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Deploying the khmer project tools on Galaxy
===========================================

We are developing the support for running normalize-by-median in `Galaxy 
<http://galaxyproject.org/>`__.

When this is mature we will make a Galaxy `Tool Shed <https://wiki.galaxyproject.org/Tool%20Shed>`__
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" />
  </section>

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
<https://wiki.galaxyproject.org/Learn/Datatypes>`__.

#. 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 :doc:`choosing-table-sizes` for assistance.