BaseSpace 開発者会議 day2

Raymond Tecotzky @rtecotzky

Reporting status and logs back to BaseSpace for the user (console log) Providing reference Genomes data (/genomes) #basedev2014

Raymond Tecotzky @rtecotzky

Uploading results back to BaseSpace (/data/output, _metadata.json file) #basedev2014

Raymond Tecotzky @rtecotzky

For More info on SpaceDock... developer.basespace.illumina.com/docs/content/d… #basedev2014

Raymond Tecotzky @rtecotzky

Step 11: simulate launch to get the contents of the AppSession.json file #basedev2014

Raymond Tecotzky @rtecotzky

In the formbuilder window, fill out the input form on the right side then click Simulate Launch. #basedev2014

Raymond Tecotzky @rtecotzky

This will show us the AppSession.json file that is generated when the app is executed. #basedev2014

Raymond Tecotzky @rtecotzky

Step 12: Put contents of the file in the JSON reader #basedev2014

Raymond Tecotzky @rtecotzky

To see the contents of AppSession.json file, copy the contents of the simulated AppSession in JSON editor. In formbuilder, #basedev2014

Raymond Tecotzky @rtecotzky

Select Create AppSession instead of launching the app. • jsoneditoronline.org #basedev2014

Raymond Tecotzky @rtecotzky

All of the input form information will be stored in the Properties field in the AppSession.json file #basedev2014

Raymond Tecotzky @rtecotzky

The python json library can parse this file and pull out the exact parameters the app needs #basedev2014

Raymond Tecotzky @rtecotzky

Step 13a: Walk through script on the Docker image "sudo docker run –i –t mtyagi/ubuntu_example /bin/bash" "apt-get install vi" #basedev2014

Raymond Tecotzky @rtecotzky

"vi Sample_python_native_apps_script.py" #basedev2014

Raymond Tecotzky @rtecotzky

Step 13b: Walk through the script on the Docker image Meta data Step 13c: Walk through the script on the Docker image #basedev2014

Raymond Tecotzky @rtecotzky

Step 14: Modify script to add your parameters (one if statement per parameter) #basedev2014

Raymond Tecotzky @rtecotzky

• The commandLine is the command line that will be sent to the docker container once it is running. #basedev2014

Raymond Tecotzky @rtecotzky

The containerImageId is the repo_name of your docker image in the registry. #basedev2014

Raymond Tecotzky @rtecotzky

The format is generally [user_name]/[docker_image_name] for the public docker registry. For docker images in private registry #basedev2014

Raymond Tecotzky @rtecotzky

Simply append docker.illumina.com to the repo_name #basedev2014

Raymond Tecotzky @rtecotzky

Step 16a: Run the app and see that output is a file with the parameters and values in it #basedev2014

Raymond Tecotzky @rtecotzky

In the Formbuilder window: Select input parameters, sample, and project. #basedev2014

Raymond Tecotzky @rtecotzky

Step 16b: Run the app and see that output is a file with the parameters and values in it #basedev2014

Raymond Tecotzky @rtecotzky

1. Run this spacedock command on the VM 2. Click "Send to Local Agent" 3. Watch the app execute in your local VM, #basedev2014

Raymond Tecotzky @rtecotzky

move on once the AppSession is marked as complete and data is done uploading. #basedev2014

Raymond Tecotzky @rtecotzky

Step 17: View app result Go to BaseSpace (basespace.illumina.com) ! Click on Projects #basedev2014