing, name it “meme-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue. For help on submitting jobs to the queue, see our SLURM User’s Guide. Scripts are provided as examples only. Your SLURM executables, tools, and options will vary.
#!/bin/bash # #SBATCH --comment=meme-test #SBATCH --ntasks=4 #SBATCH --job-name=meme-test #SBATCH --output=output.%j.meme-test #SBATCH --time=01:00:00 #### Slurm 4 processor MEME test to run for 1 hour. module add apps/meme/3.5.7 mpirun /opt/apps/meme/bin/meme
Next, you can change to your job’s directory, and run the sbatch command to submit the job:
[user@login0 ~]$ cd my/jobdir [user@login0 jobdir]$ sbatch ./meme-test.sh
More Job Information
See the following for more detailed job submission information:
Reporting Bugs
Report bugs with Meme to the IT Help Desk: rc-help@usf.edu