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- Add packages already installed via Rocker to skip file - Move scripts to src - Add comments to src/install.sh
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| # APT required | ||
| curl | ||
| libzmq3-dev | ||
| python3-pip |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| # APT skip | ||
| build-essential | ||
| clustalo # for LowMACA | ||
| default-jdk # Rocker | ||
| firefox # for packages using utils::browseURL() | ||
| #fuse # for Travel | ||
| gfortran # Rocker | ||
| git | ||
| gobjc | ||
| infernal # for inferrnal | ||
| kallisto # for rkal | ||
| #libavfilter-dev # for av/spacialHeatmap | ||
| libbz2-dev # Rocker | ||
| libcairo2-dev # Rocker | ||
| libcurl4-openssl-dev # Rocker | ||
| libfribidi-dev # for EnhancedVolcano--is this still needed? | ||
| #libfuse-dev # for Travel | ||
| libgraphviz-dev # for Rgraphviz | ||
| libicu-dev # Rocker | ||
| libjpeg-dev # Rocker | ||
| liblzma-dev # Rocker | ||
| #libmono-system-data4.0-cil # for rawr | ||
| libpcre2-dev # Rocker | ||
| libpng-dev # Rocker | ||
| libreadline-dev # Rocker | ||
| librsvg2-dev # for rsvg | ||
| libssl-dev # for openssl, mongolite | ||
| libtiff-dev # Rocker | ||
| libx11-dev | ||
| libxt-dev # Rocker | ||
| #mono-runtime # for rawr | ||
| #ocl-icd-opencl-dev # for gpuMagic | ||
| python3-minimal | ||
| zlib1g-dev # Rocker |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| cwltool | ||
| pandas | ||
| pyyaml | ||
| sklearn | ||
| tensorflow | ||
| wheel |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,61 @@ | ||
| #!/bin/bash | ||
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| set -e | ||
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| # Set variables | ||
| version="20.04" | ||
| repo="https://github.com/Bioconductor/BBS" | ||
| branch="master" | ||
| bbs="/tmp/BBS/Ubuntu-files/$version" | ||
| bioconductor_docker="/tmp/$version" | ||
| bbs_apt_files="apt_required_compile_R.txt apt_required_build.txt apt_bioc.txt apt_cran.txt" | ||
| bbs_pip_files="pip_pkgs.txt pip_spb.txt" | ||
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| # Get repository with Ubuntu-files | ||
| if [ ! -d "/tmp/BBS" ]; then | ||
| git clone -b $branch --depth 1 $repo /tmp/BBS | ||
| fi | ||
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| cd $bbs | ||
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| # Write a sorted list of BBS apt packages, skipping any commented lines. | ||
| cat $bbs_apt_files | awk '/^[^#]/ {print $1}' | sort >> /tmp/bbs_apt_pkgs | ||
| # Write a sorted list of apt packages to remove from the install list, | ||
| # excluding any commented lines. | ||
| cat $bioconductor_docker/apt_skip.txt | awk '/^[^#]/ {print $1}' | sort >> /tmp/skip_apt_pkgs | ||
| # Write a file listing the apt packages to install, removing all packages | ||
| # in skip_apt_pkgs. | ||
| 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. | ||
| cat $bbs_pip_files | awk '/^[^#]/ {print $1}' | sort >> /tmp/bbs_pip_pkgs | ||
| cat $bioconductor_docker/pip_skip.txt | awk '/^[^#]/ {print $1}' | sort >> /tmp/skip_pip_pkgs | ||
| 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 | ||
| cat $bioconductor_docker/apt_required.txt | awk '/^[^#]/ {print $1}' >> /tmp/install_apt_pkgs | ||
| apt_pkgs=$(cat /tmp/install_apt_pkgs) | ||
| pip_pkgs=$(cat /tmp/install_pip_pkgs) | ||
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| # Install dependencies | ||
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| # Install apt packages | ||
| apt-get update \ | ||
| && apt-get install -y --no-install-recommends apt-utils | ||
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| apt-get install -y --no-install-recommends $apt_pkgs \ | ||
| && apt-get clean && rm -rf /var/lib/apt/lists/* | ||
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| # Install pip packages | ||
| pip3 install $pip_pkgs | ||
| rm -rf ~/.cache/pip | ||
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| # Remove files | ||
| if test -n "$(find /tmp -maxdepth 1 -name '*_pkgs' -print -quit)"; then | ||
| cd /tmp | ||
| rm bbs_apt_files bbs_pip_files | ||
| rm -rf BBS | ||
| cd | ||
| fi |