OOD IGV: Difference between revisions
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# get a cheaha account (see [[Cheaha_GettingStarted]]) | # get a cheaha account (see [[Cheaha_GettingStarted]]) | ||
== 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|500px]] | |||
# Run/Submit the job | |||
* Click on the green "play" arrow. [[File:A2.ood job submit.png|500px]] | |||
* Status changes to "queued" [[File:A3.ood job queued.png|500px]] | |||
* wait until job completes. [[File:A4.ood job completed.png|500px]] | |||
# now open OOD desktop to launch IGV from desktop icon | |||
* see [[OOD_IGV#]] | |||
== 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]] | * Requst an OOD Desktop [[File:A.ood start desktop.png|700px]] | ||
| Line 18: | Line 35: | ||
== Running | == Running IGV from OOD Desktop == | ||
# 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]] | * [[File:G.ood desktop with icon.png|700px]] | ||
Revision as of 19:28, 16 October 2019
First time setup
- get a cheaha account (see Cheaha_GettingStarted)
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
*
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- 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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- now open OOD desktop to launch IGV from desktop icon
* see OOD_IGV#
Install via Terminal in OOD Desktop
- 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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- start a "Terminal"
* open terminal app 
- in terminal, enter /share/apps/ngs-ccts/ood-igv/2.5.sh
* enter path to installer
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- 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
- Setup should create a desktop icon called "IGV-2.5.sh"
*
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- 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