OOD IGV

Running IGV from OOD

To start an interactive IGV job using Open OnDemand (OOD), please navigate to rc.uab.edu and log in. At the top bar, click the "Interactive Apps" drop down menu and select "IGV" from the list.

You should arrive at a new page with a job resource request selection form. Please fill out the form with values appropriate for your use case, then click the "Launch" button.

Error creating thumbnail: File missing

You should be taken to a new page where all of your currently running interactive jobs are available. The job just created in the previous step should be starting up. Please be patient until the "Launch Desktop in new tab" button appears. When it does, click it to open a new tab with an interactive IGV session. If anything goes wrong, please reach out to us for Support.

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

*

Error creating thumbnail: File missing

1. Run/Submit the job

* Click on the green "play" arrow.

Error creating thumbnail: File missing

* Status changes to "queued"

Error creating thumbnail: File missing

* wait until job completes.

Error creating thumbnail: File missing

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

Error creating thumbnail: File missing

* Set Request RAM and HOURS

Error creating thumbnail: File missing

* Open the desktop, once running

Error creating thumbnail: File missing

* desktop open

Error creating thumbnail: File missing

1. start a "Terminal"

 * open terminal app 

1. in terminal, enter /share/apps/ngs-ccts/ood-igv/2.5.sh

* enter path to installer

Error creating thumbnail: File missing

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

Error creating thumbnail: File missing

Running IGV from OOD Desktop

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

*

Error creating thumbnail: File missing

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

*

Error creating thumbnail: File missing

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.

# replace <version> with one available in the list from `module avail IGV`
module load IGV/<version>

# compute memory, leave 512 for JVM, rest for heap
avail_mem=$(($SLURM_MEM_PER_CPU * $SLURM_JOB_CPUS_PER_NODE))
heap_mem=$((avail_mem - 512))

# start with heap allocation hint
igv.sh -Xmx${heap_mem}m

Script source code

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