Open OnDemand Sandbox

Open OnDemand is a web interface to Cheaha HPC resources. We have setup multiple general purpose apps, such as HPC Desktop, Jupyter, RStudio etc, on cheaha, to make the process of accessing these basic softwares easier. OnDemand also allows users to setup their own personal apps in the OnDemand, as sandbox apps.

Setting up sandbox for your profile

Setting up sandbox is pretty simple and straightforward.

• You need to create a dev folder in your $USER_DATA/ondemand folder

mkdir -p $USER_DATA/ondemand/dev

• Then go to Cheaha OnDemand , login, and under Help, click on Restart Web Server

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

Building your first dev app

Over here you have instructions to create your first example dev app:

IGV

• Under Develop tab , click on My SandBox Apps (Development)

• Now click on New App tab

• Now we are going to import an already existing git repo for an app, by clicking on Clone Existing App

• Add the following values in the form:

Directory Name: IGV
Git Remote: https://github.com/uabrc/sandbox_app_template

and Submit

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 (local git repo working directory), that you just cloned.

• Let's modify manifest.yml file (highlight the file, and click on edit) to change metadata for the sandbox app. Change the SOFTWARE_NAME and SOFTWARE_LINK variables appropriately.

In this case change then to following:

SOFTWARE_NAME : IGV
SOFTWARE_LINK : http://software.broadinstitute.org/software/igv/

• Next, highlight form.yml and click on Edit . Uncomment version section in the file, and change that section as follows:

  version:
    widget: select
    label: "IGV version"
    help: "This defines the version of IGV you want to load."
    options:
      - [ "2.5.0-Java-11", "IGV/2.5.0-Java-11" ]

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.

• Now, go into template and edit file script.sh.erb, by adding following lines at the end of the file. This is the actual job script that will be submitted to the cluster, just like you would submit with sbatch from the command line.

igvtools_gui.command &
igv.sh

Save the file, and close the tab. This script runs the app executable after loading the appropriate module, based on the version you choose in the form.

• Close the file browser for your app.

• Click on Launch IGV, and submit the job with desired parameters.

You should have your first dev app (IGV) running.

FSL

• Under Develop tab , click on My SandBox Apps (Development)

• Now click on New App tab

• Now we are going to import an already existing git repo for an app, by clicking on Clone Existing App

• Add the following values in the form:

Directory Name: FSL
Git Remote: https://github.com/uabrc/sandbox_app_template

and Submit

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 (local git repo working directory), that you just cloned.

• Let's modify manifest.yml file (highlight the file, and click on edit) to change metadata for the sandbox app. Change the SOFTWARE_NAME and SOFTWARE_LINK variables appropriately.

In this case change then to following:

SOFTWARE_NAME : FSL
SOFTWARE_LINK : https://www.fmrib.ox.ac.uk/fsl

• Next, highlight form.yml and click on Edit . Uncomment version section in the file, and change that section as follows:

  version:
    widget: select
    label: "FSL version"
    help: "This defines the version of FSL you want to load."
    options:
      - [ "6.0.3", "FSL/6.0.3" ]

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.

• Now, go into template and edit file script.sh.erb, by adding following lines at the end of the file. This is the actual job script that will be submitted to the cluster, just like you would submit with sbatch from the command line.

source /share/apps/rc/software/FSL/6.0.3/fsl/etc/fslconf/fsl.sh
fsl

Save the file, and close the tab. This script runs the app executable after loading the appropriate module, based on the version you choose in the form.

• Close the file browser for your app.

• Click on Launch IGV, and submit the job with desired parameters.

You should have your first dev app (IGV) running.

More info

To get more example apps to build or to build passenger apps, look here.

Contact us if you run into any issues, or to discuss any new app.