Galaxy tool definition for cutadapt (

Installation - Tool Shed

The recommended way to install cutadapt as a tool in Galaxy is to the use the
Galaxy Tool Shed (

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/ -id cutadapt
    See the Galaxy Wiki for more information:

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 <>

Repository: [\_galaxy\_wrapper](