headlessIGV

Modified version of the Integrative Genomics Viewer - desktop genome visualization tool for Mac, Windows, and Linux.

This modified version of IGV adds a few minor but vital capabilities to batch-mode IGV. It particular, it adds a few useful batch commands:

• panelWidth: This sets the panel width in nominal px. Note that the actual pixel width will be modified by the resolution factor, below.
• resolutionFactor: This increases the pixel density, producing larger images without shrinking the elements.
• region: this marks a specified region as a "Region of interest"

headlessIGV is primarily intended to be used with igvSnap, a wrapper program that simplifies the generation of IGV batch scripts.

You can download headlessIGV here.

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Building

These instructions are meant for developers interested in working on the IGV code. For normal use, we recommend the pre-built jar file, available in the link above.

Builds are executed from the IGV project directory. Files will be created in the 'build' subdirectory. You may need to execute 'gradle wrapper' to set up the gradle wrapper. This should be necessary the first time only, or if you clean up the local .gradle directory. Only do this if the './gradlew' calls fail.

There are two different build options, one for Java 8 and another for Java 11. The default is to build for Java 8. Java 8 builds are NOT compatible with Java 11 and vice versa.

There are other options but these cover the most common uses:

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

Java 8

• 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 (batik-codec, goby, and log4j-core) as well as helper scripts for launching.

  • These four JARs will be identical to those available in the download bundles from our website, with the exception that they will not be signed with our certificate (required for JNLP) and will have slightly different build properties (timestamp, etc) in about.properties.

  • All four JARs must be in the same location in order to run IGV. It can be run directly from 'build/IGV-dist'

  • Launch with 'igv.sh' on UNIX, 'igv.command' on Mac, and 'igv.bat' on Windows. These scripts can be edited to adjust JVM flags like maximum memory, etc.

  • All other runtime dependencies are bundled into igv.jar. There is also an igv-minimal.jar in 'build/libs' containing just the IGV classes and resources for those who prefer to manage dependencies as separate files.

• Use ./gradlew createToolsDist to build an igvtools distribution directory (found in 'build/IGVTools-dist') containing the igvtools.jar and dependencies (same as for IGV, above)
  JAR dependencies plus helper scripts for running and launching. As above, these JARs will be identical aside from signing, timestamps, etc. and all must be present together to run. See igvtools_readme.txt for more info.

• 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.

Java 11

The instructions for Java 11 are nearly identical other than the need to specify the Java 11 build file and that the results will be found in 'build_java11' rather than 'build'. More specifically:

• Use ./gradlew -b build_java11.gradle createDist to build a distribution directory with helper scripts for launching. The structure is slightly different but the concept is the same.

• Use ./gradlew -b build_java11.gradle test to run the test suite.

The full JAR build option is NOT available for Java 11 because of modularity requirements. Also, there is no separate igvtools distribution on Java 11; at present, this is folded into the normal IGV client distribution.