Mercurial > repos > bebatut > sortmerna
comparison README.md @ 6:817fb14fc739 draft
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 2feea380531495c52455aade9761b0390c235c9b-dirty
| author | bebatut |
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| date | Thu, 05 Nov 2015 08:31:34 -0500 |
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| 5:064dbe9f9333 | 6:817fb14fc739 |
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| 1 Galaxy wrapper for SortMeRNA | |
| 2 ============================ | |
| 3 | |
| 4 SortMeRNA is a tool for RNA filtering based on local sequence alignment against | |
| 5 rRNA database. For more information, check the [user manual](http://bioinfo.lifl.fr/RNA/sortmerna/code/SortMeRNA-user-manual-v1.7.pdf) | |
| 6 | |
| 7 # Installation | |
| 8 | |
| 9 ## Automated installation | |
| 10 | |
| 11 On a Galaxy instance, the wrapper can be automatically installed using the | |
| 12 ToolShed. This will automatically install the dependencies, configure the Galaxy | |
| 13 instance for the tool and data, ... | |
| 14 | |
| 15 ## Manual installation | |
| 16 | |
| 17 For manual installation, the files `sortmerna.xml` must be put in the `tools/sortmerna/` | |
| 18 folder and add the XML files to Galaxy's `tool_conf.xml` (in `config` folder) as | |
| 19 normal: | |
| 20 | |
| 21 ``` | |
| 22 <section name="Sort RNA" id="sortmerna"> | |
| 23 <tool file="sortmerna/sortmerna.xml" /> | |
| 24 </section> | |
| 25 ``` | |
| 26 | |
| 27 The SortMeRNA database must also be referenced in Galaxy. The `tool-data/sortmerna_rRNA_databases.loc.sample` | |
| 28 must be copy in Galaxy's `tool-data` folder. And Galaxy's `config/tool_data_table_conf.xml.sample` | |
| 29 have to be completed: | |
| 30 | |
| 31 ``` | |
| 32 !-- Locations of public ribosomal databases --> | |
| 33 <table name="sortmerna_rRNA_databases" comment_char="#"> | |
| 34 <columns>value, name, path</columns> | |
| 35 <file path="tool-data/sortmerna_rRNA_databases.loc" /> | |
| 36 </table> | |
| 37 ``` | |
| 38 | |
| 39 SortMeRNA must be installed somewhere on the system path. It can be done using: | |
| 40 | |
| 41 ``` | |
| 42 planemo dependency_script ~/repositories/galaxytools/tools/sortmerna/ | |
| 43 bash dep_install.sh | |
| 44 source env.sh | |
| 45 ``` | |
| 46 | |
| 47 To test the Galaxy integration, the functional tests can be runned: | |
| 48 | |
| 49 ``` | |
| 50 ./run_tests.sh -sid sortmerna | |
| 51 ``` | |
| 52 | |
| 53 # Bug Reports | |
| 54 | |
| 55 Any bug can be filed in an issue [here](https://github.com/ASaiM/galaxytools/issues). | |
| 56 | |
| 57 # Developers | |
| 58 | |
| 59 A release can be pushed to the test or main "Galaxy Tool Shed", using the following | |
| 60 Planemo commands (with required Tool Shed access detailed in `~/.planemo.yml`): | |
| 61 | |
| 62 ``` | |
| 63 planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxytools/tools/sortmerna/ | |
| 64 ``` | |
| 65 | |
| 66 or: | |
| 67 | |
| 68 ``` | |
| 69 planemo shed_update -t toolshed --check_diff ~/repositories/galaxytools/tools/sortmerna/ | |
| 70 ``` | |
| 71 | |
| 72 # License (Apache 2) | |
| 73 | |
| 74 This wrapper are released under Apache 2 License. See the [LICENSE file](https://github.com/ASaiM/galaxytools/blob/master/LICENSE) for details |