Difference between revisions of "Meme"

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 holders
RRA account holders
SC account holders

Platforms

CIRCE cluster
RRA cluster
SC 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
- http://meme-suite.org/

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

@@ Line 3: / Line 3: @@
 MEME allows discovery of motifs (highly conserved regions) in groups of related DNA or protein sequences.
-== Version ==
+{{AppStandardHeader|3.5.7|meme}}
-*3.5.7
+{{AppRunningOnAll}}
-== Authorized Users ==
-*<code>CIRCE</code> account holders
-== Platforms ==
-*<code>CIRCE</code> cluster
-== Running MEME jobs on CIRCE ==
-=== [[Modules]] ===
-Meme requires the following module file and some prerequisites to run:
-*<code>apps/meme/3.5.7</code>
-* Prerequisites:
-**<code>compilers/pgi/7.0-7.x86_64 </code>
-**<code>openmpi/1.2.6-x86_64-pgi-7.0-7</code>
-See [[Modules]] for more information.
 === Submitting a Job ===
@@ Line 33: / Line 11: @@
 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 Users|SLURM User’s Guide]]. Scripts are provided as examples only. Your SLURM executables, tools, and options will vary.
+* 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;">
@@ Line 44: / Line 22: @@
 #SBATCH --time=01:00:00
-#### Slurm 4 processor MEME test to run for 1 hour.
+#### SLURM 4 processor MEME test to run for 1 hour.
 module add apps/meme/3.5.7
@@ Line 56: / Line 34: @@
 [user@login0 jobdir]$ sbatch ./meme-test.sh</pre>
-{{MoreInformation}}
+{{Documentation}}
+*MEME Home Page
+**http://meme-suite.org/
-{{ReportingBugs}}
+{{AppStandardFooter}}