IGV Installation & Setup
This section documents the necessary steps for installation and setup of IGV for visualizing results of Omics experiments.
The installation of IGV from the source site is a moving target because the homepage and download options keep changing. In particular, many Windows users in the clinic are not able to execute installer programs. Further, you will need to enable the “strong encryption” policy of Java. If you want to try this, please go ahead (below are the relevant links) but we cannot support you in this:
Downloading and Installing IGV
Use the following link to download a standalone IGV version (including JRE and strong encryption extension):
Extract the folder.
If you are in a hospital network, make sure that the final extraction target
is on drive
C:. Otherwise, your computer’s policy might prevent IGV from
Start the program by double-clicking on the
If IGV complains that it cannot download IGV files then you have to configure your proxy properly.
See the section “Proxy Configuration” below for more details.
For good measure, visit AmIBehindAProxy.com to see whether you are behind a proxy. If you are not then you can skip the section “Proxy Configuration”.
Please visit AmIBehindAProxy.com to see whether you are behind a proxy. If you are not behind a proxy then you can skip this section.
Otherwise, you have to find out your proxy host and port (e.g., from your IP department). The instructions below use the configuration for the Charite network as an example.
Start IGV and ignore (“click away”) the notification about the failed download.
After the main window comes up, open the preference window by using the
ViewMenu, then the
Preferencesmenu item (see screenshot below).
The preferences window will appear. Go to the
Enter the following values:
Proxy host: proxy.charite.de
Proxy port: 8080
If you are outside of the Charite network then please ask your local SODAR
administrator for the values to put into the
“Remote Control” Configuration
IGV supports a “remote control” mode that allows you to load individual tracks
or whole sessions directly into IGV from SODAR. Technically, it runs an embedded
HTTP server on
localhost and clicking links redirecting there triggers
To activate this, you have to go to the
Advanced tab of the preferences,
Enable port box and ensure the port is configured as
This is only necessary in the case that you had to configure the proxy.
After restarting IGV, you should not see any more warning about genomes not being loaded.