Starting IGV

You can start IGV from either the:

Java Web Start

To start IGV from using Java Web Start:

  1. Go to the IGV downloads page:
  2. When prompted, register or log in as requested. You must register to download IGV.
  3. Click the launch icon. The browser displays the web start launch window.
  4. Select Open with Java™ Web Start and click OK. If the system displays messages about trusting the application, confirm that you trust the application. Web Start downloads and starts IGV.

Command Line

To start IGV from the command line:

  1. Be sure that Java 6 or later is installed on your machine.
  2. Download the binary distribution.
  3. Unzip the binary distribution.
  4. Open README file and use the shell scripts, which you can edit. You can also invoke Java directly.

You can optionally specify either a session file or a comma-delimited list of files to load. Other arguments that you can use from the command line include:

  • -l <locus>, --locus=<locus> a locus in the form of a locus string (e.g. chr1:100-200) or gene name
  • -b <file>, --batch=<file> Immediately run the supplied batch script after start up.
  • -g <genomeId>, --genome=<genomeId> Specify the genome by ID. You can locate the genomeId as the last entry in each line of the genome registryNEW since 2.1.28: the -g option can specify a path to a .genome or indexed fasta file.
  • -d <URL>, --dataServerURL=<URL> Specify URL to data registry file.
  • -u <URL>, --genomeServerURL=<URL> Specify URL to genome registry file.
  • -p <port>, --port=<port> Specify port IGV opens for port commands.
  • -o <file>, --preferences=<file> A user preference properties file. This can override any properties IGV supports.
  • --igvDirectory Path to the igv application directory.  This directory contains user preferes, the igv log, and cached genomes.