Mercurial > repos > bebatut > metaphlan_2
comparison README.md @ 0:8b151cff43e0 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 89a1d80e981c147c87c892384afd8411dccfd8a1-dirty
| author | bebatut |
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| date | Thu, 17 Dec 2015 04:03:29 -0500 |
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| -1:000000000000 | 0:8b151cff43e0 |
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| 1 Galaxy wrapper for MetaPhlAn2 | |
| 2 ============================= | |
| 3 | |
| 4 MetaPhlAn is a computational tool for profiling the composition of microbial | |
| 5 communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun | |
| 6 sequencing data with species level resolution. For more information, check the | |
| 7 [user manual](https://bitbucket.org/biobakery/metaphlan2) | |
| 8 | |
| 9 # Installation | |
| 10 | |
| 11 ## Automated installation | |
| 12 | |
| 13 On a Galaxy instance, the wrapper can be automatically installed using the | |
| 14 ToolShed. This will automatically install the dependencies, configure the Galaxy | |
| 15 instance for the tool and data, ... | |
| 16 | |
| 17 ## Manual installation | |
| 18 | |
| 19 For manual installation, the files `metaphlan2.xml` must be put in the `tools/metaphlan2/` | |
| 20 folder and add the XML files to Galaxy's `tool_conf.xml` (in `config` folder) as | |
| 21 normal: | |
| 22 | |
| 23 ``` | |
| 24 <section name="Profile microbial community composition" id="metaphlan2"> | |
| 25 <tool file="metaphlan2/metaphlan2.xml" /> | |
| 26 </section> | |
| 27 ``` | |
| 28 | |
| 29 MetaPhlAn2 must be installed somewhere on the system path. It can be done using: | |
| 30 | |
| 31 ``` | |
| 32 planemo dependency_script ~/repositories/galaxytools/tools/metaphlan2/ | |
| 33 bash dep_install.sh | |
| 34 source env.sh | |
| 35 ``` | |
| 36 | |
| 37 To test the Galaxy integration, the functional tests can be runned: | |
| 38 | |
| 39 ``` | |
| 40 ./run_tests.sh -sid metaphlan2 | |
| 41 ``` | |
| 42 | |
| 43 # Bug Reports | |
| 44 | |
| 45 Any bug can be filed in an issue [here](https://github.com/ASaiM/galaxytools/issues). | |
| 46 | |
| 47 # Developers | |
| 48 | |
| 49 A release can be pushed to the test or main "Galaxy Tool Shed", using the following | |
| 50 Planemo commands (with required Tool Shed access detailed in `~/.planemo.yml`): | |
| 51 | |
| 52 ``` | |
| 53 planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxytools/tools/metaphlan2/ | |
| 54 ``` | |
| 55 | |
| 56 or: | |
| 57 | |
| 58 ``` | |
| 59 planemo shed_update -t toolshed --check_diff ~/repositories/galaxytools/tools/metaphlan2/ | |
| 60 ``` | |
| 61 | |
| 62 # License (Apache 2) | |
| 63 | |
| 64 This wrapper are released under Apache 2 License. See the [LICENSE file](https://github.com/ASaiM/galaxytools/blob/master/LICENSE) for details |