[ENH] initial docker / apptainer build files

docker/Dockerfile

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+FROM neurodebian:bookworm-non-free
+
+# set up dependency versions
+ARG GO_VERSION=1.23.6
+ARG APPTAINER_VERSION=1.4.1
+ARG OS=linux
+ARG ARCH=amd64
+
+# install dependencies
+RUN	apt update && apt upgrade && apt install -y autoconf automake build-essential cryptsetup cryptsetup-bin curl dh-apparmor fakeroot fuse2fs git fuse libfuse-dev libgpgme-dev libseccomp-dev libsubid-dev libtool pkg-config python3 python3.11-venv runc squashfs-tools squashfs-tools-ng tzdata uidmap uuid-dev wget zlib1g-dev
+
+#
+# install go from precompiled binary
+#
+
+RUN	wget https://dl.google.com/go/go$GO_VERSION.$OS-$ARCH.tar.gz
+RUN	tar -C /usr/local -xzvf go$GO_VERSION.$OS-$ARCH.tar.gz
+RUN	rm go$GO_VERSION.$OS-$ARCH.tar.gz
+
+ENV GOPATH=/usr/local/go
+ENV PATH=/usr/local/go/bin:${PATH}
+
+#
+# install apptainer from source
+#
+
+ARG MCONFIG_OPTIONS="--without-suid"
+WORKDIR $GOPATH/src/github.com/apptainer
+
+RUN git clone https://github.com/apptainer/apptainer.git $GOPATH/src/github.com/apptainer
+RUN cd $GOPATH/src/github.com/apptainer
+RUN git checkout "v$APPTAINER_VERSION"
+
+RUN	./mconfig $MCONFIG_OPTIONS -p /usr/local/apptainer
+RUN	make -C $GOPATH/src/github.com/apptainer/builddir
+RUN make -C $GOPATH/src/github.com/apptainer/builddir install
+
+ENV PATH=/usr/local/apptainer/bin:$PATH
+RUN rm -rf $GOPATH/src/github.com/apptainer
+
+#
+# install nipoppy
+#
+
+# create and activate venv
+RUN	python3 -m venv /nipoppy
+ENV PATH=/nipoppy/bin:$PATH
+
+# install nipoppy
+RUN	pip install --upgrade pip setuptools wheel
+RUN	pip install nipoppy[all]==0.4.0
+
+#
+# set up container
+#
+
+# set default directory to root
+WORKDIR /
+
+# set entry command to nipoppy
+CMD	["nipoppy"]

docker/nipoppy-0.4.0.def

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+Bootstrap: docker
+From: neurodebian:bookworm-non-free
+
+%post
+	apt update && apt upgrade && apt install -y autoconf automake build-essential cryptsetup cryptsetup-bin curl dh-apparmor fakeroot fuse2fs git fuse libfuse-dev libgpgme-dev libseccomp-dev libsubid-dev libtool pkg-config python3 python3.11-venv runc squashfs-tools squashfs-tools-ng tzdata uidmap uuid-dev wget zlib1g-dev
+
+	export GOVERSION=1.23.6 OS=linux ARCH=amd64
+
+	wget https://dl.google.com/go/go$GOVERSION.$OS-$ARCH.tar.gz
+	tar -C /usr/local -xzvf go$GOVERSION.$OS-$ARCH.tar.gz
+	rm go$GOVERSION.$OS-$ARCH.tar.gz
+
+	echo "export PATH=/usr/local/go/bin:${PATH}" >> $SINGULARITY_ENVIRONMENT
+	export PATH=/usr/local/go/bin:${PATH}
+
+	export APPVERSION=1.4.1
+	git clone https://github.com/apptainer/apptainer.git
+	cd apptainer && git checkout v${APPVERSION}
+
+	./mconfig && make -C builddir && make -C builddir install
+
+	cd ..
+	rm -rf apptainer
+
+	python3 -m venv /nipoppy
+
+	. /nipoppy/bin/activate
+
+	pip install --upgrade pip setuptools wheel
+	pip install nipoppy[all]==0.4.0
+
+	echo ". /nipoppy/bin/activate" >> $SINGULARITY_ENVIRONMENT
+
+%runscript
+	nipoppy
+
+%labels
+	Author bcmcpher@gmail.com
+	Version 0.4.0