Setting up CowPi on your Aberystwyth University Galaxy Account

To run CowPi on the Aberystwyth University Galaxy server, there are a few setup steps required, the first time you use CowPi. Note, it should only be necessary to do these steps once, afterwards everything should be ready for running CowPi every time you log into Galaxy. This walkthrough has been provided on the CowPi website:  

Step 1: Register and Log in

On the homepage register for an account under the “login” link, and then log in (Figure 1).

Step 2: Navigate to the Shared workflows

The individual tools for COWPI are found on the left under the “CowPi” link, however a dedicated workflow is also available which runs all the steps together. To access this workflow, you need to import it into your account.
To do this go to “Shared Data”, and click on “Workflows” (Figure 2).

Here you will see a list of published workflows, one of which is CowPi (sometimes called BeefPi, depending on the system). On this page, click on the name of the workflow and click on “import”. This will import the workflow into your account (Figure 3).

Step 3: Import the Cowpi (Beefpie) workflow

Once imported, the workflow will appear under your list of “Workflows” in the top bar.

To run the workflow, click on the grey bar and click on “Run” (Figure 4).

This will bring you to the page where you can run the CowPi workflow (Figure 5).

Step 4: Import data files into your Galaxy History.

As some of the data files used in CowPi are too big for individual upload, we have provided a “shared data library” on Galaxy that contains the necessary data. This can be imported into your Galaxy account allowing access to these large data files.
These are the same files as available through the CowPi website (

When logged into your Galaxy account in Aberystwyth University import these data files by carrying out the following steps (note this should only ever have to be done once for any user account) :

On the main Galaxy webpage go to “Shared Data” and click on “Data Libraries” (Figure 6)

This will bring you to a page showing all available data libraries. One of these will be “CowPi Precalculated Files”, click on this link (Figure 7).

This will show you the contents of the shared data library and allow you to select those that you wish to import into your history.
To do this, tick the boxes on the left-hand side as shown below and then click on thebutton to copy the data to your history (Figure 8).

Your account should now be ready to run CowPi. Please refer to the Tutorial document on for a walkthrough on how to analsye data with CowPi.