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+Galaxy wrapper for SortMeRNA
+============================
+
+SortMeRNA is a tool for RNA filtering based on local sequence alignment against 
+rRNA database. For more information, check the [user manual](http://bioinfo.lifl.fr/RNA/sortmerna/code/SortMeRNA-user-manual-v1.7.pdf)
+
+# Installation
+
+## Automated installation
+
+On a Galaxy instance, the wrapper can be automatically installed using the 
+ToolShed. This will automatically install the dependencies, configure the Galaxy
+instance for the tool and data, ...
+
+## Manual installation
+
+For manual installation, the files `sortmerna.xml` must be put in the `tools/sortmerna/`
+ folder and add the XML files to Galaxy's `tool_conf.xml` (in `config` folder) as 
+normal:
+
+```
+<section name="Sort RNA" id="sortmerna">
+    <tool file="sortmerna/sortmerna.xml" />
+</section>
+```
+
+The SortMeRNA database must also be referenced in Galaxy. The `tool-data/sortmerna_rRNA_databases.loc.sample`
+must be copy 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="sortmerna_rRNA_databases" comment_char="#">
+    <columns>value, name, path</columns>
+    <file path="tool-data/sortmerna_rRNA_databases.loc" />
+</table>
+```
+
+SortMeRNA must be installed somewhere on the system path. It can be done using:
+
+```
+planemo dependency_script ~/repositories/galaxytools/tools/sortmerna/
+bash dep_install.sh
+source env.sh
+```
+
+To test the Galaxy integration, the functional tests can be runned:
+
+```
+./run_tests.sh -sid sortmerna
+```
+
+# 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/sortmerna/
+```
+
+or:
+
+```
+planemo shed_update -t toolshed --check_diff ~/repositories/galaxytools/tools/sortmerna/
+```
+
+# 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
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