OOD IGV

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 

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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Running IGV from OOD interactive desktop

IGV is also available from an interactive desktop job, giving the full desktop experience. Because the IGV interface is programmed in Java, we must tell IGV how much memory is available in our job context. If we don't then the default value of 2 GB is used, likely insufficient. Please see Java Xmx for more information and a more robust method of calculation. The instructions below assume an interactive desktop job has been created and prepared and that the terminal is open in that interactive desktop. This may be done using the Open OnDemand web portal.

module load IGV/<version>  # replace <version> with one available in the list from `module avail IGV`
avail_mem=$(($SLURM_MEM_PER_CPU * $SLURM_JOB_CPUS_PER_NODE))
heap_mem=$((avail_mem - 512)) # leave 512 for the JVM itself, rest for heap
igv.sh -Xmx${heap_mem}m

Script source code

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