Mercurial > repos > bebatut > rdptools
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Mon Nov 16 02:46:50 2015 -0500 @@ -0,0 +1,79 @@ +Galaxy wrapper for RDPTools +=========================== + +RDPTols is an open source command-line tool suite for performing a complete +workflow of analysis tasks of NGS data. For more information, check the +[Github repository](https://github.com/rdpstaff/RDPTools) + +# Installation + +## Automated installation + +On a Galaxy instance, the wrappers can be automatically installed using the +ToolShed. This will automatically install the dependencies, configure the Galaxy +instance for the tools and data, ... + +## Manual installation + +For manual installation, the `.xml` files must be put in the `tools/rdptools/` + folder and add the XML files to Galaxy's `tool_conf.xml` (in `config` folder) as +normal: + +``` +<section name="RDPTools" id="rdptools"> + <tool file="rdptools/framebot.xml" /> +</section> +``` + +The database must also be referenced in Galaxy. The files in `tool-data/` +must be copied in Galaxy's `tool-data` folder. And Galaxy's `config/tool_data_table_conf.xml.sample` +have to be completed: + +``` +!-- Locations of public ribosomal databases --> +<table name="framebot_ref_gene_databases" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/framebot_ref_gene_databases.loc" /> +</table> +``` + +RDPTools must be installed somewhere on the system path. It can be done using: + +``` +planemo dependency_script ~/repositories/galaxytools/packages/package_ant_1_9_6/ +bash dep_install.sh +source env.sh + +planemo dependency_script ~/repositories/galaxytools/tools/rdptools/ +bash dep_install.sh +source env.sh +``` + +To test the Galaxy integration, the functional tests can be runned: + +``` +./run_tests.sh -sid rdptools +``` + +# Bug Reports + +Any bug can be filed in an issue [here](https://github.com/ASaiM/galaxytools/issues). + +# Developers + +A release can be pushed to the test or main "Galaxy Tool Shed", using the following +Planemo commands (with required Tool Shed access detailed in `~/.planemo.yml`): + +``` +planemo shed_update -t testtoolshed --check_diff ~/repositories/galaxytools/tools/rdptools/ +``` + +or: + +``` +planemo shed_update -t toolshed --check_diff ~/repositories/galaxytools/tools/rdptools/ +``` + +# License (Apache 2) + +This wrapper are released under Apache 2 License. See the [LICENSE file](https://github.com/ASaiM/galaxytools/blob/master/LICENSE) for details \ No newline at end of file