IGV-Teaching: Difference between revisions
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To run | 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: | 1. log on to Teching cluster login node using ssh with X-forwarding being turned on: | ||
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</pre> | </pre> | ||
2. Once you log on, load | 2. Once you log on, load IGV and run with its GUI forwarded to your local machine: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
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</pre> | </pre> | ||
3. When you finished, please log out with: | 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 | |||
<pre class="gcomment"> | |||
Proxy host: webav.uga.edu | |||
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. | |||
4. When you finished, please log out with: | |||
<pre class="gcommand"> | <pre class="gcommand"> | ||
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</pre> | </pre> | ||
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 === | === Documentation === | ||
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=== System === | === System === | ||
64-bit Linux | 64-bit Linux | ||
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