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FROM rocker/r-ver:3.5.3

ENV PATH /opt/biotools/bin:$PATH
ENV ROOTSYS /opt/biotools/root
ENV LD_LIBRARY_PATH '$LD_LIBRARY_PATH:$ROOTSYS/lib'

RUN apt-get update
RUN apt-get install -yq tzdata
RUN apt-get install -y locales
RUN locale-gen "en_US.UTF-8"
RUN export LC_ALL=en_US.UTF-8
RUN export LANG=en_US.UTF-8

RUN apt-get install -y curl wget apt-utils
RUN apt-get install -y gcc fort77 aptitude
RUN aptitude install -y g++ xorg-dev libreadline-dev  gfortran
RUN apt-get install -y libssl-dev libxml2-dev libpcre3-dev liblzma-dev libbz2-dev libcurl4-openssl-dev liblapack3 git nano graphviz python3 python3-pip

RUN apt-get install -y  autotools-dev automake cmake grep sed dpkg fuse zip build-essential pkg-config bzip2 ca-certificates libglib2.0-0 libxext6 libsm6 libxrender1 mercurial subversion zlib1g-dev libncurses5-dev libncursesw5-dev

RUN apt-get clean

RUN if [ ! -d "/opt/biotools" ];then mkdir /opt/biotools; fi
RUN if [ ! -d "/opt/biotools/bin" ];then mkdir /opt/biotools/bin; fi
RUN chmod 777 -R /opt/biotools/
ENV PATH /opt/biotools/bin:$PATH

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RUN pip3 install snakemake==5.9.1 oyaml
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RUN pip3 install multiqc==1.9
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# Make table cells adapt to content (height and width)
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RUN sed -i "739s/absolute/relative/g" /usr/local/lib/python3.5/dist-packages/multiqc/templates/default/assets/css/default_multiqc.css
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RUN Rscript -e 'install.packages("yaml",Ncpus=8,repos="https://cloud.r-project.org/");library("yaml")'
RUN Rscript -e 'install.packages("DT",Ncpus=8,repos="https://cloud.r-project.org/");library("DT")'
RUN Rscript -e 'install.packages("devtools",Ncpus=8,repos="https://cloud.r-project.org/");library("devtools")'
RUN Rscript -e 'library(devtools);install.packages(c("fastmap","httpuv"),Ncpus=8,repos="https://cloud.r-project.org/");devtools::install_url("https://cloud.r-project.org/src/contrib/Archive/shiny/shiny_1.4.0.tar.gz");library("shiny")'
RUN Rscript -e 'install.packages("shinydashboard",Ncpus=8,repos="https://cloud.r-project.org/");library("shinydashboard")'
RUN Rscript -e 'install.packages("shinyjs",Ncpus=8,repos="https://cloud.r-project.org/");library("shinyjs")'
RUN Rscript -e 'install.packages("shinyFiles",Ncpus=8,repos="https://cloud.r-project.org/");library("shinyFiles")'
RUN Rscript -e 'install.packages("BiocManager",Ncpus=8,repos="https://cloud.r-project.org/");library("BiocManager")'
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RUN pip3 install cerberus