SNAP-Zoe-Teaching: Difference between revisions

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cd $SLURM_SUBMIT_DIR<br>
cd $SLURM_SUBMIT_DIR<br>
ml SNAP-Zoe/20060728-foss-2016b<br>     
ml SNAP-Zoe/20060728-foss-2016b<br>     
<u>[options]</u><br>   
snap <u>[options]</u><br>   
</div>
</div>
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.   
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.   
Line 50: Line 50:
Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.
Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster.


'''Please Note:''' '''ZOE''' is the environment variable can be used by snap to find the HMM files storing at /usr/local/apps/eb/SNAP-Zoe/20060728-foss-2016b/HMM; '''EBROOTSNAPMINZOE''' is the environment variable storing the installation path at /usr/local/apps/eb/SNAP-Zoe/20060728-foss-2016b). For example, to run a test with a sample sequence in $EBROOTSNAPMINKORF/DNA:
<pre class="gscript">
snap $ZOE/thale $EBROOTSNAPMINKORF/DNA/thale.dna.gz
</pre>


Here is an example of job submission command:
Here is an example of job submission command:

Revision as of 15:37, 10 August 2018

Category

Bioinformatics

Program On

Teaching

Version

20060728

Author / Distributor

SNAP-Zoe

Description

"SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser." More details are at SNAP-Zoe

Running Program

The last version of this application is at /usr/local/apps/eb/SNAP-Zoe/20060728-foss-2016b

To use this version, please load the module with

ml SNAP-Zoe/20060728-foss-2016b 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_SNAP-Zoe
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=SNAP-Zoe.%j.out
#SBATCH --error=SNAP-Zoe.%j.err

cd $SLURM_SUBMIT_DIR
ml SNAP-Zoe/20060728-foss-2016b
snap [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Please Note: ZOE is the environment variable can be used by snap to find the HMM files storing at /usr/local/apps/eb/SNAP-Zoe/20060728-foss-2016b/HMM; EBROOTSNAPMINZOE is the environment variable storing the installation path at /usr/local/apps/eb/SNAP-Zoe/20060728-foss-2016b). For example, to run a test with a sample sequence in $EBROOTSNAPMINKORF/DNA:

snap $ZOE/thale $EBROOTSNAPMINKORF/DNA/thale.dna.gz 

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml SNAP-Zoe/20060728-foss-2016b 
 

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Installation

Source code is obtained from SNAP-Zoe

System

64-bit Linux