OOD IGV

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== First time setup ==
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== How to use IGV ==
+
 
 +
=== Running IGV from OOD ===
 +
 
 +
To start an interactive IGV job using Open OnDemand (OOD), please navigate to [https://rc.uab.edu rc.uab.edu] and log in. At the top bar, click the "Interactive Apps" drop down menu and select "IGV" from the list.
 +
 
 +
[[File:Igv_interactive_jobs.png|border]]
 +
 
 +
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.
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 +
[[File:Igv_job_setup.png|border|960px]]
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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]].
 +
 
 +
[[File:Igv_launch.png|border]]
 +
 
 +
=== 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|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.
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<pre>
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# replace <version> with one available in the list from `module avail IGV`
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module load IGV/<version>
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# compute memory, leave 512 for JVM, rest for heap
 +
avail_mem=$(($SLURM_MEM_PER_CPU * $SLURM_JOB_CPUS_PER_NODE))
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heap_mem=$((avail_mem - 512))
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# start with heap allocation hint
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igv.sh -Xmx${heap_mem}m
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</pre>
 +
 
 +
== Legacy Setup and Run ==
 +
 
 +
IGV has been added to Open OnDemand (OOD) as a first-class application, so the steps below are no longer necessary to use IGV. The methods in the previous section are preferred due to their simplicity and are more readily supported.
 +
 
 +
=== First time setup ===
  
 
# 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'''
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  * Name: '''setup IGV 2.5'''
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  * Script Name: '''2.5.sh'''
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  * Cluster: '''Cheaha'''
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  * '''SAVE'''
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  * [[File:A1.ood job composer.jpg|700px]]
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# Run/Submit the job
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  * Click on the green "play" arrow.  [[File:A2.ood job submit.png|700px]]
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  * Status changes to "queued" [[File:A3.ood job queued.png|700px]]
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  * wait until job completes. [[File:A4.ood job completed.png|700px]]
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# now open OOD desktop to launch IGV from desktop icon
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  * see [[#Running_IGV_from_OOD_Desktop]]
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 +
=== 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]]
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   * desktop open [[File:A.ood 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.png|700px]]
+
   * 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]]  
 
   * enter path to installer [[File:C.ood terminal setup 25.png|700px]]  
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   * installer finished, IGV loading [[File:D.ood setup ivg loading.png|700px]]  
 
   * 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]]
 
   * [[File:G.ood desktop with icon.png|700px]]
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   * [[File:E.ood igv loading.png|800px]]
 
   * [[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 12:34, 17 June 2021

Contents

[edit] How to use IGV

[edit] 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.

Igv interactive jobs.png

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.

Igv job setup.png

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.

Igv launch.png

[edit] 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

[edit] Legacy Setup and Run

IGV has been added to Open OnDemand (OOD) as a first-class application, so the steps below are no longer necessary to use IGV. The methods in the previous section are preferred due to their simplicity and are more readily supported.

[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

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