Mercurial > repos > lparsons > cutadapt

Galaxy tool definition for cutadapt (http://code.google.com/p/cutadapt/)


Installation - Tool Shed
------------------------

The recommended way to install cutadapt as a tool in Galaxy is to the use the
Galaxy Tool Shed (http://wiki.galaxyproject.org/Tool%20Shed).

This will allow cutadapt to be installed automatically and keep track of older
versions of cutadapt and the tool wrapper.


Installation - Manual
---------------------

1. Install the cutadapt package and make sure it is in path for Galaxy

2. Copy cutadapt.xml to $GALAXY_HOME/tools/cutadapt

3. Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file

    **Optional steps to setup and run Galaxy functional tests**

4. Copy test-data/* to $GALAXY_HOME/test-data/

5. Set GALAXY_TEST_TOOL_CONF environment variable to a tool_conf.xml file that
    contains the tools you want to test. (e.g. 'tool_conf.xml')

6. $GALAXY_HOME/run_functional_tests.sh -id cutadapt
    See the Galaxy Wiki for more information: http://wiki.g2.bx.psu.edu/


Configuration of Adapters
-------------------------

A list of predefined adapters may be specified in the cutadapt_adapters.txt
file which resides in the tool-data directory underneath the Galaxy root.  A sample
file is provided.


Limitations of the Galaxy wrapper
---------------------------------

Reading adapters from a fasta file is not supported
Colorspace data support is not implemented
Only one "Strip suffix" is suppored


Galaxy Wrapper Development
--------------------------

Author: Lance Parsons <lparsons@princeton.edu>

Repository: [https://bitbucket.org/lance_parsons/cutadapt\_galaxy\_wrapper](https://bitbucket.org/lance_parsons/cutadapt_galaxy_wrapper)
author	lparsons
date	Mon, 06 Oct 2014 13:47:56 -0400
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