diff README @ 0:baf52103977b draft

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+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 <[e-mail]>
+
+Repository: [https://bitbucket.org/lance_parsons/cutadapt\_galaxy\_wrapper](https://bitbucket.org/lance_parsons/cutadapt_galaxy_wrapper)