Installation Instructions for PhyloMagnet

Nextflow

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

curl -s https://get.nextflow.io | bash

Singularity

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:

VERSION=2.6
wget https://github.com/singularityware/singularity/releases/download/$VERSION/singularity-$VERSION.tar.gz
tar xvf singularity-$VERSION.tar.gz
cd singularity-$VERSION
./configure --prefix=/usr/local
make
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

Note

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>

PhyloMagnet

now you can either get PhyloMagnet from github (clone or download from github.com/maxemil/PhyloMagnet) or let Nextflow handle that as well:

nextflow run maxemil/PhyloMagnet --help

# or
git clone https://github.com/maxemil/PhyloMagnet

nextflow run PhyloMagnet/main.nf --help