OOD IGV

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# get a cheaha account (see [[Cheaha_GettingStarted]])
 
# get a cheaha account (see [[Cheaha_GettingStarted]])
 
# launch an interactive desktop with OOD https://rc.uab.edu
 
# launch an interactive desktop with OOD https://rc.uab.edu
<gallery>
+
  * Requst an OOD Desktop [[File:A.ood start desktop.png|700px]]
File:A.ood start desktop.png|OOD Start Desktop Menu
+
  * Set Request RAM and HOURS [[File:A.ood set mem.png|700px]]
File:A.ood set mem.png|OOD Set Desktop memory/run-time
+
  * Open the desktop, once running [[File:A.ood launch desktop.png|700px]]
File:A.ood launch desktop.png|Launch Desktop once it's running
+
  * desktop open [[File:A.ood desktop.png|700px]]
</gallery>
+
 
# start a "Terminal"  
 
# start a "Terminal"  
 +
  * open terminal app [[File:B.ood with terminal.png|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 later ==
 
== 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

Revision as of 13:48, 15 October 2019

First time setup

  1. get a cheaha account (see Cheaha_GettingStarted)
  2. 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.png
  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 later

  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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