igv

Integrative Genomics Viewer - desktop genome visualization tool for Mac, Windows, and Linux.

Building

These instructions are meant for developers interested in working on the IGV code. For normal use, we recommend the pre-built releases available at http://software.broadinstitute.org/software/igv/download.

Builds are executed from the IGV project directory. Files will be created in the 'build' subdirectory.

IGV has been tested on Java 11. Previous (versions =< 2.6.3) running on Java8 have been deprecated.

NOTE: If on a Windows platform use ./gradlew.bat' in the instructions below

Folder structure and build targets

IGV has been tested with AdoptOpenJDK, OpenJDK and Amazon's Correto Java 11 distributions have been tested with IGV. The IGV bundles ship with embedded JREs from AdoptOpenJDK.

• Install Gradle for your platform. See https://gradle.org/ for details.

• Use ./gradlew createDist to build a distribution directory (found in build/IGV-dist) containing the igv.jar and its required runtime third-party dependencies as well as helper scripts for launching.

  • Launch IGV with igv.sh or igv_hidpi.sh on Linux, igv.command on Mac, and igv.bat on Windows. These scripts can be edited to adjust JVM flags like maximum memory, etc. See the instructions in readme.txt in that directory.

  • To run igvtools from the command line use the script igvtools on Linux and Mac, or igvtools.bat on Windows. See the instructions in igvtools_readme.txt in that directory.

  • The launcher scripts expect this folder structure in order to run IGV.

• Use ./gradlew test to run the test suite. See 'src/test/README.txt' for more information about running the tests.

Note that Gradle creates a number of other subdirectories in 'build'. These can be safely ignored.

Amazon Web Services support

For more details on how to use IGV with AWS, please refer to the UMCCR documentation.