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Conda environment

January 2020
see also:   → Installing QIIME 2 within a conda environment (conda of QIIME2-2019 includes DADA2 version 1.10)

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


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


To avoid error "Segmentation fault", conda options/channels are added to solve multithreading problems.

3) Install DADA2


# 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



4) Run DADA2

# 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