2021
see also: → original DADA2 installation page
see also: → Installing QIIME 2 within a conda environment (conda of QIIME2-2019 includes DADA2 version 1.10)
# check if conda exist already
conda info --envs
# conda environments:
#
base * /home/myname/tools/miniconda3
qiime2-2019.10 /home/myname/tools/miniconda3/envs/qiime2-2019.10
# If command "conda" does not exist
conda info --envs
conda: command not found
# Install miniconda
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh # run installation
https://docs.conda.io/en/latest/miniconda.html
# add conda channels ( repositories from which software tools will be downloaded )
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
# check order of conda channels
conda config --get channels
--add channels 'defaults' # lowest priority
--add channels 'bioconda'
--add channels 'conda-forge' # highest priority
To avoid → error "Segmentation fault", several conda channels are added to solve multithreading problems
conda create -n dada2-v1.14 -c conda-forge -c bioconda -c defaults --override-channels bioconductor-dada2
Proceed ([y]/n)? y
# check location of new environment
conda info --envs
# conda environments:
#
base * /home/myname/tools/miniconda3
dada2-v1.14 /home/myname/tools/miniconda3/envs/dada2-v1.14
qiime2-2019.10 /home/myname/tools/miniconda3/envs/qiime2-2019.10
# start the new conda environment for DADA2
conda activate dada2-v1.14
# start R within the conda environment
R
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
# In R: install DADA2 (see also: https://benjjneb.github.io/dada2/dada-installation.html )
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("dada2", version = "3.10")
Old packages
Update all/some/none? [a/s/n]: a
# close conda environment
conda deactivate
# start DADA2 conda environment
conda activate dada2-v1.14
# start R
(dada2-v1.14) username@laptop:~$ R
# start DADA2 (in R)
library(dada2); packageVersion("dada2")
Loading required package: Rcpp
[1] ‘1.14.0’
to run DADA2, see tutorial
https://benjjneb.github.io/dada2/tutorial.html
# close R
q()
Save workspace image? [y/n/c]: n
# close conda environment
conda deactivate
# Delete complete conda environment "dada2-v1.14" if not needed anymore
conda remove --name dada2-v1.14 --all
# Uninstall a singe conda package from environment (remove a package, but keep environment)
conda remove --name environmentName packageName
Read more
https://docs.conda.io/en/latest/miniconda.html
https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-pkgs.html