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Upgrade base image from Debian Bullseye (oldstable) to Bookworm (stable) #233

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Sep 5, 2024
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Upgrade base image from Debian Bullseye (oldstable) to Bookworm (stable) #233

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12 changes: 6 additions & 6 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ FROM --platform=$BUILDPLATFORM tonistiigi/xx AS xx
# Define a builder stage that runs on the build platform.
# Even if the target platform is different, instructions will run natively for
# faster compilation.
FROM --platform=$BUILDPLATFORM debian:11-slim AS builder-build-platform
FROM --platform=$BUILDPLATFORM debian:bookworm-slim AS builder-build-platform

SHELL ["/bin/bash", "-e", "-u", "-o", "pipefail", "-c"]

Expand All @@ -26,7 +26,6 @@ COPY --from=xx / /
# curl: for downloading source files
# git: used in builder-scripts/download-repo
# make: used for building from Makefiles (search for usage); may be used by package managers to build from source
# pkg-config: for building VCFtools; may be used by package managers to build from source
# nodejs: for installing Auspice
# clang: for compiling C/C++ projects; may be used by package managers to build from source
RUN apt-get update && apt-get install -y --no-install-recommends \
Expand All @@ -37,7 +36,6 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
curl \
git \
make \
pkg-config \
dpkg-dev

# Install a specific Node.js version
Expand All @@ -57,12 +55,14 @@ ARG TARGETARCH
# https://github.com/tonistiigi/xx#building-on-debian
# binutils, gcc, libc6-dev: for compiling C/C++ programs (TODO: verify)
# g++: for building VCFtools; may be used by package managers to build from source
# pkg-config: for building VCFtools; may be used by package managers to build from source
# zlib1g-dev: for building VCFtools; may be used by package managers to build from source
RUN xx-apt-get install -y \
binutils \
gcc \
g++ \
libc6-dev \
pkg-config \
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zlib1g-dev

# Add dependencies. All should be pinned to specific versions, except
Expand Down Expand Up @@ -224,7 +224,7 @@ RUN curl -fsSL https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-$
# This is in place for Python programs which are not easy to install for a
# different target platform¹.
# ¹ https://github.com/pypa/pip/issues/5453
FROM --platform=$TARGETPLATFORM python:3.10-slim-bullseye AS builder-target-platform
FROM --platform=$TARGETPLATFORM python:3.10-slim-bookworm AS builder-target-platform

SHELL ["/bin/bash", "-e", "-u", "-o", "pipefail", "-c"]

Expand Down Expand Up @@ -350,7 +350,7 @@ RUN pip3 install evofr
# ———————————————————————————————————————————————————————————————————— #

# Now build the final image.
FROM python:3.10-slim-bullseye AS final
FROM python:3.10-slim-bookworm AS final

SHELL ["/bin/bash", "-e", "-u", "-o", "pipefail", "-c"]

Expand Down Expand Up @@ -407,7 +407,7 @@ ARG TARGETPLATFORM
# ¹ https://cvxopt.org/install/#building-and-installing-from-source
RUN if [[ "$TARGETPLATFORM" == linux/arm64 ]]; then \
apt-get update && apt-get install -y --no-install-recommends \
libopenblas-base \
libopenblas0 \
; \
fi

Expand Down