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
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"
- 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