Installation - BelenJM/supeRbaits GitHub Wiki

Installing the R-package

supeRbaits is an R-package, which means that you need to have R installed in your computer. For more information about how to install R, you can find more information here.

With R installed in your computer, you can now install supeRbaits. To do this, first install the remotes package to allow installing the package from GitHub repository:

install.packages("remotes", repos = "http://cran.us.r-project.org")
library("remotes")

Install and load supeRbaits by the following command:

# install and load supeRbaits from the GitHub repo
install_github("BelenJM/supeRbaits")
library(supeRbaits)

If everything has been installed correctly, when you load supeRbaits, the following message appears:

> library(supeRbaits)
Welcome to supeRbaits!

Installing the BLAST+ software to use blast_baits()

The second function of supeRbaits is blast_baits(), which allows the user to blast the baits against the reference (or other database). If you want to use this function, you first need to have the BLAST+ software installed in your laptop/system. To do this, you need to install the software from here. BLAST+ is a group of tools to use BLAST, provided by the NCBI.

• If you are using Linux, you can follow these steps; if you have super user rights, you can try:

sudo apt install ncbi-blast+

• For Windows, you need to make sure that R finds the executable. You could do this by first locating the path to the executable "blastn" in your own system (e.g. C:/Program Files/NCBI/blast-2.12.0+/bin), and then include the path in R by using the Sys.setenv() function in R.

If the path is not correct, or BLAST+ is not correctly installed, supeRbaits will notify you with the following message "Error: Executable for makeblastdb not found! Please make sure that the software is correctly installed and, if necessary, path variables are set." when trying to run blast_baits().