BSSH Integration

Please contact Tech Support with the subject "BaseSpace Emedgene Connect app" for assistance.

Prerequisites

1. Have a BaseSpace account

2. Have an Emedgene account

3. Add this BaseSpace as a Storage Provider in Emedgene - instructions

4. Add your BaseSpace user to the Emedgene Connect App whitelist

   1. Go to

      https://<domain>.api.basespace.illumina.com/v1pre3/users/current

   2. Send the Href value to Tech Support with the subject "BaseSpace Emedgene Connect app" "Href": "v1pre3/users/00000000"

Workflow setup

1. On BaseSpace, go to Apps and search for Emedgene Connect Beta under All Categories

1. Click on the app and press Launch Application

1. Fill out the application setup

   1. Choose an Analysis Name - this will be used for the setup analysis run

   2. Choose a Biosample and Project for the setup - other projects and biosamples can be used later on

   3. Enter the Emedgene URL in which to create cases

   4. Enter your API key

   5. Enable Setup Mode

   6. Choose a Workflow name - this will be used in the BioSample Workflow sheet

   7. Press Launch Application

1. When the app launches, an additional URL will be printed to the logs. Copy this URL to another tab and give the requested access to the app. The access granted will created the workflows used later in the BioSample Workflow Sheet.

2. Once the app setup analysis is completed successfully, press View Files next to the Logs window.

1. Go to Files and find the BioSample Workflow CSV template in the outputs directory.

BioSample Workflow Sheet setup

• Columns A-J hold the data to queue the Emedgene Connect Beta app launch.

  • BioSample Name

  • Default Project - the BaseSpace project to save the outputs to. Can be different than the project used for setting up the app.

  • Analysis Group - used for pedigree grouping, define a group id and set it for all pedigree samples.

  • Analysis Workflow - in the proband row only set the workflow name define in the app setup and the size of the pedigree. emedgene-create-case_1 - singleton emedgene-create-case_3 - trio

• From column K onwards holds the data for the Emedgene Batch Upload. This data should follow the Batch Upload CSV requirements.

• Upload the BioSample Workflow Sheet on BaseSpace under Biosamples.

Sample Sheet setup

• Sample_ID needs to match the BioSampleName in the BioSample Workflow Sheet

• ProjectName needs to match the Default Project in the BioSample Workflow Sheet

Run upload

Upload the run with the Sample Sheet to BaseSpace via CLI (Command Line interface).

To set up the BaseSpace CLI see here.

<bs-path> upload run -n '<RunName>' -t <Instrument> . --concurrency=high

1. <RunName> should be set to the RunName from the Sample Sheet Headers

2. <Instrument> should be set to the InstrumentPlatform from the Sample Sheet Headers

3. <bs-path> should be set to the output of the command which bs

Next Steps

Once BCL Convert is completed for a BioSample from the BioSample Workflow sheet, the selected Analysis Workflow from the BioSample Workflow sheet will launch the Emedgene Connect Beta.