Open OnDemand Sandbox - Revision history

Ravi89@uab.edu: /* Setting up sandbox for your profile */

2020-08-11T22:44:11Z

Setting up sandbox for your profile

← Older revision		Revision as of 22:44, 11 August 2020
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	* You have successfully enabled sandbox for your environment, and you should see a new '''Develop''' tab.		* You have successfully enabled sandbox for your environment, and you should see a new '''Develop''' tab.


			'''NOTE:''' This is a one time setup

	===Building your first dev app===		===Building your first dev app===

Louistw@uab.edu at 21:03, 11 August 2020

2020-08-11T21:03:15Z

← Older revision		Revision as of 21:03, 11 August 2020
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	* Next, highlight '''form.yml''' and click on '''Edit''' . Uncomment version section in the file, and change that section as follows:		* Next, highlight '''form.yml''' and click on '''Edit''' . Uncomment version section in the file, and change that section as follows:

			Change '''SOFTWARE_NAME''' appropriately. Under options change '''display_version''' to the the version that you want to display on the form, and change '''corresponding_cheaha_module''' to matching module name on cheaha.

			Here we are specifying what the form for the app is going to look like, and changing available parameters for Cheaha.
	<pre>		<pre>
	version:		version:
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	</pre>		</pre>
	and save the file, and close the tab.		and save the file, and close the tab.

	Change '''SOFTWARE_NAME''' appropriately. Under options change '''display_version''' to the the version that you want to display on the form, and change '''corresponding_cheaha_module''' to matching module name on cheaha.

	~~Here we are specifying what the form for the app is going to look like, and changing available parameters for Cheaha.~~

	The "native" section in '''submit.yml.erb''' includes the slurm parameters you would use with sbatch and describes the resources needed for the app. These can include variable names defined in the form above which will get substituted for the user provided values when the app is run.		The "native" section in '''submit.yml.erb''' includes the slurm parameters you would use with sbatch and describes the resources needed for the app. These can include variable names defined in the form above which will get substituted for the user provided values when the app is run.

Ravi89@uab.edu: /* Building your first dev app */

2020-08-10T15:12:35Z

Building your first dev app

Show changes

Jpr@uab.edu: /* Building your first dev app */ Emphasis role or script.sh.erb

2020-08-07T18:28:23Z

Building your first dev app: Emphasis role or script.sh.erb

← Older revision		Revision as of 18:28, 7 August 2020
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	SAve the file, and close the tab		SAve the file, and close the tab

	* Now, go into '''template''' folder and create a new file '''script.sh.erb''', and add following content to it:		* Now, go into '''template''' folder and create a new file '''script.sh.erb''', and add following content to it. This is the actual job script that will be submitted to the cluster, just like you would submit with sbatch from the command line.
	<pre>		<pre>
	#!/usr/bin/env bash		#!/usr/bin/env bash

Jpr@uab.edu: /* Building your first dev app */ Clarify that the submit file uses sbatch parameters

2020-08-07T18:23:27Z

Building your first dev app: Clarify that the submit file uses sbatch parameters

← Older revision		Revision as of 18:23, 7 August 2020
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	* Now again in the file explorer for your app, click on '''New File''' with name '''submit.yml.erb'''		* Now again in the file explorer for your app, click on '''New File''' with name '''submit.yml.erb'''

	* Edit the file submit.yml.erb, with the following content.		* Edit the file submit.yml.erb, with the following content. The "native" sectino includes the slurm parameters you would use with sbatch and describes the resources needed for the app. These can include variable names defined in the form above which will get substituted for the user provided values when the app is run.
	<pre>		<pre>
	---		---

Jpr@uab.edu: /* Building your first dev app */ Clarify local git directory def

2020-08-07T18:15:57Z

Building your first dev app: Clarify local git directory def

← Older revision		Revision as of 18:15, 7 August 2020
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	'''Note:''' You can also check the line, about creating a new git repo, if you want to use it to maintain your own instance of the app.		'''Note:''' You can also check the line, about creating a new git repo, if you want to use it to maintain your own instance of the app.

	* Now click on '''Files''' to take a look at the files for the app (git repo), that you just cloned.		* Now click on '''Files''' to take a look at the files for the app (local git repo working directory), that you just cloned.

	* Highlight '''form.yml''' and click on '''Edit''' . Change the file to the following content:		* Highlight '''form.yml''' and click on '''Edit''' . Change the file to the following content:

Jpr@uab.edu: /* Setting up sandbox for your profile */ Fix variable name to $USER_DATA to match env.

2020-08-07T18:14:14Z

Setting up sandbox for your profile: Fix variable name to $USER_DATA to match env.

← Older revision		Revision as of 18:14, 7 August 2020
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	===Setting up sandbox for your profile===		===Setting up sandbox for your profile===
	Setting up sandbox is pretty simple and straightforward.		Setting up sandbox is pretty simple and straightforward.
	* You need to create a dev folder in your '''~~DATA_USER~~/ondemand''' folder		* You need to create a dev folder in your '''$USER_DATA/ondemand''' folder
	<pre>		<pre>
	mkdir -p ~~/data/user/~~$~~USER~~/ondemand/dev		mkdir -p $USER_DATA/ondemand/dev
	</pre>		</pre>

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	* You have successfully enabled sandbox for your environment, and you should see a new '''Develop''' tab.		* You have successfully enabled sandbox for your environment, and you should see a new '''Develop''' tab.


	===Building your first dev app===		===Building your first dev app===

Ravi89@uab.edu: /* Building your first dev app */

2020-08-07T17:49:02Z

Building your first dev app

← Older revision		Revision as of 17:49, 7 August 2020
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	chmod +x script.sh.erb		chmod +x script.sh.erb
	</pre>		</pre>
	This script needs to be an executable file.		, and then close the terminal. This script needs to be an executable file.

	This script runs the executable after loading the appropriate module, ~~absed~~ on the version you choose in the form.		This script runs the app executable after loading the appropriate module, based on the version you choose in the form.

	* Now close the file browser for your app.		* Now close the file browser for your app.
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	* Now click, on 'Launch IGV', and submit the job.		* Now click, on 'Launch IGV', and submit the job.

	You should have your first dev app running.		You should have your first dev app running.

	===More info===		===More info===

Ravi89@uab.edu at 17:47, 7 August 2020

2020-08-07T17:47:52Z

← Older revision		Revision as of 17:47, 7 August 2020
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	igv.sh		igv.sh
	</pre>		</pre>
	Save the file, and close the tab.		Save the file, and close the tab. Now click on '''Open in terminal''', and run
			<pre>
			chmod +x script.sh.erb
			</pre>
			This script needs to be an executable file.

	This script runs the executable after loading the appropriate module, absed on the version you choose in the form.		This script runs the executable after loading the appropriate module, absed on the version you choose in the form.
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	* Now click, on 'Launch IGV', and submit the job.		* Now click, on 'Launch IGV', and submit the job.

	You have your first dev app running.		You should have your first dev app running.

	===More info===		===More info===

Ravi89@uab.edu at 17:40, 7 August 2020

2020-08-07T17:40:21Z

← Older revision		Revision as of 17:40, 7 August 2020
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	===Building your first dev app===		===Building your first dev app===

			Over here we provide instructions to create your first example dev script:

	* Under '''Develop''' tab , click on '''My SandBox Apps (Development)'''		* Under '''Develop''' tab , click on '''My SandBox Apps (Development)'''
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	* Now click, on 'Launch IGV', and submit the job.		* Now click, on 'Launch IGV', and submit the job.

	You have your first dev app running. [mailto:support@listserv.uab.edu?Subject=OOD%20SandBox:%20 Contact us] if you run into any issues, or to discuss any new app.		You have your first dev app running.

			===More info===
			To get more example apps to build or to build passenger apps, look [https://osc.github.io/ood-documentation/master/app-development/tutorials-interactive-apps.html here].


			[mailto:support@listserv.uab.edu?Subject=OOD%20SandBox:%20 Contact us] if you run into any issues, or to discuss any new app.