OOD IGV - Revision history

Wwarr@uab.edu at 18:34, 17 June 2021

2021-06-17T18:34:21Z

← Older revision		Revision as of 18:34, 17 June 2021
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	[[File:Igv_launch.png\|border]]		[[File:Igv_launch.png\|border]]

	== Running IGV from OOD interactive desktop ==		=== 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.		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.

Wwarr@uab.edu: Deprecated older methods

2021-06-17T18:33:56Z

Deprecated older methods

@@ Line 1: / Line 1: @@
-== Running IGV from OOD ==
+== How to use IGV ==
 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.
@@ Line 13: / Line 15: @@
 [[File:Igv_launch.png|border]]
-== First time setup ==
+== Running IGV from OOD interactive desktop ==
 # get a cheaha account (see [[Cheaha_GettingStarted]])
@@ Line 22: / Line 43: @@
      * via [[#Install_via_Terminal_in_OOD_Desktop|Terminal on the OOD Desktop]]
-== Install IGV via Job ==
+=== 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'''
@@ Line 37: / Line 59: @@
    * see [[#Running_IGV_from_OOD_Desktop]]
-== Install via Terminal in OOD Desktop ==
+=== Install via Terminal in OOD Desktop ===
 # launch an interactive desktop with OOD https://rc.uab.edu
    * Requst an OOD Desktop [[File:A.ood start desktop.png|700px]]
@@ Line 52: / Line 75: @@
    * installer finished, IGV loading [[File:D.ood setup ivg loading.png|700px]]
+=== Running IGV from OOD Desktop ===
 # Setup should create a desktop icon called "IGV-2.5.sh"
@@ Line 60: / Line 82: @@
    * [[File:E.ood igv loading.png|800px]]
-== Running IGV from OOD interactive desktop ==
+=== Script source code ===
 Code can be found at https://gitlab.rc.uab.edu/CCTS-Informatics-Pipelines/ood-igv

Wwarr@uab.edu: Added update section for interactive IGV job

2021-06-17T18:29:50Z

Added update section for interactive IGV job

← Older revision		Revision as of 18:29, 17 June 2021
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			== 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.

			[[File:Igv_job_setup.png\|border\|960px]]

			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]]

	== First time setup ==		== First time setup ==

Wwarr@uab.edu: /* Running IGV from OOD interactive desktop */

2021-06-17T18:00:56Z

Running IGV from OOD interactive desktop

← Older revision		Revision as of 18:00, 17 June 2021
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	<pre>		<pre>
	~~module load IGV/<version>~~ # replace <version> with one available in the list from `module avail IGV`		# 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 * $SLURM_JOB_CPUS_PER_NODE))		avail_mem=$(($SLURM_MEM_PER_CPU * $SLURM_JOB_CPUS_PER_NODE))
	heap_mem=$((avail_mem - 512)) # ~~leave 512 for the JVM itself, rest for~~ heap		heap_mem=$((avail_mem - 512))

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

Wwarr@uab.edu: /* Running IGV from OOD interactive desktop */

2021-06-17T18:00:01Z

Running IGV from OOD interactive desktop

← Older revision		Revision as of 18:00, 17 June 2021
Line 48:		Line 48:
	== Running IGV from OOD interactive desktop ==		== 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.		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.

	<pre>		<pre>

Wwarr@uab.edu: Added new section for interactive desktop with jvm xmx flag

2021-06-17T17:55:26Z

Added new section for interactive desktop with jvm xmx flag

← Older revision		Revision as of 17:55, 17 June 2021
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	# 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]]		* [[File:E.ood igv loading.png\|800px]]

			== 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.

			<pre>
			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
			</pre>

	== 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

Curtish@uab.edu at 19:45, 16 October 2019

2019-10-16T19:45:35Z

← Older revision		Revision as of 19:45, 16 October 2019
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	# 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 ==		== Install IGV via Job ==

Curtish@uab.edu at 19:33, 16 October 2019

2019-10-16T19:33:04Z

← Older revision		Revision as of 19:33, 16 October 2019
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	* Cluster: '''Cheaha'''		* Cluster: '''Cheaha'''
	* '''SAVE'''		* '''SAVE'''
	* [[File:A1.ood job composer.jpg\|~~500px~~]]		* [[File:A1.ood job composer.jpg\|700px]]
	# Run/Submit the job		# Run/Submit the job
	* Click on the green "play" arrow. [[File:A2.ood job submit.png\|~~500px~~]]		* Click on the green "play" arrow. [[File:A2.ood job submit.png\|700px]]
	* Status changes to "queued" [[File:A3.ood job queued.png\|~~500px~~]]		* Status changes to "queued" [[File:A3.ood job queued.png\|700px]]
	* wait until job completes. [[File:A4.ood job completed.png\|~~500px~~]]		* wait until job completes. [[File:A4.ood job completed.png\|700px]]
	# now open OOD desktop to launch IGV from desktop icon		# now open OOD desktop to launch IGV from desktop icon
	* see [[~~OOD_IGV~~#]]		* see [[#Running_IGV_from_OOD_Desktop]]

	== Install via Terminal in OOD Desktop ==		== Install via Terminal in OOD Desktop ==

Curtish@uab.edu at 19:28, 16 October 2019

2019-10-16T19:28:37Z

@@ Line 3: / Line 3: @@
 # get a cheaha account (see [[Cheaha_GettingStarted]])
 # launch an interactive desktop with OOD https://rc.uab.edu
    * Requst an OOD Desktop [[File:A.ood start desktop.png|700px]]
@@ Line 18: / Line 35: @@
-== Running later ==
+== Running IGV from OOD Desktop ==
 # Setup should create a desktop icon called "IGV-2.5.sh"
    * [[File:G.ood desktop with icon.png|700px]]

Curtish@uab.edu: add graffiti around terminal start icon

2019-10-15T20:11:57Z

add graffiti around terminal start icon

← Older revision		Revision as of 20:11, 15 October 2019
Line 9:		Line 9:
	* 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]]