IGV-Teaching: Difference between revisions

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</pre>  
</pre>  


Please note, IGV GUI can run from login node with  
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:
 
<pre class="gcommand">
ssh -X MyID@teach.gacrc.uga.edu
</pre>
 
2. Once you log on, load IGV and run with its GUI forwarded to your local machine:


Example running this on login node:
<pre class="gcommand">
<pre class="gcommand">
module load IGV/2.4.4-Java-1.8.0_144
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  
sh /usr/local/apps/eb/IGV/2.4.4-Java-1.8.0_144/igv.sh  
exit
</pre>
</pre>


=== Documentation ===
3. When you start IGV for the first time, you might need to set it to use the UGA Proxy server. To do that,
once the IGV windows opens, go to '''View''' -> '''Preferences''' and click on the tab called '''Proxy'''.
more details at [http://www.broadinstitute.org/software/igv/ IGV]
On the Proxy page, select the box for "Use proxy", and fill in the following


=== Installation ===
<pre class="gcomment">
Proxy host: webav.uga.edu
source code from [http://www.broadinstitute.org/software/igv/ IGV]
=== System ===
64-bit Linux


Proxy port: 8080


Proxy type: HTTP
</pre>
Then click OK. These setting will be saved in a file called prefs.properties in a directory called igv in the user's home dir.


Then quit IGV and start it again, following step 2.


=== Category ===
4. When you finished, please log out with:


Bioinformatics
<pre class="gcommand">
exit
</pre>


=== Program On ===
Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#How_to_run_an_interactive_job_with_Graphical_User_Interface_capabilities | Run X window Jobs]] for more details of running GUI X-window jobs on Teaching cluster.


=== Documentation ===
more details at [http://www.broadinstitute.org/software/igv/ IGV]


 
=== Installation ===
=== Version ===
17.0.1
   
   
=== Author / Distributor ===
source code from [http://www.broadinstitute.org/software/igv/ IGV]
   
   
[http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act Artemis]
=== System ===
64-bit Linux
=== Description ===
"Artemis is a free genome browser and annotation tool that allows visualisation of sequence features,  next generation data and the results of analyses within the context of the sequence, and also its six-frame translation."
More details are at [http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act Artemis]
 
=== Running Program ===
 
The last version of this application is at /usr/local/apps/eb/Artemis/17.0.1-Java-1.8.0_144
 
To use this version, please load the module with
<pre class="gscript">
ml Artemis/17.0.1-Java-1.8.0_144
</pre>
 
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>

Latest revision as of 15:24, 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 IGV 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 start IGV for the first time, you might need to set it to use the UGA Proxy server. To do that, once the IGV windows opens, go to View -> Preferences and click on the tab called Proxy. On the Proxy page, select the box for "Use proxy", and fill in the following 

Proxy host: webav.uga.edu

Proxy port: 8080

Proxy type: HTTP

Then click OK. These setting will be saved in a file called prefs.properties in a directory called igv in the user's home dir.

Then quit IGV and start it again, following step 2.

4. When you finished, please log out with: 

exit

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs for more details of running GUI X-window jobs on Teaching cluster.

Documentation

more details at IGV

Installation

source code from IGV

System

64-bit Linux

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