January 2020
Install DADA2 (v1.14) using a conda environment
1) Install (Mini-)conda
# check if conda exist already
conda info --envs
# conda environments:
#
base * /home/myname/Tools/Miniconda2
qiime2-2019.10 /home/myname/Tools/Miniconda2/envs/qiime2-2019.10
# If command "conda" does not exist
conda info --envs
conda: command not found
# Install miniconda
wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
bash Miniconda2-latest-Linux-x86_64.sh # run installation
http://conda.pydata.org/miniconda.html
# add conda channels
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
# check order of conda channelsconda config --get channels --add channels 'defaults' # lowest priority
--add channels 'bioconda'
--add channels 'conda-forge' # highest priority
2) Setup a new conda environment for DADA2
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/Miniconda2
dada2-v1.14 /srv/unn/Tools/Miniconda2/envs/dada2-v1.14
qiime2-2019.10 /home/myname/Tools/Miniconda2/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"
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
> library(dada2); packageVersion("dada2")
Loading required package: Rcpp
[1] ‘1.14.0’
See more at the DADA2 tutorial
# close R
> q()
Save workspace image? [y/n/c]: n
# close conda environment
conda deactivate
