Mercurial > repos > bebatut > reago
comparison README.md @ 0:04749f9173e5 draft default tip
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/reago commit 3be2f6bc80a4743256b13ed64500448e766ddcd7
| author | bebatut |
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| date | Tue, 08 Dec 2015 10:35:06 -0500 |
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| -1:000000000000 | 0:04749f9173e5 |
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| 1 Galaxy wrapper for Reago | |
| 2 ======================== | |
| 3 | |
| 4 PRINSEQ is an assembly tool for 16S ribosomal RNA recovery from metagenomic data. | |
| 5 For more information, check the | |
| 6 [Github repository](https://github.com/chengyuan/reago-1.1) | |
| 7 | |
| 8 # Installation | |
| 9 | |
| 10 ## Automated installation | |
| 11 | |
| 12 On a Galaxy instance, the wrapper can be automatically installed using the | |
| 13 ToolShed. This will automatically install the dependencies, configure the Galaxy | |
| 14 instance for the tool and data, ... | |
| 15 | |
| 16 ## Manual installation | |
| 17 | |
| 18 For manual installation, the files `reago.xml` and `format_reago_input_files.py` | |
| 19 must be put in the `tools/reago/` folder and add the XML files to Galaxy's | |
| 20 `tool_conf.xml` (in `config` folder) as | |
| 21 normal: | |
| 22 | |
| 23 ``` | |
| 24 <section name="Assemble 16S rRNA" id="reago"> | |
| 25 <tool file="reago/reago.xml" /> | |
| 26 </section> | |
| 27 ``` | |
| 28 | |
| 29 PRINSEQ must be installed somewhere on the system path. It can be done using: | |
| 30 | |
| 31 ``` | |
| 32 planemo dependency_script ~/repositories/galaxytools/packages/package_genometools_1_5_7/ | |
| 33 bash dep_install.sh | |
| 34 source env.sh | |
| 35 | |
| 36 planemo dependency_script ~/repositories/galaxytools/tools/reago/ | |
| 37 bash dep_install.sh | |
| 38 source env.sh | |
| 39 ``` | |
| 40 | |
| 41 To test the Galaxy integration, the functional tests can be runned: | |
| 42 | |
| 43 ``` | |
| 44 ./run_tests.sh -sid reago | |
| 45 ``` | |
| 46 | |
| 47 # Bug Reports | |
| 48 | |
| 49 Any bug can be filed in an issue [here](https://github.com/ASaiM/galaxytools/issues). | |
| 50 | |
| 51 # Developers | |
| 52 | |
| 53 A release can be pushed to the test or main "Galaxy Tool Shed", using the following | |
| 54 Planemo commands (with required Tool Shed access detailed in `~/.planemo.yml`): | |
| 55 | |
| 56 ``` | |
| 57 planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxytools/tools/reago/ | |
| 58 ``` | |
| 59 | |
| 60 or: | |
| 61 | |
| 62 ``` | |
| 63 planemo shed_update -t toolshed --check_diff ~/repositories/galaxytools/tools/reago/ | |
| 64 ``` | |
| 65 | |
| 66 # License (Apache 2) | |
| 67 | |
| 68 This wrapper are released under Apache 2 License. See the [LICENSE file](https://github.com/ASaiM/galaxytools/blob/master/LICENSE) for details |