Mercurial > repos > bebatut > rdptools
comparison README.md @ 0:73b3e2f98631 draft default tip
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/rdptools commit fa8135b9b1918785c3f3b3fb7325bfe031b44ec4
| author | bebatut |
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| date | Mon, 16 Nov 2015 02:46:50 -0500 |
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| -1:000000000000 | 0:73b3e2f98631 |
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| 1 Galaxy wrapper for RDPTools | |
| 2 =========================== | |
| 3 | |
| 4 RDPTols is an open source command-line tool suite for performing a complete | |
| 5 workflow of analysis tasks of NGS data. For more information, check the | |
| 6 [Github repository](https://github.com/rdpstaff/RDPTools) | |
| 7 | |
| 8 # Installation | |
| 9 | |
| 10 ## Automated installation | |
| 11 | |
| 12 On a Galaxy instance, the wrappers can be automatically installed using the | |
| 13 ToolShed. This will automatically install the dependencies, configure the Galaxy | |
| 14 instance for the tools and data, ... | |
| 15 | |
| 16 ## Manual installation | |
| 17 | |
| 18 For manual installation, the `.xml` files must be put in the `tools/rdptools/` | |
| 19 folder and add the XML files to Galaxy's `tool_conf.xml` (in `config` folder) as | |
| 20 normal: | |
| 21 | |
| 22 ``` | |
| 23 <section name="RDPTools" id="rdptools"> | |
| 24 <tool file="rdptools/framebot.xml" /> | |
| 25 </section> | |
| 26 ``` | |
| 27 | |
| 28 The database must also be referenced in Galaxy. The files in `tool-data/` | |
| 29 must be copied in Galaxy's `tool-data` folder. And Galaxy's `config/tool_data_table_conf.xml.sample` | |
| 30 have to be completed: | |
| 31 | |
| 32 ``` | |
| 33 !-- Locations of public ribosomal databases --> | |
| 34 <table name="framebot_ref_gene_databases" comment_char="#"> | |
| 35 <columns>value, name, path</columns> | |
| 36 <file path="tool-data/framebot_ref_gene_databases.loc" /> | |
| 37 </table> | |
| 38 ``` | |
| 39 | |
| 40 RDPTools must be installed somewhere on the system path. It can be done using: | |
| 41 | |
| 42 ``` | |
| 43 planemo dependency_script ~/repositories/galaxytools/packages/package_ant_1_9_6/ | |
| 44 bash dep_install.sh | |
| 45 source env.sh | |
| 46 | |
| 47 planemo dependency_script ~/repositories/galaxytools/tools/rdptools/ | |
| 48 bash dep_install.sh | |
| 49 source env.sh | |
| 50 ``` | |
| 51 | |
| 52 To test the Galaxy integration, the functional tests can be runned: | |
| 53 | |
| 54 ``` | |
| 55 ./run_tests.sh -sid rdptools | |
| 56 ``` | |
| 57 | |
| 58 # Bug Reports | |
| 59 | |
| 60 Any bug can be filed in an issue [here](https://github.com/ASaiM/galaxytools/issues). | |
| 61 | |
| 62 # Developers | |
| 63 | |
| 64 A release can be pushed to the test or main "Galaxy Tool Shed", using the following | |
| 65 Planemo commands (with required Tool Shed access detailed in `~/.planemo.yml`): | |
| 66 | |
| 67 ``` | |
| 68 planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxytools/tools/rdptools/ | |
| 69 ``` | |
| 70 | |
| 71 or: | |
| 72 | |
| 73 ``` | |
| 74 planemo shed_update -t toolshed --check_diff ~/repositories/galaxytools/tools/rdptools/ | |
| 75 ``` | |
| 76 | |
| 77 # License (Apache 2) | |
| 78 | |
| 79 This wrapper are released under Apache 2 License. See the [LICENSE file](https://github.com/ASaiM/galaxytools/blob/master/LICENSE) for details |