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jwokatyjwokaty
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Move dependences out of Dockerfile
- Add packages already installed via Rocker to skip file - Move scripts to src - Add comments to src/install.sh
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‎Dockerfile

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Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@ ARG BIOCONDUCTOR_VERSION=3.14
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##### IMPORTANT ########
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## The PATCH version number should be incremented each time
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## there is a change in the Dockerfile.
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ARG BIOCONDUCTOR_PATCH=17
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ARG BIOCONDUCTOR_PATCH=18
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ARG BIOCONDUCTOR_DOCKER_VERSION=${BIOCONDUCTOR_VERSION}.${BIOCONDUCTOR_PATCH}
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LABEL name="bioconductor/bioconductor_docker" \
@@ -29,133 +29,15 @@ RUN dpkg --clear-avail
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# 'debconf: unable to initialize frontend: Dialog'
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ENV DEBIAN_FRONTEND noninteractive
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# Update apt-get
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RUN apt-get update \
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&& apt-get install -y --no-install-recommends apt-utils \
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&& apt-get install -y --no-install-recommends \
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## Basic deps
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gdb \
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libxml2-dev \
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python3-pip \
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libz-dev \
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liblzma-dev \
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libbz2-dev \
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libpng-dev \
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libgit2-dev \
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## sys deps from bioc_full
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pkg-config \
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fortran77-compiler \
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byacc \
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automake \
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curl \
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## This section installs libraries
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libpcre2-dev \
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libnetcdf-dev \
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libhdf5-serial-dev \
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libfftw3-dev \
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libopenbabel-dev \
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libopenmpi-dev \
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libxt-dev \
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libudunits2-dev \
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libgeos-dev \
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libproj-dev \
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libcairo2-dev \
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libtiff5-dev \
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libreadline-dev \
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libgsl0-dev \
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libgslcblas0 \
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libgtk2.0-dev \
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libgl1-mesa-dev \
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libglu1-mesa-dev \
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libgmp3-dev \
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libhdf5-dev \
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libncurses-dev \
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libbz2-dev \
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libxpm-dev \
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liblapack-dev \
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libv8-dev \
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libgtkmm-2.4-dev \
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libmpfr-dev \
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libmodule-build-perl \
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libapparmor-dev \
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libprotoc-dev \
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librdf0-dev \
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libmagick++-dev \
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libsasl2-dev \
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libpoppler-cpp-dev \
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libprotobuf-dev \
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libpq-dev \
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libperl-dev \
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## software - perl extentions and modules
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libarchive-extract-perl \
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libfile-copy-recursive-perl \
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libcgi-pm-perl \
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libdbi-perl \
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libdbd-mysql-perl \
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libxml-simple-perl \
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libmysqlclient-dev \
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default-libmysqlclient-dev \
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libgdal-dev \
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## new libs
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libglpk-dev \
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libeigen3-dev \
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## Databases and other software
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sqlite \
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openmpi-bin \
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mpi-default-bin \
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openmpi-common \
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openmpi-doc \
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tcl8.6-dev \
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tk-dev \
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default-jdk \
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imagemagick \
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tabix \
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ggobi \
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graphviz \
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protobuf-compiler \
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jags \
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## Additional resources
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xfonts-100dpi \
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xfonts-75dpi \
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biber \
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libsbml5-dev \
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libzmq3-dev \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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COPY src /tmp
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COPY Ubuntu-files /tmp
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## Python installations
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RUN apt-get update \
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&& apt-get install -y software-properties-common \
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&& add-apt-repository universe \
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&& apt-get update \
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&& apt-get -y --no-install-recommends install python2 python-dev \
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&& curl https://bootstrap.pypa.io/pip/2.7/get-pip.py --output get-pip.py \
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&& python2 get-pip.py \
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&& pip2 install wheel \
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## Install sklearn and pandas on python
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&& pip2 install sklearn \
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pandas \
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pyyaml \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* \
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&& rm -rf get-pip.py
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## FIXME
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## These two libraries don't install in the above section--WHY?
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RUN apt-get update \
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&& apt-get -y --no-install-recommends install \
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libmariadb-dev-compat \
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libjpeg-dev \
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libjpeg-turbo8-dev \
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libjpeg8-dev \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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# Install dependencies
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RUN bash /tmp/install.sh
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## Add host-site-library
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RUN echo "R_LIBS=/usr/local/lib/R/host-site-library:\${R_LIBS}" > /usr/local/lib/R/etc/Renviron.site
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ADD install.R /tmp/
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RUN R -f /tmp/install.R
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# DEVEL: Add sys env variables to DEVEL image

‎Ubuntu-files/20.04/apt_required.txt

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# APT required
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curl
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libzmq3-dev
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python3-pip

‎Ubuntu-files/20.04/apt_skip.txt

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# APT skip
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build-essential
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clustalo # for LowMACA
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default-jdk # Rocker
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firefox # for packages using utils::browseURL()
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#fuse # for Travel
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gfortran # Rocker
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git
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gobjc
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infernal # for inferrnal
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kallisto # for rkal
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#libavfilter-dev # for av/spacialHeatmap
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libbz2-dev # Rocker
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libcairo2-dev # Rocker
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libcurl4-openssl-dev # Rocker
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libfribidi-dev # for EnhancedVolcano--is this still needed?
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#libfuse-dev # for Travel
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libgraphviz-dev # for Rgraphviz
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libicu-dev # Rocker
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libjpeg-dev # Rocker
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liblzma-dev # Rocker
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#libmono-system-data4.0-cil # for rawr
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libpcre2-dev # Rocker
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libpng-dev # Rocker
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libreadline-dev # Rocker
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librsvg2-dev # for rsvg
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libssl-dev # for openssl, mongolite
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libtiff-dev # Rocker
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libx11-dev
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libxt-dev # Rocker
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#mono-runtime # for rawr
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#ocl-icd-opencl-dev # for gpuMagic
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python3-minimal
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zlib1g-dev # Rocker

‎Ubuntu-files/20.04/pip_skip.txt

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cwltool
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pandas
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pyyaml
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sklearn
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tensorflow
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wheel

‎install.R renamed to ‎src/install.R

File renamed without changes.

‎src/install.sh

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#!/bin/bash
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set -e
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# Set variables
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version="20.04"
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repo="https://github.com/Bioconductor/BBS"
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branch="master"
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bbs="/tmp/BBS/Ubuntu-files/$version"
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bioconductor_docker="/tmp/$version"
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bbs_apt_files="apt_required_compile_R.txt apt_required_build.txt apt_bioc.txt apt_cran.txt"
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bbs_pip_files="pip_pkgs.txt pip_spb.txt"
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# Get repository with Ubuntu-files
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if [ ! -d "/tmp/BBS" ]; then
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git clone -b $branch --depth 1 $repo /tmp/BBS
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fi
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cd $bbs
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# Write a sorted list of BBS apt packages, skipping any commented lines.
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cat $bbs_apt_files | awk '/^[^#]/ {print $1}' | sort >> /tmp/bbs_apt_pkgs
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# Write a sorted list of apt packages to remove from the install list,
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# excluding any commented lines.
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cat $bioconductor_docker/apt_skip.txt | awk '/^[^#]/ {print $1}' | sort >> /tmp/skip_apt_pkgs
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# Write a file listing the apt packages to install, removing all packages
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# in skip_apt_pkgs.
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comm -23 /tmp/bbs_apt_pkgs /tmp/skip_apt_pkgs >> /tmp/install_apt_pkgs
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# Write a file with pip packages to install.
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cat $bbs_pip_files | awk '/^[^#]/ {print $1}' | sort >> /tmp/bbs_pip_pkgs
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cat $bioconductor_docker/pip_skip.txt | awk '/^[^#]/ {print $1}' | sort >> /tmp/skip_pip_pkgs
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comm -23 /tmp/bbs_pip_pkgs /tmp/skip_pip_pkgs >> /tmp/install_pip_pkgs
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cd ~
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# Packages always required by Bioconductor Docker
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cat $bioconductor_docker/apt_required.txt | awk '/^[^#]/ {print $1}' >> /tmp/install_apt_pkgs
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apt_pkgs=$(cat /tmp/install_apt_pkgs)
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pip_pkgs=$(cat /tmp/install_pip_pkgs)
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# Install dependencies
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# Install apt packages
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apt-get update \
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&& apt-get install -y --no-install-recommends apt-utils
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apt-get install -y --no-install-recommends $apt_pkgs \
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&& apt-get clean && rm -rf /var/lib/apt/lists/*
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# Install pip packages
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pip3 install $pip_pkgs
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rm -rf ~/.cache/pip
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# Remove files
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if test -n "$(find /tmp -maxdepth 1 -name '*_pkgs' -print -quit)"; then
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cd /tmp
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rm bbs_apt_files bbs_pip_files
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rm -rf BBS
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cd
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fi

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