Hello new SDR user! This tutorial will take you through the basic process of using the SDR to digitise a set of samples, following these key steps:
- Uploading an input file to the SDR
- Launching the workflow to perform the digitisation
- Saving the digitisation output
Let's get ready to perform our first digitisation. To do this we need to perform a couple of preparatory steps.
For this tutorial, please download and use the following reference file.
If you have already following this tutorial and are interested in creating your own input files, please see this guide.
To use the SDR reference instance you must be a registered user. To register, please navigate to our implementation. You will need to register for an account by clicking "Register here" and then logging in with the details you provided when registering.
Now we are ready to begin digitising.
The SDR is driven by supplying an input file. This file contains some basic details about the sample to be digitised and, crucially, a URL pointing to the specimen image itself. Each row of the file is a sample to be analysed.
To allow the SDR to process our reference file, we must upload it to the SDR interface.
Once logged in, you will be presented with the main window. Which should look similar to the below:
This interface is created by the technology underlying the SDR, known as Galaxy. We wont focus on that detail here, but you can find extensive tutorials for generic Galaxy online. For a short introduction to the Galaxy interface you can go here, but for this tutorial we will show you everything you need to know.
n.b. 1
To upload a file to the SDR, click the "Upload data" button on the left hand panel. This will bring up a prompt (shown below) where you should click "Choose local files", this will open your file explorer.
Click "Choose local files"
In the file explorer, you should navigate to and select the reference file you downloaded earlier.
Select the reference file
The file is now staged for uploading. To begin the upload, press start.
Press "Start"
As the dialog turns green, the file is now uploaded. Please close the dialog.
Press "Close"
The file now appears in our history window, where workflow inputs are stored and outputs will appear.
Navigate to the Workflows list by clicking the "Workflow" link at the top of the screen.
You will be presented with a list workflows. To start running a workflow click the "Run workflow" button for the "De novo-Collections test" workflow.
Select your previously uploaded dataset and click the run button.
Your workflow will now be running. You will see Galaxy schedule the workflow steps and summarise overall job progress. You can view results for each step and its jobs as they are completed but we will explore the workflow output once all the jobs are complete. You can close your browser and come back to Galaxy while waiting for your workflow to finish.
On the right hand side of the screen you will see the Galaxy's History panel. Each step and all the associated jobs are summarised here.
To download the output of a workflow, click on the title of a step, in this case "422: sdr_output". This expands the step and provides additional buttons to interact with the outputs of the step.
Click the floppy disk icon to download a zip file containing all the outputs.
