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1. Installation
Important: The following intructuons are for Linux and assume you have Python and pip installed already. For installation on different systems, please see the links provided for the individual dependences.
The easiest way to install getphylo is using the command:
pip install getphylo
This will fetch and install the latest version from: https://pypi.org/project/getphylo/
You can also install getphylo directly from the GitHub repository. Clone the repository, using:
git clone git@github.com:drboothtj/getphylo.git
Then, navigate into the folder:
cd getphylo
Then, install getphylo using:
python setup.py develop
Important: getphylo requires DIAMOND, MUSCLE and FastTree2 to be installed to work correctly. These must be installed manually. BioPython should be installed automatically. Below are instructions to install each dependency:
You can install DIAMOND with the following command:
sudo apt install diamond-aligner
Further instructions for installing DIAMOND can be found, here: https://github.com/bbuchfink/diamond/wiki/2.-Installation.
You can install MUSCLE with the following command:
sudo apt install muscle
Further instructions for installing MUSCLE can be found, here: http://www.drive5.com/muscle/muscle.html
IMPORTANT: getphylo is not currently compatible with MUSCLE 5. We recommend using version 3.8 as this was the version used in development. Although, any version below 5.0 should work without issues.
You can install FastTree2 with the following command:
sudo apt install fasttree
Further instructions for installing FastTree2 can be found, here: http://www.microbesonline.org/fasttree/.