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OOD IGV

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# get a cheaha account (see [[Cheaha_GettingStarted]])
 
# get a cheaha account (see [[Cheaha_GettingStarted]])
 +
  * then install EITHER
 +
    * via [[#Install_IGV_via_Job|OOD job launcher]]
 +
    * OR
 +
    * via [[#Install_via_Terminal_in_OOD_Desktop|Terminal on the OOD Desktop]]
 +
 +
== Install IGV via Job ==
 +
# 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'''
 +
  * [[File:A1.ood job composer.jpg|700px]]
 +
# Run/Submit the job
 +
  * Click on the green "play" arrow.  [[File:A2.ood job submit.png|700px]]
 +
  * Status changes to "queued" [[File:A3.ood job queued.png|700px]]
 +
  * wait until job completes. [[File:A4.ood job completed.png|700px]]
 +
# now open OOD desktop to launch IGV from desktop icon
 +
  * see [[#Running_IGV_from_OOD_Desktop]]
 +
 +
== Install via Terminal in OOD Desktop ==
 
# launch an interactive desktop with OOD https://rc.uab.edu
 
# launch an interactive desktop with OOD https://rc.uab.edu
 +
  * Requst an OOD Desktop [[File:A.ood start desktop.png|700px]]
 +
  * Set Request RAM and HOURS [[File:A.ood set mem.png|700px]]
 +
  * Open the desktop, once running [[File:A.ood launch desktop.png|700px]]
 +
  * desktop open [[File:A.ood desktop.png|700px]]
 
# start a "Terminal"  
 
# start a "Terminal"  
 +
  * open terminal app [[File:B.ood with terminal highlight.jpg|700px]]
 
# in terminal, enter  <nowiki>/share/apps/ngs-ccts/ood-igv/2.5.sh</nowiki>
 
# in terminal, enter  <nowiki>/share/apps/ngs-ccts/ood-igv/2.5.sh</nowiki>
 +
  * enter path to installer [[File:C.ood terminal setup 25.png|700px]]
 
# that will install IGV locally, and launch it.  
 
# 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 [[File:D.ood setup ivg loading.png|700px]]
 +
 +
 +
== Running IGV from OOD Desktop ==
  
== Running later ==
 
 
# Setup should create a desktop icon called "IGV-2.5.sh"
 
# Setup should create a desktop icon called "IGV-2.5.sh"
 +
  * [[File:G.ood desktop with icon.png|700px]]
 
# In the future, you can just start OOD, then click on "IGV-2.5.sh"
 
# In the future, you can just start OOD, then click on "IGV-2.5.sh"
 +
  * [[File:E.ood igv loading.png|800px]]
  
 
== Script source code ==
 
== Script source code ==
 
Code can be found at https://gitlab.rc.uab.edu/CCTS-Informatics-Pipelines/ood-igv
 
Code can be found at https://gitlab.rc.uab.edu/CCTS-Informatics-Pipelines/ood-igv

Latest revision as of 14:45, 16 October 2019

Contents

[edit] 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

[edit] 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

[edit] 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 


[edit] 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

[edit] Script source code

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