Installation Instructions for PhyloMagnet


To run PhyloMagnet, you will need to install Nextflow, a pipeline execution framework. This is however quite simple:

curl -s | bash


We provide a singularity container with all necessary tools installed and configured. To use it, you first need to install Singularity (either version 2 or version 3) itself:

tar xvf singularity-$VERSION.tar.gz
cd singularity-$VERSION
./configure --prefix=/usr/local
sudo make install

# for installation of version 3 see the Singularity website

Singularity container

Then, download the container from singularity-hub or build it locally with the singularity recipe:

# singularity 2

singularity pull --name PhyloMagnet.simg shub://maxemil/PhyloMagnet:latest
# or
sudo singularity build PhyloMagnet.simg Singularity

# singularity 3

singularity pull --name PhyloMagnet.sif shub://maxemil/PhyloMagnet:latest
# or
sudo singularity build PhyloMagnet.sif Singularity


We highly recommend using the provided Singularity container to install all needed Software. Installing everything directly on the machine can be achieved using the conda environment.yml file.

If you want to see the version of the tools installed in the container, simply use conda to list all installed packages:

singularity exec PhyloMagnet.sif conda list -n PhyloMagnet-<version>


now you can either get PhyloMagnet from github (clone or download from or let Nextflow handle that as well:

nextflow run maxemil/PhyloMagnet --help

# or
git clone

nextflow run PhyloMagnet/ --help