#! Dockerfile for installing CNVkit!#

# Pull base image.
FROM ubuntu:20.04

# Python version
ARG python_version="3.9.0"
ARG htslib_version="1.16"
ARG samtools_version="1.16.1"
ARG r_version="4.1.1"

# Noninteractive environment
ENV DEBIAN_FRONTEND=noninteractive

# Install prerequisites for Python.
RUN apt-get update && apt-get install -y build-essential checkinstall \
libreadline-gplv2-dev libncursesw5-dev libssl-dev libsqlite3-dev \
tk-dev libgdbm-dev libc6-dev libbz2-dev libffi-dev wget gcc tabix liblzma-dev

# Install prerequisits for R
RUN apt-get update -y && apt-get upgrade -y && apt-get install -y \
   git \
   clang \
   g++ \
   gcc \
   bzip2 \
   pandoc \
   ca-certificates \
   software-properties-common \
   apt-transport-https \
   build-essential \
   libv8-dev \
   libgsl-dev \
   libcurl4-openssl-dev \
   curl

#Downloading, unpacking and deleting .tgz python file.
WORKDIR /usr/src
RUN wget https://www.python.org/ftp/python/${python_version}/Python-${python_version}.tgz && \
tar xzf /usr/src/Python-${python_version}.tgz && rm /usr/src/Python-${python_version}.tgz

#Install Python and remove tmp files.

WORKDIR /usr/src/Python-${python_version}
RUN ./configure && make altinstall

# Install pip.
RUN wget https://bootstrap.pypa.io/get-pip.py

RUN python3.9 get-pip.py

RUN pip3 install pandas
RUN apt-get install libatlas-base-dev gfortran -y
RUN pip3 install --upgrade pandas
RUN pip3 install numpy
RUN pip3 install --upgrade numexpr
RUN pip3 install scipy
RUN pip3 install --upgrade scipy
RUN pip3 install matplotlib
RUN pip3 install reportlab
RUN pip3 install argparse
RUN pip3 install pysam
RUN pip3 install biopython pyfaidx reportlab pyvcf --upgrade
RUN pip3 install --upgrade cython 

# Install CNVKit
RUN pip3 install cnvkit

# Define working directory.
WORKDIR /opt

#Install R
RUN apt-key adv --refresh-keys --keyserver keyserver.ubuntu.com
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
RUN apt-get clean && apt-get autoclean && apt-get update
RUN add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'

RUN apt-get update -y && apt-get upgrade -y && apt-get install -y --no-install-recommends r-base-dev 
   # r-base=${r_version}* \
   # r-recommended=${r_version}*

RUN wget -c https://cran.r-project.org/src/base/R-4/R-${r_version}.tar.gz && tar -xf R-${r_version}.tar.gz
WORKDIR /opt/R-${r_version}
RUN ./configure && make -j9 &&  make install

WORKDIR /opt/

# Install R packages
RUN echo 'options(repos = c(CRAN = "https://cloud.r-project.org"))' >> /opt/packages.R
RUN echo 'install.packages("BiocManager", version = "3.14", dependencies = TRUE)' >> /opt/packages.R
RUN echo 'install.packages("docopt", dependencies = TRUE)' >> /opt/packages.R
RUN Rscript /opt/packages.R

# Installing Bioconductor packages
RUN echo 'BiocManager::install("DNAcopy", version = "3.14")' >> /opt/bioc_packages.R
RUN Rscript /opt/bioc_packages.R

WORKDIR /opt/

# Install htslib
RUN apt-get install -y autoconf
RUN wget https://github.com/samtools/htslib/releases/download/${htslib_version}/htslib-${htslib_version}.tar.bz2
RUN tar -xjf htslib-${htslib_version}.tar.bz2
WORKDIR /opt/htslib-${htslib_version}
RUN autoreconf -i  && ./configure
RUN make && make install

WORKDIR /opt/

# Install samtools
RUN wget https://github.com/samtools/samtools/releases/download/${samtools_version}/samtools-${samtools_version}.tar.bz2
RUN tar -xjf samtools-${samtools_version}.tar.bz2
WORKDIR /opt/samtools-${samtools_version}
RUN autoheader
RUN autoconf -Wno-syntax  && ./configure
RUN make && make install

WORKDIR /opt/

# Install bcftools
RUN wget https://github.com/samtools/bcftools/releases/download/${htslib_version}/bcftools-${htslib_version}.tar.bz2
RUN tar -xjf bcftools-${htslib_version}.tar.bz2
WORKDIR /opt/bcftools-${htslib_version}
RUN autoheader
RUN autoconf -Wno-syntax  && ./configure
RUN make && make install

WORKDIR /opt/

# Remove compressed files
RUN rm -r htslib-${htslib_version}.tar.bz2
RUN rm -r samtools-${samtools_version}.tar.bz2
RUN rm -r bcftools-${htslib_version}.tar.bz2

# Set python same as python3.10
RUN ln -sf /usr/local/bin/python3.9 /usr/local/bin/python
RUN ln -sf /usr/local/bin/python3.9 /usr/local/bin/python3

# Copy Dockerfile.
COPY Dockerfile /opt/