OOD IGV

First time setup
* then install EITHER * via OOD job launcher * OR   * via Terminal on the OOD Desktop
 * 1) get a cheaha account (see Cheaha_GettingStarted)

Install IGV via Job
* Source path: /share/apps/ngs-ccts/ood-igv/jobs * Name: setup IGV 2.5 * Script Name: 2.5.sh * Cluster: Cheaha * SAVE *  * Click on the green "play" arrow. * Status changes to "queued" * wait until job completes. * see
 * 1) launch Job Composer/Create New Job/From a Specified Path: https://rc.uab.edu/pun/sys/myjobs/new_from_path and setup the job
 * 1) Run/Submit the job
 * 1) now open OOD desktop to launch IGV from desktop icon

Install via Terminal in OOD Desktop
* Requst an OOD Desktop * Set Request RAM and HOURS * Open the desktop, once running * desktop open * open terminal app * enter path to installer * installer will scroll a lot of text, some in alarming colors. * a few seconds after the text stop, the desktop icon and loading bar will appear * installer finished, IGV loading
 * 1) launch an interactive desktop with OOD https://rc.uab.edu
 * 1) start a "Terminal"
 * 1) in terminal, enter  /share/apps/ngs-ccts/ood-igv/2.5.sh
 * 1) that will install IGV locally, and launch it.

Running IGV from OOD Desktop
*  *
 * 1) Setup should create a desktop icon called "IGV-2.5.sh"
 * 1) In the future, you can just start OOD, then click on "IGV-2.5.sh"

Script source code
Code can be found at https://gitlab.rc.uab.edu/CCTS-Informatics-Pipelines/ood-igv