IGV-X

A customized version of IGV built specifically for micropeptide's research — Arabidopsis epigenetics, whole-genome bisulfite sequencing (WGBS) methylation analysis, and large multi-track sessions. Designed around those workflows while remaining fully compatible with standard IGV.

IGV-X is a robust, modern fork of the Integrative Genomics Viewer — a desktop genome visualization tool for Mac, Windows, and Linux — customized for large epigenomics sessions.

• Chromosome-name resolution that never crashes: fixes the stock IGV 2.19.5 bigWig NullPointerException on TAIR10 WGBS sessions (hundreds of methylation bigWigs with Chr1..ChrM vs RefSeq aliases); case-insensitive, alias-aware resolution across bigWig/bigBed/BAM/BED/VCF using genome alias info — never global lowercase conversion, never renaming user files.
• Large-session performance for ~900 bigWig sessions: bounded loading threads, async loads, honest progress, viewport culling, caching.
• Relative session paths by default, optional .igvx.json companion, bookmarks & highlights persisted in the session, cancelable session loading.
• High-quality PNG/SVG/PDF export, multi-track selection, configurable default quantitative ranges, trackpad navigation.
• Organize tracks by genotype → CG/CHG/CHH with editable remembered rules.
• Diagnostics & error recovery: Diagnose Track/Session, exception dedup/rate-limiting, batch command listener (port 60151).
• In-app updates from this repository's GitHub releases.
• Modern macOS app (native menu bar, fullscreen, Retina, accessibility), bundled JDK, own bundle ID and prefs (~/igvx) — safe to run alongside stock IGV.

Downloads & releases: see Releases. Full diff vs stock IGV: docs/changes-vs-igv.md · docs/whats-different.md · docs/fork-diff.md

The rest of this README is the upstream IGV documentation (fork base: 2.19.X).

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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 requires Java 21 to build and run. Later versions of Java should work but we build and test on Java 21.

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 using s3:// urls is supported by either (1) enabling OAuth access with Cognito using the UMCCR contributed AWS configuration option, or (2) setting AWS credentials and region information as described here and here.

For more details on using Cognito for OAuth access, see the UMCCR documentation on the backend and frontend for a provisioning URL step by step guide.