## Integrative Genomics Viewer (IGV) (Version 2.3)

## Install IGV

Options for installing and running IGV:

1. (Mac only) Download and run the Mac applcation; or
2. (Windows) Download and run the self-extracting archive; or
3. (All systems) Use the Java Web Start buttons (Mac users: see below for limitations); or
4. (All systems) Download the binary distribution and run IGV from the command line.

Note: IGV 2.3.x requires Java 7. Users with Java 6 (JRE 1.6) should first try to upgrade Java to the latest version. If this is not possible you will need to run a 2.2.x version available in the archive.

Mac

Download and unzip the Mac App archive, then double-click the IGV application to run it. The application can be moved to the "Applications" folder, or anywhere else. |

### Java Web Start (All Platforms)

The buttons below use Java Web Start (JWS) to install and launch IGV directly from our web site.

*Mac Users: The Java Web Start option does not work for some users due to security settings. The recommended solution is to use the bundled Mac App from the link above. Alternatively you can try to work around this by right-clicking on the buttons and saving the "jnlp" file, then right-clicking on the saved "jnlp" file and select "Open With > Java Web Start".

Chrome: Chrome does not automatically launch the Java Web Start files by default. Instead, the launch buttons below will download a "jnlp" file. This should appear in the lower left corner of the browser. Double-click the downloaded file to run, or if on a Mac right-click and select "Open With > Java Web Start"

Windows users: To run with more than 1.2 GB of memory you must install 64-bit Java. Most Windows installs do not include 64-bit Java by default, even if the operating system is 64-bit. Attempting to use the 2GB or greater launch options with 32-bit Java will result in the error "could not create virtual machine".

Launch with 750 MB | Launch with 1.2 GB Maximum usable memory for Windows OS with 32-bit Java. | Launch with 2 GB Maximum usable memory for 32-bit MacOS. | Launch with 10 GB For large memory machines with 64-bit Java.

### Windows

NOTE: for 64-bit windows only. This package provided for users unable to use the Java Web Start option above. Download the Windows package and execute the self-extracting archive. It will prompt you for a path to extract the folder, choose anywhere you like (e.g. your home folder). On completion, open the new folder. Double-click the file "igv.bat", it might appear as just "igv" depending on your settings. |

### Binary Distribution

Download and unzip the binary distribution archive in a folder of your choosing. IGV is launched from a command prompt -- follow instructions in the "readme" file. To launch igv on Mac or Linux platforms use the shell script "igv.sh". On Windows use "igv.bat". |

## igvtools

Utilities for preprocessing data files.

- igvtools

## Other IGV Versions

IGV 3.0 beta Early access release of IGV 3.0.

Development Snapshot Build Latest development snapshot; built at least nightly.

Archived Versions

## Source Code

​Source code repository is hosted at GitHub. Current release branch is 2.3.x:

- https://github.com/igvteam/igv/

## License

Permission to use this work is granted under the MIT License

## Contact

We welcome your feedback. Please send suggestions, requests, and bug reports to our help forum or open a ticket in our issue tracker.

If you are posting about a problem, please include the error message (if applicable) and your igv.log file. It will be in <your home directory>/igv. When posting a bug report, please include:

1. The version of IGV you are using
2. What you did (e.g. I opened a bedgraph file). If the problem happens when you open a file and/or view certain genomic coordinates, attach the file* (or provide a link) and specify the genomic coordinates.
3. What you expected to happen (e.g. I expected IGV to display my data)
4. What actually happened (e.g. I received an error message saying "Unknown extension: .graph")