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1 Galaxy tool definition for cutadapt (http://code.google.com/p/cutadapt/)
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2
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3
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4 Installation - Tool Shed
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5 ------------------------
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6
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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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9
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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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12
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13
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14 Installation - Manual
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15 ---------------------
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16
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17 1. Install the cutadapt package and make sure it is in path for Galaxy
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18
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19 2. Copy cutadapt.xml to $GALAXY_HOME/tools/cutadapt
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20
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21 3. Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file
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22
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23 **Optional steps to setup and run Galaxy functional tests**
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24
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25 4. Copy test-data/* to $GALAXY_HOME/test-data/
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26
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27 5. Set GALAXY_TEST_TOOL_CONF environment variable to a tool_conf.xml file that
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28 contains the tools you want to test. (e.g. 'tool_conf.xml')
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29
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30 6. $GALAXY_HOME/run_functional_tests.sh -id cutadapt
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31 See the Galaxy Wiki for more information: http://wiki.g2.bx.psu.edu/
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32
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33
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34 Configuration of Adapters
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35 -------------------------
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36
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37 A list of predefined adapters may be specified in the cutadapt_adapters.txt
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38 file which resides in the tool-data directory underneath the Galaxy root. A sample
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39 file is provided.
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40
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41
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42 Limitations of the Galaxy wrapper
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43 ---------------------------------
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44
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45 Reading adapters from a fasta file is not supported
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46 Colorspace data support is not implemented
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47 Only one "Strip suffix" is suppored
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48
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49
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50 Galaxy Wrapper Development
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51 --------------------------
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52
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53 Author: Lance Parsons <lparsons@princeton.edu>
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54
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55 Repository: [https://bitbucket.org/lance_parsons/cutadapt\_galaxy\_wrapper](https://bitbucket.org/lance_parsons/cutadapt_galaxy_wrapper)
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