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Ecological-and-Evolutionary-Genomics / eeg2016

Ecological and Evolutionary Genomics 2016
GNU General Public License v3.0
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KRONA AND MOTHUR #54

Open jwdrew opened 8 years ago

jwdrew commented 8 years ago

https://github.com/accaldwell/mothur_krona

https://github.com/marbl/Krona/wiki/Importing%20text%20and%20XML%20data

rec3141 commented 8 years ago

First need to install dependencies

# lxml should already be installed on biolinux but here's the command      
sudo apt-get install python3-lxml 

# download, unpack, and install Krona tools
wget https://github.com/marbl/Krona/releases/download/v2.6.1/KronaTools-2.6.1.tar
tar xvf KronaTools-2.6.1.tar   
sudo ./install.pl     
./updateTaxonomy.sh

# download mothur_krona
https://raw.githubusercontent.com/accaldwell/mothur_krona/master/mothur_krona_XML.py

# run krona_mothur on mothur *.tax.summary output file
mothur_krona_XML.py /path/to/tax.summary > output.xml
ktImportXML output.xml