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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 tag::
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 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.