Set up dependencies and working directory

If you are a participant in a workshop, please go to the section For participants in workshops.

If you are not a participant in an workshop, please follow the next sections to set up your working directory:

Installing dependencies

Download BUCKy
Download MrBayes
Download Tree-QMC
Download Julia and follow instructions to install julia

Install the necessary packages: open julia then type

  using Pkg # to use functions that manage packages
  Pkg.add("PhyloNetworks") # to download & install package PhyloNetworks
  Pkg.add("SNaQ")
  Pkg.add("PhyloTraits")
  Pkg.add("PhyloPlots")
  Pkg.add("RCall")      # packaage to call R from within julia
  Pkg.add("CSV")        # to read from / write to text files, e.g. csv files
  Pkg.add("DataFrames") # to create & manipulate data frames
  Pkg.add("StatsModels")# for regression formulas
  using PhyloNetworks   # may take some time: pre-compiles functions in that package
  using PhyloPlots

and close julia with exit().

You also want to create a folder that will have the data and the dependencies. We can call this folder my-analysis, and make sure to move inside this folder in the terminal with:

mkdir my-analysis
cd my-analysis

Download the TICR scripts

In the project directory my-analysis, you have to git clone the PhyloUtilities repo with the TICR scripts and QuartetMaxCut. These scripts were originally in the TICR repo.

pwd ## you are in your working directory
git clone https://github.com/JuliaPhylo/PhyloUtilities.git

We will be using the standard scripts to run on a local machine or server, but note that there are SLURM scripts available here and more information here.

Download data via git clone

In your project directory my-analysis, you can clone this repository with the data:

pwd ## you are in your working directory
git clone https://github.com/solislemuslab/snaq-tutorial.git

This will download the learning materials and the data (in folder data).

If you are using your own data, simply create a folder with your data.

For participants in workshops

For participants in the MBL workshop

Login to your particular virtual machine (VM) using the IP address on the sticker attached to the back of your name tag. If, for example, your IP address was 123.456.789.321, you would type the following into the terminal on your local computer (i.e. your laptop) and press the enter key:

ssh -X moleuser@123.456.789.321

After login, you want to copy the phylo-networks in your home directory:

cp -r moledata/phylo-networks ./
cd phylo-networks

We will not cover the alternative RAxML+ASTRAL pipeline (which you could cover outside the workshop).