Galaxy is a platform for doing reproducible bioinformatics research. It provides a friendly interface to a vast number of complex command line tools, and it encourages consistent science by using identical software and interfaces across all Galaxy instances.
At the CPT we depend on Galaxy for all of our computer-based analysis; we can launch long running jobs and return to our lab work, while Galaxy keeps track of where and how far along our analysis is, during runs of our pipelines.
Galaxy consists of a three panel interface. On the left are your tools, in the center you’ll do your analysis and view the results, and on the right is your history.
These are all groups of tools you can run in Galaxy. A tool is something that generates or transforms data. Some examples of tools would be a Gene Caller, which reads your genome and returns a list of gene locations, or Blast, which would search your protein sequences against a database.
In Galaxy, tools are simple interfaces to the complex software behind them. Galaxy tools enhance productivity by ensuring that your input files are the correct format at every step.
The history panel keeps track of what you’ve done. Each entry is called a “dataset” in Galaxy terminology. Datasets are usually just a single file (like a fasta genome), but may be complex files (like html web pages). The colors indicate in which of the three states a job could be; grey for jobs that have been submitted to Galaxy, yellow for a jobs that are currently running, and red/green for a jobs that are completed.
Warning
Sometimes jobs fail and turn red! If they do, don’t worry–it likely isn’t your fault. Just be sure to click the bug icon so we can be made aware of what went wrong.
Tools are the central feature of Galaxy, they’re what Galaxy is all about: easy-to-use access to powerful command line tools. We use the language “tool” to describe some command line program that has been “wrapped” for use in Galaxy. Many of the command line options are available to be tweaked and fiddled with in the Galaxy tool interface.
To run a tool, first read the tool’s help box at the bottom, it may give you very important information regarding running the tool, and the options available to you.
Next go over the options in the tool interface, many are set to default values and those options may not be what you intended to happen.
Nearly all Galaxy tools process some input files and produce some output files. When you have an input box that lets you select a file, Galaxy will ensure that you cannot pass datasets of an incorrect format to a tool.
When you’ve finished configuring a tool, and execute it, it will show up as a set of output files in the history on the right, which we’ll cover in the next section..
A job is a tool run with a set of parameters, and it sits somewhere in Galaxy’s queue. We have lots of Galaxy users and can only run so many jobs at once. Jobs produce one or more output files.
Looking at an individual output dataset, there will be several features that will be of interest to you, and a couple that won’t:
In this example we see dataset #29, which is a table of Start Codon Usages.
This is the collapsed view of a dataset. You’ll see three icons, an eye, a pencil, and an X.
When you delete a dataset accidentally, don’t worry! It isn’t gone permanently.
See the text “6 deleted”? Clicking on the word “deleted” will show you the deleted items in your history.
Clicking anywhere on the title of the dataset, “Start Codon Usages” will expand to the full view:
At the bottom of the dataset you can see a preview of the table. Near the top you’ll note the it is a “tabular” format. Galaxy keeps track of file formats to ensure you only use correctly-formatted data for tools.
The history dataset view is information dense, so we’ll go over the icons, their colloquial names, and their functions.
Histories are used to separate out your analyses and help you keep track of what you’ve done. You might make a new history for a task like assembling a genome, annotating a genome, or doing some comparative analysis between phages. It’s good practice to title your history something that will be useful to you when you come back later. Who knows what “Untitled History” last edited on 2012-02-01 was for? Good names are important!
At the top right of your history you’ll see a couple icons. A refresh symbol, a gear, and the new history view.
The refresh button can be used to refresh your history if you’re impatient, like I can be. The gear icon provides you with the old interface to switch histories and modify the view. We’ll be using the new “View all histories” view:
At the top left you’ll see a done button, which will let you exit this view when you’re done. On the left is your current history. To the right of that are your other histories. The switch to button allows you to switch histories. Any new tools you run will be done in this history.
Switch back to the main view of Galaxy (i.e. click done if you’re still in the switch history menu from above). If you ever find yourself lost in Galaxy, you can always click Analyze Data on the big blue bar at the top, and it’ll take you home.
This button will bring up your upload menu and allow you to import data into Galaxy.
You can drag and drop files to upload them, or use the Choose Local File button in the bottom menu.
There are a couple other options for advanced users:
Once the file has been detected by Galaxy, you’ll see it pop up in the upload window:
You can set the file type if Galaxy doesn’t detect it properly, but that is a rare case, and before overriding Galaxy you should double check that your file is formatted properly.
When you’ve selected all the files you wish to upload, click Start in the bottom right of the upload menu.
The dataset will indicate to you that it is uploaded in the upload window,
at which time you can close that window with Escape or the Close button in the bottom right.
The dataset will turn yellow
And then green when it is ready.
Workflows are merely collections of jobs where some jobs depend on the outputs of other jobs. Say you’re faced with a task like the following:
If you did these tasks one by one, you would have to keep track of at least 4 different files, one as the output of each step. You have to wait for each program to finish, before you can execute the next one. What if step 2 took 10 minutes? And Step 3 took 15? You would have to check back every few minutes to see if your job was done before you could start the next.
Thus, enter workflows:
Workflows solve numerous problems for us:
You will often be asked to import workflows. You can do this by going to the Published Workflow page, and finding a workflow you’re interested in.
Workflows which you have created, or imported, are available under the Workflow menu at the top of Galaxy.
The run workflow interface can be somewhat overwhelming. For the large part, the tools are pre-configured for you. As the course progresses we’ll cover in detail what each portion of the workflow does.
Just like with tools, there is an Execute button at the bottom which will launch the workflow.
At this point you should be fairly comfortable: