Launches the Integrative Genomics Viewer (IGV) with the provided file and input parameters.
Author: Barbara Hill, Marc-Danie Nazaire, Jim Robinson, Peter Carr (Broad Institute)
This module launches IGV on a specified data file or IGV session file. For full documentation and more information about IGV, please visit the IGV website. (http://broadinstitute.org/igv). Each run of the module creates a Java WebStart file named igv_job_<gp_job_id>.jnlp. A corresponding launch button is also displayed on the IGV job status page. Click on this button to launch IGV. Note that in some Web browsers you must download the file, and then directly launch it from your client computer. The launcher automatically installs or updates to the latest released version of IGV.IGV will prompt you for your GenePattern username and password before it opens the data or session file. Once you have IGV running, you can also directly open GenePattern files by selecting File>Load from URL… from the IGV menu and entering the URL of the GenePattern file. Right-click (CTRL-click on the Mac) on a filename in GenePattern to copy the URL link address and then paste it into the IGV URL entry box. Note that accessing your GenePattern files from IGV will only work with GenePattern Server versions 3.3.2 or later.
Helga Thorvaldsdóttir, James T. Robinson, Jill P. Mesirov. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in Bioinformatics 2012.
James T. Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov. Integrative Genomics Viewer. Nature Biotechnology 29, 24–26 (2011).
|[parameter name]||[parameter description] Default: [value]|
* - required
[provide example data, including input files and parameter settings]. (we’ll put the input files on the ftp site and link to them from the doc)
[any software requirements for running this, e.g., version of R, licensing]