This section describes how a user with an account with which they can log in on the Rstudio webserver can further customize their environment for dada2.
Cutadapt is a python program that can be installed with pip. As an RStudio server user this can be done through the “terminal” tab in the browser interface:
python3 -m pip install --user --upgrade cutadapt
Note that as a non-root user, the program is installed under
~/.local, so the environment variables PYTHONPATH and PATH
need to be updated so that the executable script is found and
it can load its library dependencies.
Within the RStudio server interface, users can install packages as needed through the console:
install.packages('BiocManager', 'magrittr', 'dplyr')
library(BiocManager)
BiocManager::install('dada2')
BiocManager::install('ShortRead')
BiocManager::install('Biostrings')