How to build dada2 environment

not the most straighforward install, here's how i've been doing it.

in your home directory, download and install miniconda3

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

install mamba in your base environment

conda install mamba -c conda-forge

create new conda environment, put it in a place with all your other conda environments and where there is lots of spaces (e.g. data, not home or scratch)

mamba create --prefix /gpfs/home/ibishop/data/ibishop/condas/dada2

activate

conda activate /gpfs/home/ibishop/data/ibishop/condas/dada2

install r then devtools

mamba install -c conda-forge r-base=4.0
mamba install -c conda-forge r-devtools=2.4.2

start R

R

load libraries and install via dada2 via github

library("devtools")
devtools::install_github("benjjneb/dada2", ref="v1.16")

check version

packageVersion("dada2")
help(package="dada2")