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: www.cowpi.org.
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 (www.cowpi.org).
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 the
button to copy the data to your history (Figure 8).
button 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 http://www.cowpi.org/p/tutorial.html for
a walkthrough on how to analsye data with CowPi.