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author bebatut
date Tue, 10 Nov 2015 04:05:25 -0500
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1 Galaxy wrapper for SortMeRNA
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2 ============================
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4 SortMeRNA is a tool for RNA filtering based on local sequence alignment against
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5 rRNA database. For more information, check the [user manual](http://bioinfo.lifl.fr/RNA/sortmerna/code/SortMeRNA-user-manual-v1.7.pdf)
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7 # Installation
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9 ## Automated installation
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11 On a Galaxy instance, the wrapper can be automatically installed using the
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12 ToolShed. This will automatically install the dependencies, configure the Galaxy
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13 instance for the tool and data, ...
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15 ## Manual installation
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17 For manual installation, the files `sortmerna.xml` must be put in the `tools/sortmerna/`
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18 folder and add the XML files to Galaxy's `tool_conf.xml` (in `config` folder) as
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19 normal:
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21 ```
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22 <section name="Sort RNA" id="sortmerna">
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23 <tool file="sortmerna/sortmerna.xml" />
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24 </section>
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25 ```
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27 The SortMeRNA database must also be referenced in Galaxy. The `tool-data/sortmerna_rRNA_databases.loc.sample`
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28 must be copy in Galaxy's `tool-data` folder. And Galaxy's `config/tool_data_table_conf.xml.sample`
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29 have to be completed:
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31 ```
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32 !-- Locations of public ribosomal databases -->
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33 <table name="sortmerna_rRNA_databases" comment_char="#">
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34 <columns>value, name, path</columns>
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35 <file path="tool-data/sortmerna_rRNA_databases.loc" />
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36 </table>
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37 ```
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39 SortMeRNA must be installed somewhere on the system path. It can be done using:
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41 ```
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42 planemo dependency_script ~/repositories/galaxytools/tools/sortmerna/
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43 bash dep_install.sh
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44 source env.sh
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45 ```
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47 To test the Galaxy integration, the functional tests can be runned:
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49 ```
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50 ./run_tests.sh -sid sortmerna
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51 ```
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53 # Bug Reports
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55 Any bug can be filed in an issue [here](https://github.com/ASaiM/galaxytools/issues).
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57 # Developers
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59 A release can be pushed to the test or main "Galaxy Tool Shed", using the following
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60 Planemo commands (with required Tool Shed access detailed in `~/.planemo.yml`):
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62 ```
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63 planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxytools/tools/sortmerna/
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64 ```
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66 or:
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68 ```
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69 planemo shed_update -t toolshed --check_diff ~/repositories/galaxytools/tools/sortmerna/
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70 ```
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72 # License (Apache 2)
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74 This wrapper are released under Apache 2 License. See the [LICENSE file](https://github.com/ASaiM/galaxytools/blob/master/LICENSE) for details