This is a three part tutorial. Part 1 focuses on installation of TOAST.
Note that TOAST requires R version 3.6.1 or higher for installation of dependencies and functionality.
Update R prior to going any further
Part 2 focuses on gathering public data using BUSCO. Note that ONLY MAC and LINUX users can use BUSCO!
Part 3 focuses on visualization of missing data patterns and alignment assembly. This functionality works on all platforms.
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")
You can also download the R scripts from github and install it manually.
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
If you did the above and only wish to visualize missing data patterns/assemble concatenated alignments you are ready to move on to part 2.
If you are a MAC OR LINUX user and wish to harness BUSCO orthologs, keep reading!
BUSCO is limited to only running on Mac and Linux machines and requires Python3, please update if you are using earlier versions. If you plan to use TOAST to visualize missing data patterns, these functions will work also work on Windows and do not use python.
However, you need to be using Mac or LINUX to use any functions that involve BUSCO harvesting of data. Further, MafftOrientAlign requires a Unix (Linux or OSX) environment.
Please see the BUSCO manual for instructions on installation.
Note that BUSCO recommends specific releases of HMMER and BLAST. But, we have found more recent versions of HMMER to work while the lastest BLAST (2.9+) will occassionally crash.
We recommend following the BUSCO instructions to ensure compatibility. There are several options availabel when installing BUSCO and we suggest using the following command to ensure no mismatch of python versions in R (This is particularly important for mac users!)
sudo python3 setup.py install
After you have successfully installed BUSCO you will need to copy and modify the config.ini file to direct BUSCO to both BLAST and HMMER.
Please see the BUSCO manual and follow these directions carefully.
CHECK that you have successfully installed BUSCO prior to proceeding any further!
TOAST requires you install MAFFT and place this into your global path (e.g., modify your ~/.bashrc file).