fixed-tree-experiments

Dependencies

This project requires the following phylogenetic inference tools:

Program	Version
BEAGLE	4.0.1
BEAST	1.10.5pre_thorney_0.1.2
iqtree	2.2.2.6
lsd	2.3
treetime	0.11.4

Pipeline with docker or singularity

There is no need to install dependencies with docker or singularity.

Running the pipeline with docker

nextflow run main.nf -profile docker

Running the pipeline with singularity and PBS

nextflow -C configs/pbs.config run main.nf -profile singularity

Since the pipeline will take weeks to run to completion one should use a high performance computer. An example of configuration file for PBS Pro can be found in the configs folder.

Installation

git clone 4ment/fixed-tree-experiments.git

Install phylogenetic programs

Install BEAST, IQ-TREE and LSD in the bin directory.

conda setup

Other Python dependencies, including TreeTime, are managed with Anaconda:

conda env create -f environment.yml
conda activate fixed-tree

You may need to set the NXF_CONDA_CACHEDIR variable for nextflow to locate the conda environment

export NXF_CONDA_CACHEDIR=$HOME/miniconda3/envs

Running the pipeline

nextflow run main.nf

This command creates a results/ directory in the pipeline working directory. The directory contains all intermediate and final outputs needed to generate the figures.

Generate figures

The results can be visualized using the included R Markdown report. Required R packages are managed with renv. Run once:

Rscript -e 'renv::restore()'

Then render the results to a PDF:

Rscript -e 'rmarkdown::render("plot.Rmd")'

Generate network graphs

python scripts/build-net.py --multi --results results --out plot.pdf

This script will create a pdf file containing the graphs and it will also generate a file containing z-scores contained in the manuscript.