5  Upload Data to Galaxy

Using data in Galaxy

For Galaxy to be able to use your data, that data must be in your history on the Galaxy instance.

Caution

Data is not shared between Galaxy instances. For instance, if you upload data to usegalaxy.eu it will not automatically be available on usegalaxy.org or usegalaxy.au.

5.1 Uploading your data

There are three main routes to uploading your data onto the Galaxy instance.

5.1.1 Use the You can load your own data link in an empty workflow

This option is only visible when you have an empty workflow. Click on the You can load your own data link under This history is empty. This will bring up a dialogue box. You can drag and drop a file or files into the dialogue box, or use the Choose local file button to navigate to the location of your files.

1. Click on the You can load your own data link.
2. Drag the three workshop data files starting with SARS_AY278741 into the dialogue box.
3. Click on the Start button.
4. The files will appear in the History sidebar.
5. Click the Close button in the file dialogue.

Data file colours

When the data files are first added to the workflow, they have a grey background. This indicates that Galaxy knows about the files, and is preparing to upload them.

When Galaxy begins to upload the files, the background changes to orange.

When the upload is complete, the background turns green.

If there is a problem with uploading, the background turns red (please signal to a demonstrator if this happens for you).

Data file types

You will have noticed the Auto-detect dropdown boxes when you uploaded your files. Galaxy is able to process files that describe many data types, including genome sequence data, transcriptome data, mass spectrometry data, and so on. Each individual file contains a single type of data.

Galaxy is usually clever enough to determine for itself what data is in a particular file, but sometimes it cannot recognise the contents, and you may have to specify the file type by choosing from the options in this drop-down box.

Video: Uploading files with the You can load your own data link

5.1.2 Use the Upload Data button in the Tools sidebar

There is an Upload button at the top left of the Galaxy window, in the left-most toolbar. It has a green background and an upload icon. At any point in the analysis, you can click on this button to upload data into the workflow.

1. Click on the Upload button.
2. Drag the trimmed_pe_aln.qsorted.mapped.fixed.1.fastq.gz file into the dialogue box.
3. Click on the Start button.
4. The file will appear in the History sidebar.
5. Click the Close button in the file dialogue.

This file is substantially larger than the files you uploaded above, and will take longer to turn orange, and then green, to indicate that it has uploaded correctly.

Video: Uploading files with the Upload button

5.1.3 Drag and drop data onto the workspace

You can also drag and drop data files directly into the central workspace window of Galaxy. This will trigger the file upload dialogue box.

1. Drag the trimmed_pe_aln.qsorted.mapped.fixed.2.fastq.gz file into the Galaxy workspace.
2. A Drag files here to upload overlay will appear.
3. Drop the file in the overlay. A file upload dialogue box will appear.
4. Click on the Start button.
5. The file will appear in the History sidebar.
6. Click the Close button in the file dialogue.

Video: Uploading files by dragging them into the workspace

5.2 Inspecting Data

You can inspect the data you have uploaded to Galaxy visually in two ways.

5.2.1 In the History

To view the contents of an uploaded data file in the History.

1. Click on the file name (e.g. SARS_AY278741.fasta). The file descriptor will enlarge.

• The descriptor shows the file’s datatype (e.g. “format fasta”)
• At the bottom of the descriptor, a preview of the dataset is shown, with the first few lines of the data.

2. Click on the file name again to close the file descriptor.

5.2.2 In the Workspace

You can view the complete file contents (or at least a large preview of up to 1MB of data) in the main workspace window, by clicking on the eye icon in the file descriptor.

1. Click on the eye icon of one of the file descriptors (e.g. SARS_AY278741.gff3). A representation of the data in the file will be shown in the workspace window.

Video: Inspecting a data file in the History and the Workspace

5.2.3 Using additional tools

The open file descriptor presents several icons, just above the data preview. These allow you to:

1. Download the dataset to your computer
2. Obtain a direct URL link to the data
3. View details about the dataset
4. Visualise the data interactively using an appropriate tool
5. Show related dataset

View the video below to see some examples of this output.

Video: Using interactive data inspection tools