OOD IGV

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Attention: Research Computing Documentation has Moved
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Please use the new documentation url https://docs.rc.uab.edu/ for all Research Computing documentation needs.


As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.

Thank you,

The Research Computing Team

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

*

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  1. Run/Submit the job

* Click on the green "play" arrow.

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* Status changes to "queued"

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* wait until job completes.

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  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

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* Set Request RAM and HOURS

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* Open the desktop, once running

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* desktop open

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  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

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  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

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Running IGV from OOD Desktop

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

*

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

*

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Script source code

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

Retrieved from "https://docs.uabgrid.uab.edu/w/index.php?title=OOD_IGV&oldid=5982"