SnpEff-Teaching: Difference between revisions
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The last version of this application is at /usr/local/apps/eb/snpEff/4.3t-Java-1.8.0_144 | The last version of this application is at /usr/local/apps/eb/snpEff/4.3t-Java-1.8.0_144 | ||
To use this version, please | To use this version, please load the module with | ||
<pre class="gscript"> | <pre class="gscript"> | ||
ml snpEff/4.3t-Java-1.8.0_144 | ml snpEff/4.3t-Java-1.8.0_144 | ||
</pre> | </pre> | ||
Here is an example of a shell script, sub.sh, to run on | Here is an example of a shell script, sub.sh, to run on the batch queue: | ||
<div class="gscript2"> | <div class="gscript2"> | ||
| Line 40: | Line 40: | ||
<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | <nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | ||
<nowiki>#</nowiki>SBATCH --output=snpEff.%j.out<br> | <nowiki>#</nowiki>SBATCH --output=snpEff.%j.out<br> | ||
<nowiki>#</nowiki>SBATCH --error=snpEff.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml snpEff/4.3t-Java-1.8.0_144<br> | ml snpEff/4.3t-Java-1.8.0_144<br> | ||
java- | java -jar snpEff.jar <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 59: | Line 60: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
ml snpEff/4.3t-Java-1.8.0_144 | ml snpEff/4.3t-Java-1.8.0_144 | ||
java- | java -jar snpEff.jar | ||
Error: Unable to access jarfile snpEff.jar | |||
</pre> | </pre> | ||
Latest revision as of 15:24, 15 August 2018
Category
Bioinformatics
Program On
Teaching
Version
4.3t
Author / Distributor
Description
"SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes)." More details are at snpEff
Running Program
The last version of this application is at /usr/local/apps/eb/snpEff/4.3t-Java-1.8.0_144
To use this version, please load the module with
ml snpEff/4.3t-Java-1.8.0_144
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_snpEff
#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=snpEff.%j.out
#SBATCH --error=snpEff.%j.err
cd $SLURM_SUBMIT_DIR
ml snpEff/4.3t-Java-1.8.0_144
java -jar snpEff.jar [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.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml snpEff/4.3t-Java-1.8.0_144 java -jar snpEff.jar Error: Unable to access jarfile snpEff.jar
Installation
Source code is obtained from snpEff
System
64-bit Linux