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author bebatut
date Thu, 05 Nov 2015 10:31:59 -0500
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1 Galaxy wrapper for MetaPhlAn2
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2 =============================
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4 MetaPhlAn is a computational tool for profiling the composition of microbial
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5 communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun
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6 sequencing data with species level resolution. For more information, check the
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7 [user manual](https://bitbucket.org/biobakery/metaphlan2)
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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 `metaphlan2.xml` must be put in the `tools/metaphlan2/`
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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 community composition" id="metaphlan2">
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25 <tool file="metaphlan2/metaphlan2.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/metaphlan2/
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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 metaphlan2
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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/metaphlan2/
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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/metaphlan2/
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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