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Support for cutadapt 0.9.5, added quality trimming and additional output options
author Lance Parsons <lparsons@princeton.edu>
date Fri, 22 Jul 2011 11:03:00 -0400
parents 8b064ea16722
children 2d6671b10919
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Galaxy tool definition for cutadapt (http://code.google.com/p/cutadapt/)

Installation
------------

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/


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

Colorspace data support is not implemented
Prefix and Suffix to read names not implemented
Length-tag addition to read name not implemented