Dockerfile

#
# NOTE: THIS DOCKERFILE IS GENERATED VIA "apply-templates.sh"
#
# PLEASE DO NOT EDIT IT DIRECTLY.
#

FROM debian:bookworm-slim

# ensure local python is preferred over distribution python
ENV PATH /usr/local/bin:$PATH

# http://bugs.python.org/issue19846
# > At the moment, setting "LANG=C" on a Linux system *fundamentally breaks Python 3*, and that's not OK.
ENV LANG C.UTF-8

# runtime dependencies
RUN set -eux; \
	apt-get update; \
	apt-get install -y --no-install-recommends \
		ca-certificates \
		netbase \
		tzdata \
	; \
	rm -rf /var/lib/apt/lists/*

ENV GPG_KEY A035C8C19219BA821ECEA86B64E628F8D684696D
ENV PYTHON_VERSION 3.10.13

RUN set -eux; \
	\
	savedAptMark="$(apt-mark showmanual)"; \
	apt-get update; \
	apt-get install -y --no-install-recommends \
		dpkg-dev \
		gcc \
		gnupg \
		libbluetooth-dev \
		libbz2-dev \
		libc6-dev \
		libdb-dev \
		libexpat1-dev \
		libffi-dev \
		libgdbm-dev \
		liblzma-dev \
		libncursesw5-dev \
		libreadline-dev \
		libsqlite3-dev \
		libssl-dev \
		make \
		tk-dev \
		uuid-dev \
		wget \
		xz-utils \
		zlib1g-dev \
	; \
	\
	wget -O python.tar.xz "https://www.python.org/ftp/python/${PYTHON_VERSION%%[a-z]*}/Python-$PYTHON_VERSION.tar.xz"; \
	wget -O python.tar.xz.asc "https://www.python.org/ftp/python/${PYTHON_VERSION%%[a-z]*}/Python-$PYTHON_VERSION.tar.xz.asc"; \
	GNUPGHOME="$(mktemp -d)"; export GNUPGHOME; \
	gpg --batch --keyserver hkps://keys.openpgp.org --recv-keys "$GPG_KEY"; \
	gpg --batch --verify python.tar.xz.asc python.tar.xz; \
	gpgconf --kill all; \
	rm -rf "$GNUPGHOME" python.tar.xz.asc; \
	mkdir -p /usr/src/python; \
	tar --extract --directory /usr/src/python --strip-components=1 --file python.tar.xz; \
	rm python.tar.xz; \
	\
	cd /usr/src/python; \
	gnuArch="$(dpkg-architecture --query DEB_BUILD_GNU_TYPE)"; \
	./configure \
		--build="$gnuArch" \
		--enable-loadable-sqlite-extensions \
		--enable-optimizations \
		--enable-option-checking=fatal \
		--enable-shared \
		--with-lto \
		--with-system-expat \
		--without-ensurepip \
	; \
	nproc="$(nproc)"; \
	EXTRA_CFLAGS="$(dpkg-buildflags --get CFLAGS)"; \
	LDFLAGS="$(dpkg-buildflags --get LDFLAGS)"; \
	LDFLAGS="${LDFLAGS:--Wl},--strip-all"; \
	make -j "$nproc" \
		"EXTRA_CFLAGS=${EXTRA_CFLAGS:-}" \
		"LDFLAGS=${LDFLAGS:-}" \
		"PROFILE_TASK=${PROFILE_TASK:-}" \
	; \
# https://github.com/docker-library/python/issues/784
# prevent accidental usage of a system installed libpython of the same version
	rm python; \
	make -j "$nproc" \
		"EXTRA_CFLAGS=${EXTRA_CFLAGS:-}" \
		"LDFLAGS=${LDFLAGS:--Wl},-rpath='\$\$ORIGIN/../lib'" \
		"PROFILE_TASK=${PROFILE_TASK:-}" \
		python \
	; \
	make install; \
	\
	cd /; \
	rm -rf /usr/src/python; \
	\
	find /usr/local -depth \
		\( \
			\( -type d -a \( -name test -o -name tests -o -name idle_test \) \) \
			-o \( -type f -a \( -name '*.pyc' -o -name '*.pyo' -o -name 'libpython*.a' \) \) \
		\) -exec rm -rf '{}' + \
	; \
	\
	ldconfig; \
	\
	apt-mark auto '.*' > /dev/null; \
	apt-mark manual $savedAptMark; \
	find /usr/local -type f -executable -not \( -name '*tkinter*' \) -exec ldd '{}' ';' \
		| awk '/=>/ { so = $(NF-1); if (index(so, "/usr/local/") == 1) { next }; gsub("^/(usr/)?", "", so); printf "*%s\n", so }' \
		| sort -u \
		| xargs -r dpkg-query --search \
		| cut -d: -f1 \
		| sort -u \
		| xargs -r apt-mark manual \
	; \
	apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false; \
	rm -rf /var/lib/apt/lists/*; \
	\
	python3 --version

# make some useful symlinks that are expected to exist ("/usr/local/bin/python" and friends)
RUN set -eux; \
	for src in idle3 pydoc3 python3 python3-config; do \
		dst="$(echo "$src" | tr -d 3)"; \
		[ -s "/usr/local/bin/$src" ]; \
		[ ! -e "/usr/local/bin/$dst" ]; \
		ln -svT "$src" "/usr/local/bin/$dst"; \
	done

# if this is called "PIP_VERSION", pip explodes with "ValueError: invalid truth value '<VERSION>'"
ENV PYTHON_PIP_VERSION 23.0.1
# https://github.com/docker-library/python/issues/365
ENV PYTHON_SETUPTOOLS_VERSION 65.5.1
# https://github.com/pypa/get-pip
ENV PYTHON_GET_PIP_URL https://github.com/pypa/get-pip/raw/dbf0c85f76fb6e1ab42aa672ffca6f0a675d9ee4/public/get-pip.py
ENV PYTHON_GET_PIP_SHA256 dfe9fd5c28dc98b5ac17979a953ea550cec37ae1b47a5116007395bfacff2ab9

RUN set -eux; \
	\
	savedAptMark="$(apt-mark showmanual)"; \
	apt-get update; \
	apt-get install -y --no-install-recommends wget; \
	\
	wget -O get-pip.py "$PYTHON_GET_PIP_URL"; \
	echo "$PYTHON_GET_PIP_SHA256 *get-pip.py" | sha256sum -c -; \
	\
	apt-mark auto '.*' > /dev/null; \
	[ -z "$savedAptMark" ] || apt-mark manual $savedAptMark > /dev/null; \
	apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false; \
	rm -rf /var/lib/apt/lists/*; \
	\
	export PYTHONDONTWRITEBYTECODE=1; \
	\
	python get-pip.py \
		--disable-pip-version-check \
		--no-cache-dir \
		--no-compile \
		"pip==$PYTHON_PIP_VERSION" \
		"setuptools==$PYTHON_SETUPTOOLS_VERSION" \
	; \
	rm -f get-pip.py; \
	\
	pip --version

CMD ["python3"]

CMD git clone https://github.com/AlexandrovLab/DupCaller.git && cd DupCaller && pip install .