Installation

Dependencies

ThorAxe needs Python version 3.6.1 or higher, but less than 3.9 and:

ProGraphMSA

ThorAxe needs ProGraphMSA to perform the multiple sequence alignments. Follow the instructions on that link to install it or download one of the following compiled binaries:

It is important to rename the program to ProGraphMSA and to put it in the path. If you are using Windows 10, you can use ProGraphMSA through Ubuntu with the Windows Subsystem for Linux. For example, to install the 64 bits version in Ubuntu you can do:

wget  https://github.com/PhyloSofS-Team/ProGraphMSA/raw/master/bin/ProGraphMSA_64
chmod a+x ProGraphMSA_64
sudo mv ProGraphMSA_64 /bin/ProGraphMSA

ThorAxe

Finally, the easiest way to install ThorAxe is from PyPI using pip with Python 3:

python -m pip install thoraxe

In Ubuntu, you may need to use python3 instead of python.

python3 -m pip install thoraxe

Installation from source

If you want to install the latest and in-development version of ThorAxe, clone its source code from the thoraxe GitHub repo using git:

git clone https://github.com/PhyloSofS-Team/thoraxe.git

Then, you can use the pip module of Python 3 to install it:

cd thoraxe
python -m pip install -e .

The -e flag allows you to update the thoraxe repo using git pull and get the changes reflected in the installed version.

Docker image

We offer a Docker image with ThorAxe and all its dependencies installed. To run this image, you need to install Docker from the Docker website.

The following example is going to run the ThorAxe Docker image using Windows PowerShell. The local directory is going to be bind mounted in /project. The actual folder is ${PWD} in Windows PowerShell and $(pwd) in Unix. Please note that in Ubuntu, you may need sudo to run docker.

docker run -ti --rm --mount type=bind,source=${PWD},target=/project diegozea/thoraxe

After this, we have access to the bash terminal of an Ubuntu 18.04 image with ThorAxe, tree to help explore the results and ipython3 to make easier the use of the thoraxe Python module.

_images/docker.gif — ThorAxe example using Docker in Windows 10.