Uploading with the Uploader Tool
This is a quick tutorial on how to upload data to IRIDA using the IRIDA MiSeq Uploader Tool. You should use the IRIDA MiSeq uploader tool if you’re uploading an entire MiSeq run to IRIDA. Usually you only want to use the uploader tool if you’re a sequencing facility doing sequencing on behalf of a client.
This tutorial assumes that your client has already created the project where they want their data to reside in IRIDA. Clients must tell you what the numeric identifier for their project is so that you can use that information when setting up the run in the Illumina Experiment Manager.
- Downloading and Installing the Uploader
- Launching the Uploader
- Configuring the Uploader
- Modifying the Sample Sheet
- Uploading Data
Downloading and Installing the Uploader
The Illumina MiSeq platform has a Windows 7 PC installed inside the sequencer. A Windows installer for the Illumina MiSeq uploader tool can be downloaded at: https://irida.corefacility.ca/downloads/tools/IRIDA_Uploader_latest.exe
You can safely accept all default options once you launch the installer.
What does the installer install?
For complete transparency, the installer will install several components required by the uploader:
- Python 2.7.9 (32-bit)
- PyLauncher for Windows (https://bitbucket.org/vinay.sajip/pylauncher)
- The IRIDA MiSeq Uploader source code (https://github.com/phac-nml/irida-miseq-uploader)
Launching the Uploader
The installer will create a Start menu entry on your system:
You can launch the uploader by clicking on the entry in the Start menu.
Configuring the Uploader
Creating a client in IRIDA
Before you can prepare the uploader to connect, you must create a client ID and secret in IRIDA.
Start by clicking on the “Admin” menu (in the top, right-hand corner of the screen) and selecting “Clients”:
The clients list shows all clients that are currently allowed to access the IRIDA REST API.
You can add a new client by clicking on the “Add Client” button:
When you add a client, you’ll be required to provide the following information:
- A unique client ID,
- How long a token should be valid for once issued,
- The type of OAuth2 flow that a client should use,
- Whether to allow refresh tokens.
- The scopes that the client is allowed to use (should the client be allowed to read, write, or both with the REST API).
Important: When you’re creating a client entry for your uploader, you must select the
password grant type, and you must select both the
Configuring the Uploader Settings
Once you’ve created the client ID and secret in the IRIDA web interface, you need to enter that information into the settings dialog of the uploader. Open the settings dialog by clicking on the Options menu and selecting Settings:
The default settings for the uploader will not work with your IRIDA install:
- Server URL: The server URL is the location that the uploader should upload data to. If you navigate to your instance of IRIDA in your web browser, the URL (after you’ve logged in) will often look like:
https://irida.corefacility.ca/irida/. The URL you should enter into the Server URL field is that URL, with
api/at the end. So in the case of
https://irida.corefacility.ca/irida/, you should enter the URL
- Client authorization
- User authorization
- Username: This is the username that you will use to connect to upload data to IRIDA. This user account must have the Sequencer or Administrator role.
- Password: The password for the user account.
- Completion command: This is an arbitrary command that will be executed after an upload has finished (for example, you may want to use the Windows utility Robocopy to copy the complete run folder to a different location on your network).
On successful connection, your settings dialog should have green checkmarks on each setting:
Modifying the Sample Sheet
You must enter the numeric project ID number into the sample sheet for every sample that’s going to be uploaded using the uploader tool. You can enter this number in the Illumina Experiment Manager tool in the
Sample Project column:
You may also alter this value after the sequencer has completed the run using a spreadsheet tool like Microsoft Excel. Find the file named
SampleSheet.csv in the directory containing the results of your experiment and open the file with Microsoft Excel. Enter the numeric project ID in the
Sample_Project column for each sample in the list. Make sure that you save the file as a CSV file.
The uploader tool will create samples in the project(s) using the
Sample ID field as the sample name. If a sample in the project already has a name in the
Sample ID column (as might be the case with a top-up run), then the uploader will simply upload the new data to the existing sample.
Launch the uploader and choose the directory that contains your experiment results by clicking on the “Choose directory” button:
Use the dialog that appears to select the directory containing one or more sequencing run data directories, then click OK. You will see a success message indicating that the upload is ready to proceed if you’ve selected a directory that contains a valid
When you’re ready to proceed with uploading, click on the “Upload” button at the bottom of the window. The upload will begin, and you will see the progress of individual files and the overall run indicated at the bottom of the window, along with an estimated time remaining before the upload is complete:
Depending on the size of your experiment and your connection speed to your instance of IRIDA, upload can take several minutes to hours of time.