We are developing the support for running normalize-by-median in Galaxy.
When this is mature we will make a Galaxy Tool Shed version available for easier installation.
If your installation uses a virtualenv be sure to activate it in your terminal before continuing.
pip install --no-clean khmer
Move to the tools directory in your Galaxy installation and copy in the tool definition file.:
cd tools
mkdir khmer
ln -s build/khmer/scripts/normalize-by-median.xml .
Add the following to your tool_conf.xml inside the <toolbox> tag:
<section id="khmer-protocols-extra" name="khmer protocols">
<tool file="khmer/normalize-by-median.xml" />
</section>
Then (re)start Galaxy.
For one or more files into a single file:
#. Choose ‘Normalize By Median’ from the ‘khmer protocols’ section of the ‘Tools’ menu.
#. Compatible files already uploaded to your Galaxy instance should be listed. If not then you may need to set their datatype manually.
#. After selecting the input files specift if they are paired-interleaved or not.
#. Specify the sample type or show the advanced parameters to set the hashsize yourself. Consult Choosing hash sizes for khmer for assistance.
This file can be edited directly through the Web. Anyone can update and fix errors in this document with few clicks -- no downloads needed.
For an introduction to the documentation format please see the reST primer.