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+Galaxy wrapper for HUMAnN2
+==========================
+
+HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence 
+and abundance of microbial pathways in a community from metagenomic or 
+metatranscriptomic sequencing data. For more information, check the 
+[user manual](http://huttenhower.sph.harvard.edu/humann2/manual)
+
+# 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 `humann2.xml` must be put in the `tools/humann2/`
+ folder and add the XML files to Galaxy's `tool_conf.xml` (in `config` folder) as 
+normal:
+
+```
+<section name="Profile microbial pathways in a community" id="humann2">
+    <tool file="humann2/humann2.xml" />
+</section>
+```
+
+MetaPhlAn2 must be installed somewhere on the system path. It can be done using:
+
+```
+planemo dependency_script ~/repositories/galaxytools/tools/humann2/
+bash dep_install.sh
+source env.sh
+```
+
+To test the Galaxy integration, the functional tests can be runned:
+
+```
+./run_tests.sh -sid humann2
+```
+
+# 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/humann2/
+```
+
+or:
+
+```
+planemo shed_update -t toolshed --check_diff ~/repositories/galaxytools/tools/humann2/
+```
+
+# 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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