Add files for building docker image for rtools

# Dockerfile for rtools used in https://gitlab.fi.muni.cz/lexa/hic-te

FROM rocker/r-ver:4.1.3

RUN mkdir -p /install_script

COPY /install_script/install_packages.R /install_script/install_packages.R

RUN apt-get update \

    && apt-get install -y -qq --no-install-recommends --purge \

        libxml2 \

        libz-dev \

        libbz2-dev \

        liblzma-dev \

        libcurl4-openssl-dev \

    && Rscript "/install_script/install_packages.R" \

    && apt-get autoclean \

    && rm -rf /var/lib/apt/lists/* \

    && rm -rf /tmp/*

install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))

# in case there is some issues with installing packages, comment line 1 and uncomment line 4 

# install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/devel/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))

pak::pkg_install("GenomicRanges")

pak::pkg_install("Rsamtools")

pak::pkg_install("circlize")

pak::pkg_install("dplyr")

pak::pkg_install("ggplot2")

pak::pkg_install("gplots")

pak::pkg_install("karyoploteR")

pak::pkg_install("ragg")

pak::pkg_install("reshape2")

pak::pkg_install("rtracklayer")

pak::pkg_install("stringr")

pak::pak_cleanup(package_cache = TRUE, metadata_cache = TRUE, force = TRUE)