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OOD IGV

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Contents

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: convert: unable to open image `/research/apps/rnb/docs/htdocs/tgw/images/e/e1/A1.ood_job_composer.jpg': No such file or directory @ error/blob.c/OpenBlob/2589.
convert: missing an image filename `/tmp/transform_1598819-1.jpg' @ error/convert.c/ConvertImageCommand/3015.
  1. Run/Submit the job
* Click on the green "play" arrow.
Error creating thumbnail: convert: unable to open image `/research/apps/rnb/docs/htdocs/tgw/images/2/2d/A2.ood_job_submit.png': No such file or directory @ error/blob.c/OpenBlob/2589.
convert: unable to open file `/research/apps/rnb/docs/htdocs/tgw/images/2/2d/A2.ood_job_submit.png' @ error/png.c/ReadPNGImage/3639.
convert: missing an image filename `/tmp/transform_47debfd-1.png' @ error/convert.c/ConvertImageCommand/3015.
* Status changes to "queued"
Error creating thumbnail: convert: unable to open image `/research/apps/rnb/docs/htdocs/tgw/images/4/42/A3.ood_job_queued.png': No such file or directory @ error/blob.c/OpenBlob/2589.
convert: unable to open file `/research/apps/rnb/docs/htdocs/tgw/images/4/42/A3.ood_job_queued.png' @ error/png.c/ReadPNGImage/3639.
convert: missing an image filename `/tmp/transform_26048bd-1.png' @ error/convert.c/ConvertImageCommand/3015.
* wait until job completes.
Error creating thumbnail: convert: unable to open image `/research/apps/rnb/docs/htdocs/tgw/images/6/6f/A4.ood_job_completed.png': No such file or directory @ error/blob.c/OpenBlob/2589.
convert: unable to open file `/research/apps/rnb/docs/htdocs/tgw/images/6/6f/A4.ood_job_completed.png' @ error/png.c/ReadPNGImage/3639.
convert: missing an image filename `/tmp/transform_1b4fb48-1.png' @ error/convert.c/ConvertImageCommand/3015.
  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: convert: unable to open image `/research/apps/rnb/docs/htdocs/tgw/images/c/cc/A.ood_start_desktop.png': No such file or directory @ error/blob.c/OpenBlob/2589.
convert: unable to open file `/research/apps/rnb/docs/htdocs/tgw/images/c/cc/A.ood_start_desktop.png' @ error/png.c/ReadPNGImage/3639.
convert: missing an image filename `/tmp/transform_3e21672-1.png' @ error/convert.c/ConvertImageCommand/3015.
* Set Request RAM and HOURS
Error creating thumbnail: convert: unable to open image `/research/apps/rnb/docs/htdocs/tgw/images/0/0b/A.ood_set_mem.png': No such file or directory @ error/blob.c/OpenBlob/2589.
convert: unable to open file `/research/apps/rnb/docs/htdocs/tgw/images/0/0b/A.ood_set_mem.png' @ error/png.c/ReadPNGImage/3639.
convert: missing an image filename `/tmp/transform_448ef9d-1.png' @ error/convert.c/ConvertImageCommand/3015.
* Open the desktop, once running
Error creating thumbnail: convert: unable to open image `/research/apps/rnb/docs/htdocs/tgw/images/a/a1/A.ood_launch_desktop.png': No such file or directory @ error/blob.c/OpenBlob/2589.
convert: unable to open file `/research/apps/rnb/docs/htdocs/tgw/images/a/a1/A.ood_launch_desktop.png' @ error/png.c/ReadPNGImage/3639.
convert: missing an image filename `/tmp/transform_281eb38-1.png' @ error/convert.c/ConvertImageCommand/3015.
* desktop open
Error creating thumbnail: convert: unable to open image `/research/apps/rnb/docs/htdocs/tgw/images/a/ae/A.ood_desktop.png': No such file or directory @ error/blob.c/OpenBlob/2589.
convert: unable to open file `/research/apps/rnb/docs/htdocs/tgw/images/a/ae/A.ood_desktop.png' @ error/png.c/ReadPNGImage/3639.
convert: missing an image filename `/tmp/transform_2d6d317-1.png' @ error/convert.c/ConvertImageCommand/3015.
  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
Error creating thumbnail: convert: unable to open image `/research/apps/rnb/docs/htdocs/tgw/images/d/d8/C.ood_terminal_setup_25.png': No such file or directory @ error/blob.c/OpenBlob/2589.
convert: unable to open file `/research/apps/rnb/docs/htdocs/tgw/images/d/d8/C.ood_terminal_setup_25.png' @ error/png.c/ReadPNGImage/3639.
convert: missing an image filename `/tmp/transform_3758020-1.png' @ error/convert.c/ConvertImageCommand/3015.
  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: convert: unable to open image `/research/apps/rnb/docs/htdocs/tgw/images/3/3f/D.ood_setup_ivg_loading.png': No such file or directory @ error/blob.c/OpenBlob/2589.
convert: unable to open file `/research/apps/rnb/docs/htdocs/tgw/images/3/3f/D.ood_setup_ivg_loading.png' @ error/png.c/ReadPNGImage/3639.
convert: missing an image filename `/tmp/transform_31a01de-1.png' @ error/convert.c/ConvertImageCommand/3015.


Running IGV from OOD Desktop

  1. Setup should create a desktop icon called "IGV-2.5.sh"
*
Error creating thumbnail: convert: unable to open image `/research/apps/rnb/docs/htdocs/tgw/images/7/7b/G.ood_desktop_with_icon.png': No such file or directory @ error/blob.c/OpenBlob/2589.
convert: unable to open file `/research/apps/rnb/docs/htdocs/tgw/images/7/7b/G.ood_desktop_with_icon.png' @ error/png.c/ReadPNGImage/3639.
convert: missing an image filename `/tmp/transform_40a7a00-1.png' @ error/convert.c/ConvertImageCommand/3015.
  1. In the future, you can just start OOD, then click on "IGV-2.5.sh"
*
Error creating thumbnail: convert: unable to open image `/research/apps/rnb/docs/htdocs/tgw/images/d/de/E.ood_igv_loading.png': No such file or directory @ error/blob.c/OpenBlob/2589.
convert: unable to open file `/research/apps/rnb/docs/htdocs/tgw/images/d/de/E.ood_igv_loading.png' @ error/png.c/ReadPNGImage/3639.
convert: missing an image filename `/tmp/transform_1ef1f26-1.png' @ error/convert.c/ConvertImageCommand/3015.

Script source code

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