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#LABEL maintainer="Combiz Khozoie, Ph.D. [email protected], Alan Murphy, [email protected]"
## Use rstudio installs binaries from RStudio's RSPM service by default,
## Uses the latest stable ubuntu, R and Bioconductor versions. Created on unbuntu 20.04, R 4.0 and BiocManager 3.12
FROM rocker/rstudio
## Add packages dependencies
RUN apt-get update \
&& apt-get install -y --no-install-recommends apt-utils \
&& apt-get install -y --no-install-recommends \
## Basic deps
gdb \
## libxml2-dev \
# python3-pip \
libz-dev \
liblzma-dev \
libbz2-dev \
libpng-dev \
libgit2-dev \
## sys deps from bioc_full
pkg-config \
# fortran77-compiler \
byacc \
automake \
curl \
## This section installs libraries
libpcre2-dev \
libnetcdf-dev \
libhdf5-serial-dev \
libfftw3-dev \
libopenbabel-dev \
#libopenmpi-dev \
libxt-dev \
libudunits2-dev \
libgeos-dev \
libproj-dev \
#libcairo2-dev \
libtiff5-dev \
libreadline-dev \
libgsl0-dev \
libgslcblas0 \
libgtk2.0-dev \
#libgl1-mesa-dev \
#libglu1-mesa-dev \
libgmp3-dev \
libhdf5-dev \
libncurses-dev \
libbz2-dev \
libxpm-dev \
#liblapack-dev \
libv8-dev \
libgtkmm-2.4-dev \
libmpfr-dev \
libmodule-build-perl \
libapparmor-dev \
libprotoc-dev \
librdf0-dev \
libmagick++-dev \
libsasl2-dev \
libpoppler-cpp-dev \
libprotobuf-dev \
libpq-dev \
libperl-dev \
## software - perl extentions and modules
# libarchive-extract-perl \
# libfile-copy-recursive-perl \
# libcgi-pm-perl \
# libdbi-perl \
# libdbd-mysql-perl \
# libxml-simple-perl \
# libmysqlclient-dev \
# default-libmysqlclient-dev \
# libgdal-dev \
## new libs
libglpk-dev \
## Databases and other software
# sqlite \
# openmpi-bin \
# mpi-default-bin \
# openmpi-common \
# openmpi-doc \
# tcl8.6-dev \
# tk-dev \
default-jdk \
#imagemagick \
tabix \
#ggobi \
#graphviz \
protobuf-compiler \
jags \
## Additional resources
xfonts-100dpi \
xfonts-75dpi \
#biber \
libsbml5-dev \
## qpdf needed to stop R CMD Check warning
pandoc \
## qpdf needed to stop R CMD Check warning
qpdf \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
RUN install2.r -e \
anndata \
#stringr \
#cli \
#dplyr \
#data.table \
R.utils \
#ggpubr \
#ggplot2 \
rmarkdown \
rlang \
#future \
#plotly \
#rliger \
argparse \
#Hmisc \
rcmdcheck \
devtools \
#shiny \
remotes
## Install remaining packages from source
COPY ./misc/requirements-src.R .
RUN Rscript requirements-src.R
## Install Bioconductor packages
COPY ./misc/requirements-bioc.R .
COPY ./misc/requirements-bioc.R .
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
libfftw3-dev \
gcc && apt-get clean \
&& rm -rf /var/lib/apt/lists/*
RUN Rscript -e 'requireNamespace("BiocManager"); BiocManager::install(ask=F);' \
&& Rscript requirements-bioc.R
## Install from GH the following
RUN installGithub.r mojaveazure/seurat-disk
## Install scFlow package
# Copy description
WORKDIR scKirby
ADD . .
# Run R CMD check - will fail with any errors or warnings
#Run Rscript -e 'devtools::check()'
# Install R package from source
RUN Rscript -e "remotes::install_local()"
RUN rm -rf *