ptato_img.def

# singularity definition file

Bootstrap: docker
From: ubuntu:22.04

%post
   ln -snf /usr/share/zoneinfo/$CONTAINER_TIMEZONE /etc/localtime && echo $CONTAINER_TIMEZONE > /etc/timezone

%post
   apt-get -y update && apt-get install -y python3 \
   make \
   wget \
   curl \
   openjdk-11-jdk \
   git \
   build-essential \
   libssl-dev \
   uuid-dev \
   libgpgme11-dev \
   squashfs-tools \
   libseccomp-dev \
   openjdk-11-jdk \
   tabix \
   libncurses-dev libbz2-dev liblzma-dev r-base r-base-core r-recommended r-base-dev \
   r-cran-rgl r-cran-rjags r-cran-snow r-cran-ggplot2 r-cran-igraph \
   r-cran-lme4 r-cran-rjava r-cran-devtools r-cran-roxygen2 r-cran-rjava \
   libxml2-dev libcairo2-dev libsqlite3-dev libmariadbd-dev \
   libpq-dev libssh2-1-dev unixodbc-dev libcurl4-openssl-dev libssl-dev coinor-libcbc-dev coinor-libclp-dev libglpk-dev
   apt-get install -y software-properties-common
   Rscript -e 'install.packages("BiocManager")'
   Rscript -e 'install.packages("randomForest")'
   Rscript -e 'BiocManager::install(c("BSgenome", "copynumber", "MutationalPatterns", "StructuralVariantAnnotation", "VariantAnnotation", "BSgenome.Hsapiens.UCSC.hg38"))'
   add-apt-repository -y ppa:apptainer/ppa
   apt update
   apt install -y apptainer
   git clone https://github.com/nextflow-io/nextflow
   cd nextflow && make compile && make pack && make install
   chmod 777 /nextflow/nextflow
   echo $PWD