| 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
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