view README @ 8:2d6671b10919 draft

Updated to support cutadapt version 1.1 (also include automatic dependency installation)

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 fastx_clipper_sequences.txt
file which resides in the tool-data directory underneath the Galaxy root.  A sample
file is provided.


Limitations
-----------

Colorspace data support is not implemented
Name adapters support is not implemented