/igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

Primary LanguageJavaMIT LicenseMIT

igv

Build Status GitHub issues GitHub closed issues

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 is 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

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.

    • 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.

  • See this README for tips about using the IGV launcher scripts.

  • This dashboard describes project structure and dependencies.

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

Amazon Web Services support

Public data files hosted in Amazon S3 buckets can be loaded into IGV using https endpoints. Authenticated access can be configured using the UMCCR contributed AWS configuration option. For more details, refer to the UMCCR documentation. Note authenticated access is currently restricted to the following file formats: BAM, CRAM, tabix indexed VCF (vcf.gz / vcf.gz.tbi), and non-indexed feature file formats.