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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/prinseq/ commit 283fe2285a4e95f4505133fc7fa1eee96a4d274d
author bebatut
date Tue, 17 Nov 2015 06:02:09 -0500
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1 Galaxy wrapper for PRINSEQ
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2 ===========================
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4 PRINSEQ is a tool for easy and rapid quality control and data processing of
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5 metagenomic and metatranscriptomic datasets. This tool allow to process the
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6 sequences with filtering and trimming. For more information, check the
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7 [user manual](http://prinseq.sourceforge.net/manual.html)
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9 # Installation
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11 ## Automated installation
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13 On a Galaxy instance, the wrapper can be automatically installed using the
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14 ToolShed. This will automatically install the dependencies, configure the Galaxy
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15 instance for the tool and data, ...
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17 ## Manual installation
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19 For manual installation, the files `prinseq.xml` must be put in the `tools/prinseq/`
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20 folder and add the XML files to Galaxy's `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="Control quality" id="prinseq">
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25 <tool file="prinseq/prinseq.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/tools/prinseq/
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33 bash dep_install.sh
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34 source env.sh
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35 ```
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37 To test the Galaxy integration, the functional tests can be runned:
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39 ```
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40 ./run_tests.sh -sid prinseq
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41 ```
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43 # Bug Reports
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45 Any bug can be filed in an issue [here](https://github.com/ASaiM/galaxytools/issues).
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47 # Developers
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49 A release can be pushed to the test or main "Galaxy Tool Shed", using the following
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50 Planemo commands (with required Tool Shed access detailed in `~/.planemo.yml`):
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52 ```
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53 planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxytools/tools/prinseq/
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54 ```
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56 or:
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58 ```
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59 planemo shed_update -t toolshed --check_diff ~/repositories/galaxytools/tools/prinseq/
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60 ```
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62 # License (Apache 2)
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64 This wrapper are released under Apache 2 License. See the [LICENSE file](https://github.com/ASaiM/galaxytools/blob/master/LICENSE) for details