IGV-Teaching: Difference between revisions

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Please refer to [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] for more details.
Please refer to [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] for more details.
Here is an example of a shell script, sub.sh, to run on the batch queue:
<div class="gscript2">
<nowiki>#</nowiki>!/bin/bash<br>
<nowiki>#</nowiki>SBATCH --job-name=j_Artemis<br>
<nowiki>#</nowiki>SBATCH --partition=batch<br>       
<nowiki>#</nowiki>SBATCH --mail-type=ALL<br>
<nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u><br> 
<nowiki>#</nowiki>SBATCH --ntasks=<u>1</u><br> 
<nowiki>#</nowiki>SBATCH --mem=<u>10gb</u><br>   
<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> 
<nowiki>#</nowiki>SBATCH --output=Artemis.%j.out<br>
<nowiki>#</nowiki>SBATCH --error=Artemis.%j.err<br>
cd $SLURM_SUBMIT_DIR<br>
ml Artemis/17.0.1-Java-1.8.0_144<br>   
act <u>[options]</u><br> 
</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. 
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.
Here is an example of job submission command:
<pre  class="gcommand">
sbatch ./sub.sh
</pre>


=== Documentation ===
=== Documentation ===

Revision as of 09:55, 7 February 2019

Category

Bioinformatics

Program On

Teaching

Version

2.4.4

Author / Distributor

To cite your use of IGV in your publication:

James T. Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov. Integrative Genomics Viewer. Nature Biotechnology 29, 24–26 (2011), or

Helga Thorvaldsdottir, James T. Robinson, Jill P. Mesirov. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.

Briefings in Bioinformatics 2012.

Description

"The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations." more details at IGV

Running Program

Also refer to Running Jobs on Sapelo2

  • Version 2.4.4, installed in /usr/local/apps/eb/IGV/2.4.4-Java-1.8.0_144

To use this version of IGV, please first load the module with 

module load IGV/2.4.4-Java-1.8.0_144

To run IGV GUI, please follow steps as below:

1. log on to Teching cluster login node using ssh with X-forwarding being turned on: 

ssh -X MyID@teach.gacrc.uga.edu

2. Once you log on, load TASSEL and run with its GUI forwarded to your local machine: 

module load IGV/2.4.4-Java-1.8.0_144
sh /usr/local/apps/eb/IGV/2.4.4-Java-1.8.0_144/igv.sh

3. When you finished, please log out with: 

exit

Please refer to Run X window Jobs for more details.

Documentation

more details at IGV

Installation

source code from IGV

System

64-bit Linux

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