Mercurial > repos > george-weingart > lefse
view Readme_lefse_Galaxy.txt @ 0:e7cd19afda2e draft
Lefse
author | george-weingart |
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date | Tue, 13 May 2014 21:57:00 -0400 |
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Installation instructions for lefse in a galaxy environment. These instructions require the Mercurial versioning system, galaxy, and an internet connection. 1. In the "galaxy-dist/tools" directory install lefse by cloning the repository: bitbucket.org/biobakery/lefse_galaxy 2. Rename the galaxy_lefse directory thus created to "lefse" 3. Update member tool_conf.xml in the galaxy directory adding the following: <section name="LEfSe" id="lefse"> <tool file="lefse/format_input.xml" /> <tool file="lefse/run_lefse.xml" /> <tool file="lefse/plot_res.xml" /> <tool file="lefse/plot_cladogram.xml" /> <tool file="lefse/plot_single_feature.xml" /> <tool file="lefse/plot_features.xml" /> </section> 4. Update member datatypes_conf.xml in the galaxy directory adding the following: <datatype extension="lefse" type="galaxy.datatypes.data:Lefse" display_in_upload="true"/> <datatype extension="lefse_res" type="galaxy.datatypes.tabular:LefseRes" display_in_upload="true"/> 5. Copy the *.png members to galaxy-dist/static/images 6. Recycle galaxy