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In the terminal connected to Lonestar, figure out the complete path to the IGV directory.
Open a new terminal window on your Desktop. Fill in the parts in brackets <> in this command:
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Launching IGV
There are two ways, in you're web browser or by downloading the binaries locally and running IGV from your machine.
In Browser
Navigate a web browser to this page:http://www.broadinstitute.org/software/igv/download
Go ahead and click on the "Launch with 2 GB" option. This will download a "Java Web Start" file that you can launch by locating it on your Desktop and double-clicking.
Locally
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wget http://www.broadinstitute.org/igv/projects/downloads/IGV_2.1.14.zip unzip IGV_2.1.14.zip cd IGV_2.1.14 java -Xmx4g -jar igv.jar |
Load genome into IGV
From the main window of IGV, click on File -> Import Genome and you should be presented with the following window.
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