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author bebatut
date Mon, 16 Nov 2015 02:46:50 -0500
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73b3e2f98631 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/rdptools commit fa8135b9b1918785c3f3b3fb7325bfe031b44ec4
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1 Galaxy wrapper for RDPTools
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2 ===========================
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4 RDPTols is an open source command-line tool suite for performing a complete
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5 workflow of analysis tasks of NGS data. For more information, check the
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6 [Github repository](https://github.com/rdpstaff/RDPTools)
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8 # Installation
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10 ## Automated installation
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12 On a Galaxy instance, the wrappers can be automatically installed using the
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13 ToolShed. This will automatically install the dependencies, configure the Galaxy
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14 instance for the tools and data, ...
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16 ## Manual installation
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18 For manual installation, the `.xml` files must be put in the `tools/rdptools/`
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19 folder and add the XML files to Galaxy's `tool_conf.xml` (in `config` folder) as
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20 normal:
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22 ```
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23 <section name="RDPTools" id="rdptools">
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24 <tool file="rdptools/framebot.xml" />
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25 </section>
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26 ```
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28 The database must also be referenced in Galaxy. The files in `tool-data/`
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29 must be copied in Galaxy's `tool-data` folder. And Galaxy's `config/tool_data_table_conf.xml.sample`
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30 have to be completed:
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32 ```
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33 !-- Locations of public ribosomal databases -->
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34 <table name="framebot_ref_gene_databases" comment_char="#">
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35 <columns>value, name, path</columns>
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36 <file path="tool-data/framebot_ref_gene_databases.loc" />
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37 </table>
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38 ```
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40 RDPTools must be installed somewhere on the system path. It can be done using:
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42 ```
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43 planemo dependency_script ~/repositories/galaxytools/packages/package_ant_1_9_6/
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44 bash dep_install.sh
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45 source env.sh
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47 planemo dependency_script ~/repositories/galaxytools/tools/rdptools/
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48 bash dep_install.sh
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49 source env.sh
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50 ```
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52 To test the Galaxy integration, the functional tests can be runned:
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54 ```
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55 ./run_tests.sh -sid rdptools
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56 ```
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58 # Bug Reports
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59
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60 Any bug can be filed in an issue [here](https://github.com/ASaiM/galaxytools/issues).
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62 # Developers
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64 A release can be pushed to the test or main "Galaxy Tool Shed", using the following
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65 Planemo commands (with required Tool Shed access detailed in `~/.planemo.yml`):
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67 ```
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68 planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxytools/tools/rdptools/
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69 ```
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71 or:
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73 ```
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74 planemo shed_update -t toolshed --check_diff ~/repositories/galaxytools/tools/rdptools/
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75 ```
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77 # License (Apache 2)
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79 This wrapper are released under Apache 2 License. See the [LICENSE file](https://github.com/ASaiM/galaxytools/blob/master/LICENSE) for details