The impatient guide to running CowPi on Galaxy

Step 1: Set up an account and import the necessary pre-calculated files

The CowPi workflow is provided free for use by the wider scientific community at Aberystwyth University. A full description of how to set up your Galaxy account, the work flow and how to import pre-calculated files is provided here:

Step 2: Upload your files to Galaxy.

You need a fasta formatted OTU file like in Figure 1 and a tab-delimited OTU count table for each of your samples as shown in Figure 2. Two example files are provided ‘timecourseOTU.fa’ and ‘OTU_Table.txt’.

Step 3: In the CowPi workflow, select the correct files for each step.

Choose the following options (as shown in :
1: (Usearch):
Select the OTU fasta file (timecourseOTU.fa) in step 1 and enter country and institute information.

2: (Extract Names):
Change nothing.

3: (Rstep)
Select the OTU count data (timecourseOTU.fa).

4: (Convert BIOM)
            Change nothing.

5: (Normalize)
            Select the precalcuated 16S copy-number file (

6: (Predict Metagenome)
            Select the precalcaulted KO abundance files (

7: (Categorize)
            Change nothing.

Then click “Run Workflow”.