Dockerfile

# FROM ubuntu:bionic
FROM tomkellygenetics/universc:latest

#---[2021/03/22 15:53] update apt-get, grab R 3.6.3 and perl
RUN apt-get update -qq \
 && apt-get install -y --no-install-recommends software-properties-common dirmngr \
 && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 \
 && add-apt-repository -y "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" \
 && echo "deb http://cloud.r-project.org/bin/linux/ubuntu bionic-cran40/" >>/etc/apt/sources.list \
 && apt-get update \
 && apt-get upgrade -y \
 && apt-get install -y perl git wget \
 && apt-get install -y --allow-unauthenticated r-base-core r-base

#---[2021/03/22 15:54] install missing libs for compile R packages
RUN apt-get -y install libcurl4-gnutls-dev \
 && apt-get -y install libssl-dev \
 && apt-get -y install libxml2-dev \
 && apt-get -y install libfontconfig1-dev \
 && apt-get -y install libharfbuzz-dev \
 && apt-get -y install libfribidi-dev \
 && apt-get -y install libfreetype6-dev \
 && apt-get -y install libtiff5-dev \
 && apt-get -y install libjpeg-dev \
 && apt-get -y install libpng-dev \
 && apt-get -y install libudunits2-dev \
 && apt-get -y install libgdal-dev

#---[2021/03/22 15:54] install common R packages
RUN Rscript -e 'install.packages("Matrix", repos="http://R-Forge.R-project.org")' \
 && Rscript -e 'install.packages("R.utils")' \
 && Rscript -e 'install.packages("data.table")' \
 && Rscript -e 'install.packages("docopt")' \
 && Rscript -e 'install.packages("ROCR")' \
 && Rscript -e 'install.packages("PRROC")' \
 && Rscript -e 'install.packages("caret")' \
 && Rscript -e 'install.packages("e1071")' \
 && Rscript -e 'install.packages("ggplot2")' \
 && Rscript -e 'install.packages("scales")' \
 && Rscript -e 'install.packages("reshape2")'
 
#---[2021/03/22 15:54] install monocle and cicero
RUN Rscript -e 'install.packages("devtools")' \
 && Rscript -e 'install.packages("BiocManager")' \
 && Rscript -e 'devtools::install_version("RcppAnnoy", "0.0.16")' \
 && Rscript -e 'install.packages("BiocManager")' \
 && Rscript -e 'BiocManager::install(c("BiocGenerics", "DelayedArray", \
    "DelayedMatrixStats","limma", "S4Vectors", "SingleCellExperiment", \
    "SummarizedExperiment", "batchelor", "Matrix.utils"))' \
 && Rscript -e 'devtools::install_github("cole-trapnell-lab/leidenbase")' \
 && Rscript -e 'devtools::install_github("cole-trapnell-lab/monocle3")' \
 && Rscript -e 'BiocManager::install(c("Gviz", "GenomicRanges", "rtracklayer"))' \
 && Rscript -e 'devtools::install_github("cole-trapnell-lab/cicero-release", ref = "monocle3")'

#---[2021/03/22 15:54] clone the git
RUN git clone -v https://github.com/chung-lab/SCAFE 2>2021032308

#---[2021/03/22 15:54] install the paths
WORKDIR ./SCAFE

RUN chmod 755 -R ./scripts/ \
 && chmod 755 -R ./resources/bin/ \
 && echo "export PATH=\$PATH:/SCAFE/scripts" >>~/.bashrc

#---[2021/03/22 15:54] start bash when run
CMD ["/bin/bash"]