Deploying the khmer project tools on Galaxy

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.

Install the tools & tool description

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" />

Then (re)start Galaxy.

Single Output Usage

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.

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