Apptainer

Bootstrap: docker
From: rocker/r-ubuntu:22.04

%post

apt-get update && apt-get install -y --no-install-recommends build-essential python3-pip libssl-dev libbz2-dev libsdl1.2-dev liblzma-dev libcurl4-openssl-dev zlib1g-dev libxml2-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev trf bwa bcftools samtools default-jre pandoc jq parallel && rm -rf /var/lib/apt/lists/*
pip install cutadapt==4.4 pandas==2.0.3 bio==1.5.9 

mkdir -p /usr/local/lib/R/etc/ /usr/lib/R/etc/
echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl', Ncpus = 4)" | tee /usr/local/lib/R/etc/Rprofile.site | tee /usr/lib/R/etc/Rprofile.site
R -e 'install.packages("remotes")'

# Update apt-get
Rscript -e 'install.packages("remotes", version = "2.4.2")'
Rscript -e 'remotes::install_cran("tidyverse", version = "2.0.0")'
Rscript -e 'remotes::install_cran("ggbeeswarm", upgrade="never", version="0.6.1")'
Rscript -e 'remotes::install_cran("gridExtra",upgrade="never", version = "2.3")'
Rscript -e 'remotes::install_cran("rmarkdown",upgrade="never", version = "2.17")'
Rscript -e 'remotes::install_cran("gridExtra",upgrade="never", version = "2.3")'
Rscript -e 'remotes::install_cran("foreach",upgrade="never", version = "1.5.2")'
Rscript -e 'remotes::install_cran("doMC",upgrade="never", version = "1.3.8")'
Rscript -e 'remotes::install_cran("argparse",upgrade="never", version = "2.1.6")'

Rscript -e 'if (!require("BiocManager", quietly = TRUE)) { install.packages("BiocManager"); }; BiocManager::install(version = "3.16");'

Rscript -e 'BiocManager::install("dada2", version = "3.16", ask = FALSE)'
Rscript -e 'BiocManager::install("muscle", version = "3.16", ask = FALSE)'
Rscript -e 'BiocManager::install("BSgenome", version = "3.16", ask = FALSE)'

%runscript
exec /bin/bash "$@"
%startscript
exec /bin/bash "$@"