BootStrap: docker
From: ubuntu:22.04

%help 
This is a singularity container packing R version 4.3.3 and all the dependencies necessary to run the FRASER ("Find RAre Splicing Events in RNA-seq") package, version 1.14.1, for rnaseq analysis.
(BiocManager version : 3.18)
run the command 'apptainer test <image_name>.sif' to see the actual versions of R and FRASER installed
built-in R packages are installed in /usr/lib/R/library
other R packages were added in /usr/local/lib/R/site-library
Authors : valentin.vautrot@u-bourgogne.fr

%post

# export R_VERSION=4.3.3
# echo "export R_VERSION=${R_VERSION}" >> $SINGULARITY_ENVIRONMENT
export DEBIAN_FRONTEND=noninteractive

apt-get update
apt-get install -y --no-install-recommends apt-utils
apt-get install -y --no-install-recommends \
    locales \
    software-properties-common \
    dirmngr \
    wget \

wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc
add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu jammy-cran40/"

apt-get install -y --no-upgrade --no-install-recommends -t jammy-cran40 r-base-core=4.3.3-1.2204.0 r-base=4.3.3-1.2204.0 r-recommended=4.3.3-1.2204.0 r-base-dev=4.3.3-1.2204.0

echo "installed R version :"
R --version

apt-get install -y --no-upgrade --no-install-recommends build-essential libcurl4-openssl-dev zlib1g-dev libxml2-dev libssl-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev libbz2-dev gfortran

echo "installed R version :"
R --version

# # install R packages :
Rscript -e 'install.packages("devtools")'
Rscript -e 'devtools::install_version("vegan", version ="2.6-4", repos = "https://cran.r-project.org")'
Rscript -e 'devtools::install_version("RcppArmadillo", version ="0.12.8.1.0", repos = "https://cran.r-project.org")'
Rscript -e 'install.packages("BiocManager", dependencies=TRUE)'
Rscript -e 'BiocManager::install("FRASER", version = "3.18")'
Rscript -e 'BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene", version = "3.18")'
Rscript -e 'BiocManager::install("org.Hs.eg.db", version = "3.18")'

# Clean up
rm -rf /var/lib/apt/lists/*

%test
echo "installed R version :"
R --version
echo "installed FRASER package version :"
Rscript -e 'packageVersion("FRASER")'

%labels 
Auhtors valentin.vautrot@u-bourgogne.fr
Contained_OS_version Ubuntu_22.04_LTS_JammyJellyfish
Contained_R_version 4.3.3
Contained_FRASER_version 1.14.1