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Dockerfile
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# Image for INTERVENE Synthetic data pipeline
FROM debian:bullseye-slim
RUN set -eux; \
apt-get update; \
apt-get install -y --no-install-recommends \
ca-certificates \
curl \
; \
rm -rf /var/lib/apt/lists/*
# ********************* Build basic julia image ******************************************
ENV JULIA_PATH /usr/local/julia
ENV PATH $JULIA_PATH/bin:$PATH
# https://julialang.org/juliareleases.asc
# Julia (Binary signing key) <[email protected]>
ENV JULIA_GPG 3673DF529D9049477F76B37566E3C7DC03D6E495
# https://julialang.org/downloads/
ENV JULIA_VERSION 1.6.4
RUN set -eux; \
\
savedAptMark="$(apt-mark showmanual)"; \
if ! command -v gpg > /dev/null; then \
apt-get update; \
apt-get install -y --no-install-recommends \
gnupg \
dirmngr \
; \
rm -rf /var/lib/apt/lists/*; \
fi; \
\
# https://julialang.org/downloads/#julia-command-line-version
# https://julialang-s3.julialang.org/bin/checksums/julia-1.6.4.sha256
arch="$(dpkg --print-architecture)"; \
case "$arch" in \
'amd64') \
url='https://julialang-s3.julialang.org/bin/linux/x64/1.6/julia-1.6.4-linux-x86_64.tar.gz'; \
sha256='52244ae47697e8073dfbc9d1251b0422f0dbd1fbe1a41da4b9f7ddf0506b2132'; \
;; \
'armhf') \
url='https://julialang-s3.julialang.org/bin/linux/armv7l/1.6/julia-1.6.4-linux-armv7l.tar.gz'; \
sha256='9ad3f6bd71eb6840d4cef1569855da20c0b4931a2bdf77703a64df672b0702a1'; \
;; \
'arm64') \
url='https://julialang-s3.julialang.org/bin/linux/aarch64/1.6/julia-1.6.4-linux-aarch64.tar.gz'; \
sha256='072daac7229c15fa41d0c1b65b8a3d6ee747323d02f5943da3846b075291b48b'; \
;; \
'i386') \
url='https://julialang-s3.julialang.org/bin/linux/x86/1.6/julia-1.6.4-linux-i686.tar.gz'; \
sha256='9d43d642174cf22cf0fde18dc2578c84f357d2c619b9d846d3a6da4192ba48cf'; \
;; \
*) \
echo >&2 "error: current architecture ($arch) does not have a corresponding Julia binary release"; \
exit 1; \
;; \
esac; \
\
curl -fL -o julia.tar.gz.asc "$url.asc"; \
curl -fL -o julia.tar.gz "$url"; \
\
echo "$sha256 *julia.tar.gz" | sha256sum --strict --check -; \
\
export GNUPGHOME="$(mktemp -d)"; \
gpg --batch --keyserver keyserver.ubuntu.com --recv-keys "$JULIA_GPG"; \
gpg --batch --verify julia.tar.gz.asc julia.tar.gz; \
command -v gpgconf > /dev/null && gpgconf --kill all; \
rm -rf "$GNUPGHOME" julia.tar.gz.asc; \
\
mkdir "$JULIA_PATH"; \
tar -xzf julia.tar.gz -C "$JULIA_PATH" --strip-components 1; \
rm julia.tar.gz; \
\
apt-mark auto '.*' > /dev/null; \
[ -z "$savedAptMark" ] || apt-mark manual $savedAptMark; \
apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false; \
\
# smoke test
julia --version
# **************************** Install tools ***********************************
ENV TOOLS_DIR /opt/tools
ENV DOWNLOAD_DIR /home/Downloads
ENV PLINK_PATH "$TOOLS_DIR/plink"
ENV PLINK2_PATH "$TOOLS_DIR/plink2"
ENV KING_PATH "$TOOLS_DIR/king"
ENV VCFTOOLS_PATH "$TOOLS_DIR/vcftools"
ENV BCFTOOLS_PATH "$TOOLS_DIR/bcftools"
ENV MAPTHIN_PATH "$TOOLS_DIR/mapthin"
# Add tools to PATH
ENV PATH $PLINK_PATH:$PLINK2_PATH:$KING_PATH:$VCFTOOLS_PATH/bin:$BCFTOOLS_PATH/bin:$MAPTHIN_PATH:$PATH
# Setup compression tools
RUN set -eux; \
apt-get update; \
apt-get install -y --no-install-recommends \
unzip \
git \
autoconf automake build-essential pkg-config zlib1g-dev cmake \
libbz2-dev liblzma-dev
RUN set -eux; \
# Setup tools directory
mkdir -p $TOOLS_DIR; \
mkdir -p $DOWNLOAD_DIR; \
# Setup Plink 1.9
echo "Setting up Plink 1.9"; \
curl -fL -o $DOWNLOAD_DIR/plink1.zip "http://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20201019.zip"; \
unzip $DOWNLOAD_DIR/plink1.zip -d "$PLINK_PATH"; \
# Setup Plink2
echo "Setting up Plink 2.0"; \
curl -fL -o $DOWNLOAD_DIR/plink2.zip "https://s3.amazonaws.com/plink2-assets/plink2_linux_avx2_latest.zip"; \
unzip $DOWNLOAD_DIR/plink2.zip -d "$PLINK2_PATH"; \
# Setup KING
echo "Setting up KING"; \
curl -fL -o $DOWNLOAD_DIR/king.tar.gz "https://www.kingrelatedness.com/Linux-king.tar.gz"; \
mkdir "$KING_PATH"; \
tar -xzf $DOWNLOAD_DIR/king.tar.gz -C "$KING_PATH"; \
# Setup vcftools
echo "Setting up vcftools"; \
cd "$DOWNLOAD_DIR"; \
git clone https://github.com/vcftools/vcftools.git; \
cd vcftools; \
./autogen.sh; \
./configure --prefix="$VCFTOOLS_PATH"; \
make; \
make install; \
cd -; \
# Setup bcftools
echo "Setting up bcftools"; \
cd "$DOWNLOAD_DIR"; \
curl -fL -o bcftools.tar.bz2 https://github.com/samtools/bcftools/releases/download/1.13/bcftools-1.13.tar.bz2; \
mkdir -p bcftools; \
tar -xf bcftools.tar.bz2 -C "bcftools" --strip-components 1; \
cd bcftools; \
./configure --prefix="$BCFTOOLS_PATH"; \
make; \
make install; \
cd -; \
# Setup mapthin
echo "Setting up mapthin"; \
cd "$DOWNLOAD_DIR"; \
curl --insecure -fL -o mapthin.zip https://www.staff.ncl.ac.uk/richard.howey/mapthin/mapthin-v1.11-linux-x86_64.zip; \
unzip mapthin.zip; \
mkdir $MAPTHIN_PATH; \
mv mapthin-v1.11-linux-x86_64/* $MAPTHIN_PATH; \
chmod +x $MAPTHIN_PATH/mapthin; \
# Setup plinkio
echo "Setting up plinkio"; \
cd "$DOWNLOAD_DIR"; \
curl -fL -o libplinkio.zip https://github.com/mfranberg/libplinkio/archive/refs/tags/v0.9.8.zip; \
unzip libplinkio.zip; \
cd libplinkio-0.9.8; \
mkdir build; \
cd build; \
cmake ../; \
make && make test && make install; \
# Debug
# ls -la $TOOLS_DIR; \
# ls -la $PLINK_PATH; \
# ls -la $PLINK2_PATH; \
# ls -la $KING_PATH; \
# ls -la $BCFTOOLS_PATH; \
# ls -ls $BCFTOOLS_PATH/bin; \
# ls -ls $BCFTOOLS_PATH/libexec; \
# ls -la $MAPTHIN_PATH; \
\
# Test
# plink --version; \
# plink2 --version; \
# which king; \
# vcftools --version; \
# bcftools --version; \
# mapthin; \
# Clean up
rm -rf $DOWNLOAD_DIR
# ************************* Add INTERVENE scripts *********************************
WORKDIR /opt/intervene
ENV SCRIPT_DIR "/opt/intervene/scripts"
ENV DATA_DIR "/data"
ENV JULIA_PROJECT $SCRIPT_DIR
RUN mkdir -p $DATA_DIR
# ENV JULIA_DEPOT_PATH "/opt/intervene/.julia/"
# RUN mkdir -p $JULIA_DEPOT_PATH
RUN echo "cat banner.txt\n" >> ~/.bashrc
# Copy source files
WORKDIR $SCRIPT_DIR
COPY . .
RUN ln -s $DATA_DIR .
# Install Julia packages
RUN set -eux; \
julia --project=$SCRIPT_DIR -e \
"using Pkg; Pkg.instantiate(); using Conda; Conda.add(\"bed-reader\")"
# Install dependencies for phenotype generation
RUN set -eux; \
apt-get update; \
apt-get install -y --no-install-recommends \
libgsl-dev \
libblas-dev liblapack-dev
# Build phenotype generation binary
ENV PHENO_BIN_PATH "$TOOLS_DIR/phenotype"
RUN mkdir -p $PHENO_BIN_PATH
ENV PATH $PHENO_BIN_PATH:$PATH
RUN set -eux; \
cd algorithms/phenotype; \
gcc Main.c Support.c -o $PHENO_BIN_PATH/phenoalg -L. -lm -lgsl -fPIC -lblas -lplinkio
# Setup path for commands
ENV PATH "$SCRIPT_DIR/commands":$PATH