Difference between revisions of "Meme"
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MEME allows discovery of motifs (highly conserved regions) in groups of related DNA or protein sequences. | MEME allows discovery of motifs (highly conserved regions) in groups of related DNA or protein sequences. | ||
{{AppStandardHeader|3.5.7|meme}} | |||
{{AppRunningOnAll}} | |||
=== Submitting a Job === | === Submitting a Job === | ||
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If, for example, you have an MEME input file named meme.in, you would set up a submit script like this: | 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 | * 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. | ||
<pre style="white-space:pre-wrap; width:45%; border:1px solid lightgrey; background:#E0E0E0; color:black;"> | <pre style="white-space:pre-wrap; width:45%; border:1px solid lightgrey; background:#E0E0E0; color:black;"> | ||
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#SBATCH --time=01:00:00 | #SBATCH --time=01:00:00 | ||
#### | #### SLURM 4 processor MEME test to run for 1 hour. | ||
module add apps/meme/3.5.7 | module add apps/meme/3.5.7 | ||
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[user@login0 jobdir]$ sbatch ./meme-test.sh</pre> | [user@login0 jobdir]$ sbatch ./meme-test.sh</pre> | ||
{{ | {{Documentation}} | ||
*MEME Home Page | |||
**http://meme-suite.org/ | |||
{{ | {{AppStandardFooter}} |
Latest revision as of 21:54, 20 February 2017
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 holdersRRA
account holdersSC
account holders
Platforms
CIRCE
clusterRRA
clusterSC
cluster
Modules
Meme requires the following module file to run:
apps/meme/3.5.7
- See Modules for more information.
Running Meme on CIRCE/SC
The Meme user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.
- Note on CIRCE: Make sure to run your jobs from your $WORK directory!
- Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.
Submitting a Job
If, for example, you have an MEME input file named meme.in, you would set up a submit script like this:
- The script below (for testing, name it “meme-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue.
#!/bin/bash # #SBATCH --comment=meme-test #SBATCH --ntasks=4 #SBATCH --job-name=meme-test #SBATCH --output=output.%j.meme-test #SBATCH --time=01:00:00 #### SLURM 4 processor MEME test to run for 1 hour. module add apps/meme/3.5.7 mpirun /opt/apps/meme/bin/meme
Next, you can change to your job’s directory, and run the sbatch command to submit the job:
[user@login0 ~]$ cd my/jobdir [user@login0 jobdir]$ sbatch ./meme-test.sh
Documentation
Home Page, User Guides, and Manuals
- MEME Home Page
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