OOD IGV: Difference between revisions
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# get a cheaha account (see [[Cheaha_GettingStarted]]) | # get a cheaha account (see [[Cheaha_GettingStarted]]) | ||
# 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]] | |||
File:A.ood start desktop.png| | * Set Request RAM and HOURS [[File:A.ood set mem.png|700px]] | ||
File:A.ood set mem.png| | * Open the desktop, once running [[File:A.ood launch desktop.png|700px]] | ||
File:A.ood launch desktop.png| | * desktop open [[File:A.ood desktop.png|700px]] | ||
# start a "Terminal" | # start a "Terminal" | ||
* open terminal app [[File:B.ood with terminal.png|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]] | |||
# that will install IGV locally, and launch it. | # 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 [[File:D.ood setup ivg loading.png|700px]] | |||
== Running later == | == 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]] | |||
# 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]] | |||
== 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 | ||
Revision as of 19:48, 15 October 2019
First time setup
- get a cheaha account (see Cheaha_GettingStarted)
- launch an interactive desktop with OOD https://rc.uab.edu
* Requst an OOD Desktop
Error creating thumbnail: File missing
* Set Request RAM and HOURS
Error creating thumbnail: File missing
* Open the desktop, once running
Error creating thumbnail: File missing
* desktop open
Error creating thumbnail: File missing
- start a "Terminal"
* open terminal app
Error creating thumbnail: File missing
- in terminal, enter /share/apps/ngs-ccts/ood-igv/2.5.sh
* enter path to installer
Error creating thumbnail: File missing
- 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: File missing
Running later
- Setup should create a desktop icon called "IGV-2.5.sh"
*
Error creating thumbnail: File missing
- In the future, you can just start OOD, then click on "IGV-2.5.sh"
*
Error creating thumbnail: File missing
Script source code
Code can be found at https://gitlab.rc.uab.edu/CCTS-Informatics-Pipelines/ood-igv