SNAKEFILE TO USE FOR BASIC HYPHY ANALYSES

This application is currently designed to run in an HPC environment.

There is an assumption that the freely availible Anaconda software has been installed on your machine, as well as the HyPhy (MPI enabled) package. The error filtering script requires the hyphy develop branch

Save hyphy and hyphy-analyses in your home directory

To install:

Step 1: clone the repository

git clone https://github.com/agselberg/hyphy_snakefile.git

cd hyphy_snakefile

Step 2: set the enviornment

Use the following commands to set up the conda environment before starting the analysis:

conda env create -f environment.yml

conda activate HYPHY_SNAKEMAKE

Step 3: Set config

1. Set full paths for data directories and set extensions for data files.
2. Specify if gene trees or species trees will be used:

• GENE TREES:
  • Update config file to "trees" : "gene"
  • Include one gene tree for each msa file with the same basename (ex: gene1.fasta and gene1.nwk)
• SPECIES TREES:
  • Update config file to "trees" : "species"
  • There should be one species tree in the specified tree directory
• BUILD TREES with RAXML:
  • Update config file to `"trees" : "raxml"

Step 4: Choose HyPhy models to run

The specified snakefile will run the following models: BUSTED-E, BUSTED-PH, Contrast-FEL, aBSREL, MEME, RELAX. To skip a model, comment out undesired models in rule all in the Snakefile.

Step 5:

Run Snakemake:

bash RUN_SNAKEFILE.sh