weeder2: motif discovery in sequences from coregulated genes of a single species
================================================================================

Galaxy tool for the Weeder2 motif discovery package:

- Zambelli, F., Pesole, G. and Pavesi, G. 2014. Using Weeder, Pscan, and PscanChIP
  for the Discovery of Enriched Transcription Factor Binding Site Motifs in
  Nucleotide Sequences. Current Protocols in Bioinformatics. 47:2.11:2.11.1–2.11.31.
  http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0211s47/full

See http://159.149.160.51/modtools/

Automated installation
======================

Installation via the Galaxy Tool Shed will take of installing the tool wrapper and
the Weeder2 program and data, and setting the appropriate environment variables.

Manual Installation
===================

There are two files to install:

- ``weeder2_wrapper.xml`` (the Galaxy tool definition)
- ``weeder2_wrapper.sh`` (the shell script wrapper)

The suggested location is in a ``tools/weeder2/`` folder. You will then
need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
by adding the line:

    <tool file="weeder2/weeder2_wrapper.xml" />

You will also need to install ``weeder2`` from:

- http://159.149.160.51/modtools/downloads/weeder2.html

The tool wrapper uses the following environment variables in order to find the
appropriate files:

- ``WEEDER_FREQFILES_DIR`` should point to the ``FreqFiles`` directory

Also the directory holding the Weeder2 executables should be on your ``PATH``.

If you want to run the functional tests, copy the sample test files under
sample test files under Galaxy's ``test-data/`` directory. Then:

    ./run_tests.sh -id trimmomatic

You will need to have set the environment variables above.

History
=======

========== ======================================================================
Version    Changes
---------- ----------------------------------------------------------------------
2.0.0.0    - Initial version
========== ======================================================================


Developers
==========

This tool is developed on the following GitHub repository:
https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/weeder2

For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
the ``package_weeder2.sh`` script.


Licence (MIT)
=============

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in the Software without restriction, including without limitation the rights
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