OOD IGV: Difference between revisions
(add images) |
mNo edit summary |
||
| (9 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
== First time setup == | == 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. | |||
[[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]] | |||
=== 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. | |||
<pre> | |||
# 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 | |||
</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''' | |||
* Name: '''setup IGV 2.5''' | |||
* Script Name: '''2.5.sh''' | |||
* Cluster: '''Cheaha''' | |||
* '''SAVE''' | |||
* [[File:A1.ood job composer.jpg|700px]] | |||
# Run/Submit the job | |||
* Click on the green "play" arrow. [[File:A2.ood job submit.png|700px]] | |||
* Status changes to "queued" [[File:A3.ood job queued.png|700px]] | |||
* wait until job completes. [[File:A4.ood job completed.png|700px]] | |||
# now open OOD desktop to launch IGV from desktop icon | |||
* see [[#Running_IGV_from_OOD_Desktop]] | |||
=== 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 9: | Line 67: | ||
* 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. | * 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]] | ||
| Line 17: | Line 75: | ||
* 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 === | |||
# 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]] | ||
| Line 24: | Line 82: | ||
* [[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 18:34, 17 June 2021
How to use 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.
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.
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
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)
* then install EITHER * via OOD job launcher * OR * via 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 * Name: setup IGV 2.5 * Script Name: 2.5.sh * Cluster: Cheaha * SAVE
*
- Run/Submit the job
* Click on the green "play" arrow.
* Status changes to "queued"
* wait until job completes.
- now open OOD desktop to launch IGV from desktop icon
* see #Running_IGV_from_OOD_Desktop
Install via Terminal in OOD Desktop
- launch an interactive desktop with OOD https://rc.uab.edu
* Requst an OOD Desktop
* Set Request RAM and HOURS
* Open the desktop, once running
* desktop open
- start a "Terminal"
* open terminal app 
- in terminal, enter /share/apps/ngs-ccts/ood-igv/2.5.sh
* enter path to installer
- 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
Running IGV from OOD Desktop
- Setup should create a desktop icon called "IGV-2.5.sh"
*
- In the future, you can just start OOD, then click on "IGV-2.5.sh"
*
Script source code
Code can be found at https://gitlab.rc.uab.edu/CCTS-Informatics-Pipelines/ood-igv