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annotate README @ 8:2d6671b10919 draft

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Updated to support cutadapt version 1.1 (also include automatic dependency installation)
author lparsons
date Mon, 26 Nov 2012 17:37:26 -0500
parents 1dada50cca8a
children 93d58ffe39f1
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1 Galaxy tool definition for cutadapt (http://code.google.com/p/cutadapt/)
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4 Installation - Tool Shed
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5 ---------------------------
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7 The recommended way to install cutadapt as a tool in Galaxy is to the use the
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8 Galaxy Tool Shed (http://wiki.galaxyproject.org/Tool%20Shed).
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10 This will allow cutadapt to be installed automatically and keep track of older
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11 versions of cutadapt and the tool wrapper.
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14 Installation - Manual
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15 ---------------------
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17 1 - Install the cutadapt package and make sure it is in path for Galaxy
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18 2 - Copy cutadapt.xml to $GALAXY_HOME/tools/cutadapt
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19 3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file
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21 Optional steps to setup and run Galaxy functional tests
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23 4 - Copy test-data/* to $GALAXY_HOME/test-data/
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24 5 - Set GALAXY_TEST_TOOL_CONF environment variable to a tool_conf.xml file that
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25 contains the tools you want to test. (e.g. 'tool_conf.xml')
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26 6 - $GALAXY_HOME/run_functional_tests.sh -id cutadapt
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27 See the Galaxy Wiki for more information: http://wiki.g2.bx.psu.edu/
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30 Configuration of Adapters
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31 -------------------------
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33 A list of predefined adapters may be specified in the fastx_clipper_sequences.txt
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34 file which resides in the tool-data directory underneath the Galaxy root. A sample
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35 file is provided.
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38 Limitations
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39 -----------
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41 Colorspace data support is not implemented
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42 Name adapters support is not implemented