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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
author bebatut
date Tue, 08 Dec 2015 10:35:06 -0500
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04749f9173e5 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
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1 Galaxy wrapper for Reago
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2 ========================
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4 PRINSEQ is an assembly tool for 16S ribosomal RNA recovery from metagenomic data.
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5 For more information, check the
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6 [Github repository](https://github.com/chengyuan/reago-1.1)
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8 # Installation
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10 ## Automated installation
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12 On a Galaxy instance, the wrapper 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 tool and data, ...
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16 ## Manual installation
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18 For manual installation, the files `reago.xml` and `format_reago_input_files.py`
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19 must be put in the `tools/reago/` folder and add the XML files to Galaxy's
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20 `tool_conf.xml` (in `config` folder) as
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21 normal:
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23 ```
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24 <section name="Assemble 16S rRNA" id="reago">
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25 <tool file="reago/reago.xml" />
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26 </section>
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27 ```
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29 PRINSEQ must be installed somewhere on the system path. It can be done using:
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31 ```
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32 planemo dependency_script ~/repositories/galaxytools/packages/package_genometools_1_5_7/
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33 bash dep_install.sh
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34 source env.sh
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36 planemo dependency_script ~/repositories/galaxytools/tools/reago/
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37 bash dep_install.sh
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38 source env.sh
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39 ```
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41 To test the Galaxy integration, the functional tests can be runned:
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43 ```
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44 ./run_tests.sh -sid reago
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45 ```
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47 # Bug Reports
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49 Any bug can be filed in an issue [here](https://github.com/ASaiM/galaxytools/issues).
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51 # Developers
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53 A release can be pushed to the test or main "Galaxy Tool Shed", using the following
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54 Planemo commands (with required Tool Shed access detailed in `~/.planemo.yml`):
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56 ```
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57 planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxytools/tools/reago/
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58 ```
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60 or:
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62 ```
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63 planemo shed_update -t toolshed --check_diff ~/repositories/galaxytools/tools/reago/
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64 ```
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66 # License (Apache 2)
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68 This wrapper are released under Apache 2 License. See the [LICENSE file](https://github.com/ASaiM/galaxytools/blob/master/LICENSE) for details