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 specify if they are paired-interleaved or not.
#. Specify the sample type or show the advanced parameters to set the tablesize yourself. Consult Choosing table sizes for khmer for assistance.