PICRUSt within Galaxy

This repository provides the configuration files allowing PICRUSt to be used within Galaxy.

These files are not needed to run PICRUSt from the command line.

Install

This describes the steps of getting PICRUSt installed in Galaxy.

1. Install Galaxy. Note that you will need to create new versions of the configuration files you want to edit with ".sample" removed.

2. Install PICRUSt. Including the download of ALL precalculated PICRUSt files from this page: http://picrust.github.io/picrust/picrust_precalculated_files.html. You may need to install this tool and others in the Galaxy Python virtual environment by running ". galaxy/.venv/bin/activate" first.

3. From within your galaxy-dist/tools directory, download the picrust_galaxy files:

   git clone git://github.com/picrust/picrust_galaxy.git picrust_galaxy

4. Copy or link to the following installed PICRUSt scripts (typically found in /usr/bin/local) to galaxy-dist/tools/picrust_galaxy directory.

   • normalize_by_copy_number.py
   • predict_metagenomes.py
   • categorize_by_function.py
   • metagenome_contributions.py

5. Add the following to the file galaxy-dist/tool_conf.xml:

   <section name="PICRUSt" id="PICRUSt">  
       <tool file="picrust_galaxy/normalize.xml"/>  
       <tool file="picrust_galaxy/predict.xml"/>  
       <tool file="picrust_galaxy/categorize.xml"/>  
       <tool file="picrust_galaxy/metagenome.xml"/>  
   </section>  

6. Add the following to the file galaxy-dist/datatypes_conf.xml:

   <datatype extension="biom" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true" />  

7. Restart Galaxy