Prior to the workshop, participants are expected to install the software below. Prior experience using command line programs and something like R can be helpful but is not necessary for participation. A primer will be delivered at the beginning of the workshop and material will be delivered at an introductory level to keep material accessible.

George will hold office hours on 2 and 3 Nov from 15:00-17:00 to help troubleshoot pre-workshop problems in person at Kew and via Teams. A link has been sent to registered participants via email.

Keep in mind that if you are using an institution-owned machine, you may need to reach out to your IT team in advance for software installs.

HPC Access for the Workshop

The workshop is supported by the UK Crop Diversity Cluster. In order to access the cluster, you will need to create an account here.

The form will ask you institutional affiliation. If you are attending the workshop but not associated with one of the listed institutions, please clarify that you are attending the workshop on phylogenetic networks.

After successful registration, you will need to follow instructions on generating an ssh key and sharing the public key with the cluster admin here.

It is best to register and have your ssh key in place as early as possible so as to not overwhelm the admin, but George is available during the office hours if any of the registration and key instructions are unclear.

Some Common Prerequisites

The below instructions are for installation on your own computer. All necessary software and dependencies for analyses have be pre-installed on the cluster for you.

If you do not already, please install the following:

  • install Julia
    • it can be helpful to add Julia to your PATH
  • install R
  • install a text editor for editing or writing code if you do not already have one. Some free suggestions include:
  • if you are on a Windows computer, you will need a way to log into the institutional cluster.
    • I highly recommend gitbash
    • A tried and true alternative is PuTTY

BPP

We will run the latest version of BPP on the cluster, which can be accessed with the release page of the BPP GitHub.

However, we will also use R and some R packages to analyze results from BPP that will require installation on your own computer. After R is installed we will install the bppr R package. The package can be installed after launching R or Rstudio by

install.packages("devtools")
devtools::install_github("dosreislab/bppr")

You should also install Tracer, which is an interactive program used for evaluating the quality of Bayesian posterior samples.

PhyloNetworks

The bulk of analysis will be carried out on the cluster, but the visualization steps are best carried out on your own computer. This will require installing Julia and the associated packages for PhyloNetworks:

  • 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("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().