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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit e5b8f29dde45dddcda6ee283212dd1bdde487f87-dirty
author bebatut
date Fri, 18 Dec 2015 09:04:07 -0500
parents 947012405a6e
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1 Galaxy wrapper for HUMAnN2
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2 ==========================
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4 HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence
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5 and abundance of microbial pathways in a community from metagenomic or
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6 metatranscriptomic sequencing data. For more information, check the
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7 [user manual](http://huttenhower.sph.harvard.edu/humann2/manual)
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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 `humann2.xml` must be put in the `tools/humann2/`
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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="Profile microbial pathways in a community" id="humann2">
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25 <tool file="humann2/humann2.xml" />
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26 </section>
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27 ```
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29 MetaPhlAn2 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/humann2/
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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 humann2
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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/humann2/
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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/humann2/
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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