tutorial.md

layout	title	zenodo_link	level	questions	objectives	time_estimation	key_points	subtopic	contributors
tutorial_hands_on	A short introduction to Galaxy	https://doi.org/10.5281/zenodo.582600	Introductory	How to get started in Galaxy	Learn how to upload a file Learn how to use a tool Learn how to view results Learn how to view histories	30m	The Galaxy interface has tools on the left, viewing pane in the middle, and a history of your data analysis on the right. You can create a new history for each analysis. All your histories are saved. To get data into Galaxy, you can upload a file by pasting in a web address. There are other ways to get data into Galaxy (not covered in this tutorial): you can upload a file from your computer, and you can import an entire history. Choose a tool and change any settings for your analysis. Run the tool. The output files will be saved at the top of your history. View the output files by clicking on the eye icon. View all your histories and move files between them. Switch to a different history. Log out of your Galaxy server. When you log back in (to the same server), your histories will all be there.	core	annasyme

Overview

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• This is a short introduction to the Galaxy user interface - the web page that you interact with.
• We will cover key tasks in Galaxy: uploading files, using tools, and viewing histories.

Agenda

1. TOC {:toc}

{: .agenda}

What does Galaxy look like?

{% icon hands_on %} Hands-on: Log in to Galaxy

1. Open your favorite browser (Chrome, Safari or Firefox as your browser, not Internet Explorer!)
2. Browse to your Galaxy instance
3. Log in or register

{% icon comment %} Different Galaxy servers

This is an image of Galaxy Australia, located at usegalaxy.org.au

The particular Galaxy server that you are using may look slightly different and have a different web address:

• The main Galaxy server is usegalaxy.org
• The European Galaxy server is usegalaxy.eu

You can also find more possible Galaxy servers at the top of this tutorial in Available on these Galaxies {: .comment} {: .hands_on}

The Galaxy homepage is divided into three panels:

• Tools on the left
• Viewing panel in the middle
• History of analysis and files on the right

The first time you use Galaxy, there will be no files in your history panel.

Key Galaxy actions

Name your current history

Your "History" is in the panel at the right.

{% icon hands_on %} Hands-on: Name history

1. Go to the History panel (on the right)

2. Click on the history name (which by default is "Unnamed history")

   {:width="320px"}

3. Type in a new name, for example, "My-Analysis"

4. Press Enter on your keyboard to save it

{% icon comment %} Renaming not an option?

If renaming does not work, it is possible you aren't logged in, so try logging in to Galaxy first. Anonymous users are only permitted to have one history, and they cannot rename it. {: .comment}

{: .hands_on}

Upload a file

Your "Tools" are in the panel at the left.

{% icon hands_on %} Hands-on: Upload a file from URL

1. At the top of the Tools panel (on the left), click {% icon galaxy-upload %} Upload

   

   This brings up a box:

   {:width="500px"}

2. Click Paste/Fetch data

3. Paste in the address of a file:

   https://zenodo.org/record/582600/files/mutant_R1.fastq
   

4. Click Start

5. Click Close

{: .hands_on}

Your uploaded file is now in your current history. When the file has uploaded to Galaxy, it will turn green.

{% icon comment %} Comment

After this you will see your first history item (called a "dataset") in Galaxy's right panel. It will go through the gray (preparing/queued) and yellow (running) states to become green (success).

{: .comment}

What is this file?

{% icon hands_on %} Hands-on: View the dataset content

1. Click on the {% icon galaxy-eye %} (eye) icon next to the dataset name, to look at the file content

   {:width="320px"} {: .hands_on}

The contents of the file will be displayed in the central Galaxy panel.

This file contains DNA sequencing reads from a bacteria, in FASTQ format:

{:width="620px"}

Use a tool

Let's look at the quality of the reads in this file.

{% icon hands_on %} Hands-on: Use a tool

1. Type FastQC in the tools panel search box (top)

2. Click on the {% tool FastQC %} tool

   The tool will be displayed in the central Galaxy panel.

3. Select the following parameters:

   • {% icon param-file %} "Short read data from your current history": the FASTQ dataset that we uploaded
   • No change in the other parameters

4. Click Execute

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This tool will run and two new output datasets will appear at the top of your history panel.

View results

We will look at the output dataset called FastQC on data 1: Webpage.

{% icon comment %} Comment

• Note that Galaxy has given this dataset a name according to both the tool name ("FastQC") and the input ("data 1") that it used.
• The name "data 1" means the dataset number 1 in Galaxy's current history (our FASTQ file).

{: .comment}

{% icon hands_on %} Hands-on: View results

• Click on the {% icon galaxy-eye %} (eye) icon next to the "Webpage" output dataset.

  The information is displayed in the central panel

  {:width="620px"} {: .hands_on}

This tool has summarised information about all of the reads in our FASTQ file.

{% icon question %} Questions

1. What was the length of the reads in the input FASTQ file?
2. Do these reads have higher quality scores in the centre or at the ends?

{% icon solution %} Solutions

1. 150 bp
2. In the center {: .solution} {: .question}

Run another tool

Let's run a tool to filter out lower-quality reads from our FASTQ file.

{% icon hands_on %} Hands-on: Run another tool

1. Type Filter by quality in the tools panel search box (top)
2. Click on the tool {% tool Filter by quality %}
3. Set the following parameters:
   • {% icon param-file %} "Input FASTQ file": our initial FASTQ dataset
   • "Quality cut-off value": 35
   • "Percent of bases in sequence that must have quality equal to / higher than cut-off value": 80
4. Click Execute {: .hands_on}

After the tool has run, its output dataset will appear at the top of your History panel.

• This dataset will be called "Filter by quality on data 1".
• Remember that Galaxy has named this file according to the tool it used ("Filter by quality") and the input dataset ("data 1").
• The actual numbers in front of the datasets in the history are not important.

What are the results from this filtering tool?

We could click on the eye icon to view the contents of this output file, but it will not be very informative - we will just see a list of reads.

{% icon hands_on %} Hands-on: Get metadata about a file

1. Click on the output dataset name in the History panel.

   This expands the information about the file.

   

{: .hands_on}

{% icon question %} Questions

How many read has been discarded

{% icon solution %} Solutions

1786 low-quality reads were discarded {: .solution} {: .question}

Re-run that tool with changed settings

We have now decided that our input reads have to be filtered to an even higher standard. We will change the filter settings and re-run the tool.

{% icon hands_on %} Hands-on: Re-run the tool

1. Click on the {% icon galaxy-refresh %} icon (Run this job again) for the output dataset of Filter by quality {% icon tool %}

   

   This brings up the tool interface in the central panel with the parameters set to the values used previously to generate this dataset.

2. Change the settings to something even stricter

   For example, you might decide you want 80 percent of bases to have a quality of 36 or higher, instead of 35.

3. Click Execute

4. View the results: Click on the output dataset name to expand the information. (Note: not the {% icon galaxy-eye %} (eye) icon.) {: .hands_on}

{% icon question %} Questions

How many reads were discarded under these new filtering conditions?

{: .question}

You can re-run a tool many times with different settings. Each time you re-run the tool, its new output datasets will appear at the top of your current history.

Create a new history

Let's create a new history.

{% icon hands_on %} Hands-on: New history

1. Create a new history

   {% include snippets/create_new_history.md %}

2. Rename your history, e.g. "Next-analysis"

   {% include snippets/rename_history.md %}

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This new history does not have any datasets in it yet.

Look at all your histories

Where is your first history, called "my-analysis"?

{% icon hands_on %} Hands-on: View histories

1. Click on the View all histories ({% icon galaxy-columns %} icon) at the top right of your history

   {:width="320px"}

   A new page will appear with all your histories displayed here.

2. Copy a dataset into your new history

   1. Click on the FASTQ dataset in "my-analysis" history
   2. Drag it into the "Next-analysis" history

   This makes a copy of the dataset in the new history (without actually using additional disk space).

3. Click on Analyze Data in the top panel to go back to your analysis window

{: .hands_on}

Your main Galaxy window will now show the current history as "Next-analysis", and it will have one dataset in it.

At any time, you can go back into the "View all histories" page and "Switch to" a different history.

Conclusion

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{% icon trophy %} Well done! You have completed the short introduction to Galaxy, where you named the history, uploaded a file, used a tool, and viewed results. Additional tutorials are available for a more in-depth introduction to Galaxy's features.