OOD IGV

First time setup

1. get a cheaha account (see Cheaha_GettingStarted)

 * then install EITHER
   * via OOD job launcher
   * OR
   * via Terminal on the OOD Desktop

Install IGV via Job

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

 * Source path: /share/apps/ngs-ccts/ood-igv/jobs
 * Name: setup IGV 2.5
 * Script Name: 2.5.sh
 * Cluster: Cheaha
 * SAVE

*

Error creating thumbnail: File missing

1. Run/Submit the job

* Click on the green "play" arrow.

Error creating thumbnail: File missing

* Status changes to "queued"

Error creating thumbnail: File missing

* wait until job completes.

Error creating thumbnail: File missing

1. now open OOD desktop to launch IGV from desktop icon

 * see #Running_IGV_from_OOD_Desktop

Install via Terminal in OOD Desktop

1. launch an interactive desktop with OOD https://rc.uab.edu

* Requst an OOD Desktop

Error creating thumbnail: File missing

* Set Request RAM and HOURS

Error creating thumbnail: File missing

* Open the desktop, once running

Error creating thumbnail: File missing

* desktop open

Error creating thumbnail: File missing

1. start a "Terminal"

 * open terminal app 

1. in terminal, enter /share/apps/ngs-ccts/ood-igv/2.5.sh

* enter path to installer

Error creating thumbnail: File missing

1. that will install IGV locally, and launch it.

 * 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

Error creating thumbnail: File missing

Running IGV from OOD Desktop

1. Setup should create a desktop icon called "IGV-2.5.sh"

*

Error creating thumbnail: File missing

1. In the future, you can just start OOD, then click on "IGV-2.5.sh"

*

Error creating thumbnail: File missing

Script source code

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