OOD IGV

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Contents

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
 * A1.ood job composer.jpg
  1. Run/Submit the job
 * Click on the green "play" arrow.  A2.ood job submit.png
 * Status changes to "queued" A3.ood job queued.png
 * wait until job completes. A4.ood job completed.png
  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 A.ood start desktop.png
 * Set Request RAM and HOURS A.ood set mem.png
 * Open the desktop, once running A.ood launch desktop.png
 * desktop open A.ood desktop.png
  1. start a "Terminal"
 * open terminal app B.ood with terminal highlight.jpg
  1. in terminal, enter /share/apps/ngs-ccts/ood-igv/2.5.sh
 * enter path to installer C.ood terminal setup 25.png 
  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 D.ood setup ivg loading.png 


Running IGV from OOD Desktop

  1. Setup should create a desktop icon called "IGV-2.5.sh"
 * G.ood desktop with icon.png
  1. In the future, you can just start OOD, then click on "IGV-2.5.sh"
 * E.ood igv loading.png

Script source code

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

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