Docker/Singularity container for PolyAtailor?

[SergeWielhouwer]

Hi,

I would like to try out PolyAtailor as it seems a really promising tool!
However, I experienced a lot of difficulty installing the many dependencies required for this tool.

Do you maybe have a container image or recipe for this tool ready for use?

Below you can see my current recipe, it should contain all the tools but many dependencies are not available in their repositories anymore for this R version or require a lot of other dependencies which are hard to find.

Bootstrap: docker
#From: rocker/r-ver:3.6.2
From: rocker/r-ver:3.6.3

%post
	# Update the system
	apt-get update && apt-get -y upgrade

	# Install R and required packages
	# apt-get -y install r-base

	# Install system dependencies
	apt-get -y install libssl-dev libcurl4-openssl-dev libxml2-dev wget libfontconfig1-dev libharfbuzz-dev libfribidi-dev
	apt-get -y install apt-utils
	apt-get -y install make zlib1g-dev build-essential ncurses-dev libbz2-dev liblzma-dev
	apt-get -y install gfortran libreadline-dev libx11-dev libcairo2-dev libxt-dev
	apt-get -y install evince xorg openbox
	apt-get -y install texlive-base  libpcre3-dev libgdal-dev libudunits2-dev
	apt-get -y install libcurl4-gnutls-dev

	# Install curl manually for devtools
	wget https://github.com/curl/curl/releases/download/curl-7_55_0/curl-7.55.0.tar.gz
	tar -xf curl-7.55.0.tar.gz
	cd curl-7.55.0
	./configure
	make 
	make install
	cd ..

	# Install devtools and its dependencies
	Rscript -e "install.packages(c('usethis', 'pkgdown', 'rcmdcheck', 'roxygen2', 'rversions', 'urlchecker'), repos = 'https://cloud.r-project.org/', dependencies = TRUE)"
	Rscript -e "install.packages('devtools', repos = 'https://cloud.r-project.org/', dependencies = TRUE)"

    # Install additional R packages
    Rscript -e "install.packages(c('dplyr', 'reshape2', 'RColorBrewer', 'data.table', 'ggplot2'), repos = 'https://cloud.r-project.org/', dependencies = TRUE)"
	R -e 'install.packages("BiocManager", repos="http://cran.us.r-project.org", dependencies = TRUE)'
	R -e 'local({r <- getOption("repos"); r["CRAN"] <- "http://cran.r-project.org"; options(repos=r)}); install.packages("BiocManager", repos="http://cran.r-project.org", dependencies = TRUE)'
	R -e 'local({r <- getOption("repos"); r["CRAN"] <- "http://cran.r-project.org"; options(repos=r)}); BiocManager::install("IRanges")'
	R -e 'local({r <- getOption("repos"); r["CRAN"] <- "http://cran.r-project.org"; options(repos=r)}); BiocManager::install("GenomicFeatures")'
	R -e 'local({r <- getOption("repos"); r["CRAN"] <- "http://cran.r-project.org"; options(repos=r)}); BiocManager::install("GenomicRanges")'
	R -e 'local({r <- getOption("repos"); r["CRAN"] <- "http://cran.r-project.org"; options(repos=r)}); BiocManager::install("Biostrings")'
	R -e 'local({r <- getOption("repos"); r["CRAN"] <- "http://cran.r-project.org"; options(repos=r)}); BiocManager::install("BSgenome")'
	R -e 'local({r <- getOption("repos"); r["CRAN"] <- "http://cran.r-project.org"; options(repos=r)}); BiocManager::install("ggbio")'
	R -e 'local({r <- getOption("repos"); r["CRAN"] <- "http://cran.r-project.org"; options(repos=r)}); BiocManager::install("rtracklayer")'
	R -e 'local({r <- getOption("repos"); r["CRAN"] <- "http://cran.r-project.org"; options(repos=r)}); BiocManager::install("DESeq2")'
	R -e 'local({r <- getOption("repos"); r["CRAN"] <- "http://cran.r-project.org"; options(repos=r)}); BiocManager::install("DEXSeq")'

	# Install PolyAtailor from GitHub
	R -e 'local({r <- getOption("repos"); r["CRAN"] <- "http://cran.r-project.org"; options(repos=r)}); Rscript -e "devtools::install_github(YuLab-SMU/ggmsa, dependencies = TRUE)"'
	R -e 'local({r <- getOption("repos"); r["CRAN"] <- "http://cran.r-project.org"; options(repos=r)}); Rscript -e "devtools::install_github(BMILAB/movAPA, dependencies = TRUE)"'
	R -e 'local({r <- getOption("repos"); r["CRAN"] <- "http://cran.r-project.org"; options(repos=r)}); Rscript -e "devtools::install_github(BMILAB/PolyAtailor, dependencies = TRUE)"'


%runscript
    exec Rscript "$@"