<commit_before>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.

Checkout and install the branch of the Git repository where development of
this feature is ongoing.::

  pip install -e git+https://github.com/ged-lab/khmer.git@output_naming1#khmer


Move to the `tools` directory in your Galaxy installation and copy in the
tool definition file.::

  cd tools
  mkdir khmer
  ln -s ../src/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.

Usage
-----

<commit_msg>more deets<commit_after>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.

Checkout and install the branch of the Git repository where development of
this feature is ongoing.::

  pip install -e git+https://github.com/ged-lab/khmer.git@output_naming1#khmer


Move to the `tools` directory in your Galaxy installation and copy in the
tool definition file.::

  cd tools
  mkdir khmer
  ln -s ../src/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 specift if they are paired-interleaved
or not.

#. Specify the sample type or show the advanced parameters to set the hashsize
yourself. Consult :doc:`choosing-hash-sizes` for assistance.


{'fraction_non_alphanumeric': 0.14175167077031306, 'fraction_numerical': 0.002110446711220542, 'mean_word_length': 3.700826446280992, 'pattern_counts': {'":': 0, '<': 16, '<?xml version=': 0, '>': 16, 'https://': 5, 'lorem ipsum': 0, 'www.': 0, 'xml': 6}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1249010', 'n_tokens_mistral': 823, 'n_tokens_neox': 769, 'n_words': 318}