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Dockerfile
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# ----- Dockerfile Re-analysis Mathys et al., 2019-----
#LABEL maintainer="Alan Murphy, [email protected]"
#
FROM bioconductor/bioconductor_docker:RELEASE_3_15
## 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 \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
# Install R dependencies
RUN install2.r -e \
RcppParallel \
pacman \
qs \
data.table \
ggplot2 \
cowplot \
viridis \
ggrepel \
Hmisc \
reshape2 \
wesanderson \
Seurat \
&& rm -rf /tmp/downloaded_packages
# Install Bioc dependencies
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 -e 'options(timeout=2000);requireNamespace("BiocManager");BiocManager::install(c("SingleCellExperiment","biomaRt","edgeR","EnsDb.Hsapiens.v79"),ask=F)'