TOAST INSTALLATION

Before getting started

Note that TOAST requires R version 3.6.1 or higher for installation of dependencies and functionality.

Update R prior to going any further

TOAST also requires you install MAFFT and place this into your global path (e.g., modify your ~/.bashrc file).

Please ensure MAFFT is working before proceeding

1. Installation

TOAST can be installed from github, but relies on dependencies not yet on CRAN. The easiest way to install TOAST and all dependencies is to copy the following code 
#if you do not already have devtools
                install.packages("devtools")

                library(devtools)
                devtools::install_github("carolinafishes/toast")
                library("toast")

2. R Dependencies

TOAST is built upon the efforts of several other R packages including: 

gplot
rentrez
ggplot2 
devtools 
viridis 
packcircles 
gridExtra 
data.tree 
circlepackeR 
foreach 
doParallel 
seqinr 
reshape 
usethis 
streamgraph
LINUX USERS ONLY: Please note that rentrez makes use of several dependencies that may not be on your computer. If you encounter errors during the installation of this package here is a list of dependencies you may need to install as follows in terminal 

sudo apt install openssl
sudo apt install libssl-dev
sudo apt install libcurl4-opensll-dev
sudo apt install libxml2-dev
From here you are are ready to get started!

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