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https://github.com/jupyter/docker-stacks.git
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Add a setup script to install Julia + IJulia (#1927)
This commit is contained in:
Yuvi Panda
@@ -12,12 +12,6 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
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USER root
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# Julia installation
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# Default values can be overridden at build time
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# (ARGS are in lower case to distinguish them from ENV)
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# Check https://julialang.org/downloads/
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ARG julia_version="1.9.1"
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# R pre-requisites
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RUN apt-get update --yes && \
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apt-get install --yes --no-install-recommends \
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@@ -29,36 +23,16 @@ RUN apt-get update --yes && \
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# Julia dependencies
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# install Julia packages in /opt/julia instead of ${HOME}
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ENV JULIA_DEPOT_PATH=/opt/julia \
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JULIA_PKGDIR=/opt/julia \
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JULIA_VERSION="${julia_version}"
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JULIA_PKGDIR=/opt/julia
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WORKDIR /tmp
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# hadolint ignore=SC2046
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RUN set -x && \
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julia_arch=$(uname -m) && \
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julia_short_arch="${julia_arch}" && \
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if [ "${julia_short_arch}" == "x86_64" ]; then \
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julia_short_arch="x64"; \
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fi; \
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julia_installer="julia-${JULIA_VERSION}-linux-${julia_arch}.tar.gz" && \
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julia_major_minor=$(echo "${JULIA_VERSION}" | cut -d. -f 1,2) && \
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mkdir "/opt/julia-${JULIA_VERSION}" && \
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wget --progress=dot:giga "https://julialang-s3.julialang.org/bin/linux/${julia_short_arch}/${julia_major_minor}/${julia_installer}" && \
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tar xzf "${julia_installer}" -C "/opt/julia-${JULIA_VERSION}" --strip-components=1 && \
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rm "${julia_installer}" && \
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ln -fs /opt/julia-*/bin/julia /usr/local/bin/julia
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# Show Julia where conda libraries are \
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RUN mkdir /etc/julia && \
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echo "push!(Libdl.DL_LOAD_PATH, \"${CONDA_DIR}/lib\")" >> /etc/julia/juliarc.jl && \
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# Create JULIA_PKGDIR \
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mkdir "${JULIA_PKGDIR}" && \
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chown "${NB_USER}" "${JULIA_PKGDIR}" && \
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fix-permissions "${JULIA_PKGDIR}"
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# Setup Julia
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RUN /opt/setup-scripts/setup-julia.bash
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USER ${NB_UID}
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# Setup IJulia kernel & other packages
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RUN /opt/setup-scripts/setup-julia-packages.bash
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# R packages including IRKernel which gets installed globally.
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# r-e1071: dependency of the caret R package
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RUN mamba install --yes \
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@@ -86,18 +60,3 @@ RUN mamba install --yes \
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mamba clean --all -f -y && \
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fix-permissions "${CONDA_DIR}" && \
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fix-permissions "/home/${NB_USER}"
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# Add Julia packages.
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# Install IJulia as jovyan and then move the kernelspec out
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# to the system share location. Avoids problems with runtime UID change not
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# taking effect properly on the .local folder in the jovyan home dir.
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RUN julia -e 'import Pkg; Pkg.update()' && \
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julia -e 'import Pkg; Pkg.add("HDF5")' && \
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julia -e 'using Pkg; pkg"add IJulia"; pkg"precompile"' && \
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# move kernelspec out of home \
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mv "${HOME}/.local/share/jupyter/kernels/julia"* "${CONDA_DIR}/share/jupyter/kernels/" && \
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chmod -R go+rx "${CONDA_DIR}/share/jupyter" && \
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rm -rf "${HOME}/.local" && \
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fix-permissions "${JULIA_PKGDIR}" "${CONDA_DIR}/share/jupyter"
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WORKDIR "${HOME}"
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@@ -12,56 +12,15 @@ SHELL ["/bin/bash", "-o", "pipefail", "-c"]
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USER root
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# Julia installation
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# Default values can be overridden at build time
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# (ARGS are in lower case to distinguish them from ENV)
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# Check https://julialang.org/downloads/
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ARG julia_version="1.9.1"
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# Julia dependencies
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# install Julia packages in /opt/julia instead of ${HOME}
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ENV JULIA_DEPOT_PATH=/opt/julia \
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JULIA_PKGDIR=/opt/julia \
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JULIA_VERSION="${julia_version}"
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JULIA_PKGDIR=/opt/julia
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WORKDIR /tmp
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# hadolint ignore=SC2046
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RUN set -x && \
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julia_arch=$(uname -m) && \
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julia_short_arch="${julia_arch}" && \
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if [ "${julia_short_arch}" == "x86_64" ]; then \
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julia_short_arch="x64"; \
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fi; \
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julia_installer="julia-${JULIA_VERSION}-linux-${julia_arch}.tar.gz" && \
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julia_major_minor=$(echo "${JULIA_VERSION}" | cut -d. -f 1,2) && \
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mkdir "/opt/julia-${JULIA_VERSION}" && \
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wget --progress=dot:giga "https://julialang-s3.julialang.org/bin/linux/${julia_short_arch}/${julia_major_minor}/${julia_installer}" && \
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tar xzf "${julia_installer}" -C "/opt/julia-${JULIA_VERSION}" --strip-components=1 && \
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rm "${julia_installer}" && \
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ln -fs /opt/julia-*/bin/julia /usr/local/bin/julia
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# Show Julia where conda libraries are \
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RUN mkdir /etc/julia && \
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echo "push!(Libdl.DL_LOAD_PATH, \"${CONDA_DIR}/lib\")" >> /etc/julia/juliarc.jl && \
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# Create JULIA_PKGDIR \
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mkdir "${JULIA_PKGDIR}" && \
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chown "${NB_USER}" "${JULIA_PKGDIR}" && \
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fix-permissions "${JULIA_PKGDIR}"
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# Setup Julia
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RUN /opt/setup-scripts/setup-julia.bash
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USER ${NB_UID}
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# Add Julia packages.
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# Install IJulia as jovyan and then move the kernelspec out
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# to the system share location. Avoids problems with runtime UID change not
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# taking effect properly on the .local folder in the jovyan home dir.
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RUN julia -e 'import Pkg; Pkg.update()' && \
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julia -e 'import Pkg; Pkg.add("HDF5")' && \
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julia -e 'using Pkg; pkg"add IJulia"; pkg"precompile"' && \
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# move kernelspec out of home \
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mv "${HOME}/.local/share/jupyter/kernels/julia"* "${CONDA_DIR}/share/jupyter/kernels/" && \
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chmod -R go+rx "${CONDA_DIR}/share/jupyter" && \
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rm -rf "${HOME}/.local" && \
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fix-permissions "${JULIA_PKGDIR}" "${CONDA_DIR}/share/jupyter"
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WORKDIR "${HOME}"
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# Setup IJulia kernel & other packages
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RUN /opt/setup-scripts/setup-julia-packages.bash
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@@ -43,3 +43,6 @@ USER ${NB_UID}
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# Add R mimetype option to specify how the plot returns from R to the browser
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COPY --chown=${NB_UID}:${NB_GID} Rprofile.site /opt/conda/lib/R/etc/
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# Add setup scripts that may be used by downstream images or inherited images
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COPY setup-scripts/ /opt/setup-scripts/
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24
minimal-notebook/setup-scripts/setup-julia-packages.bash
Executable file
24
minimal-notebook/setup-scripts/setup-julia-packages.bash
Executable file
@@ -0,0 +1,24 @@
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#!/bin/bash
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# Requirements:
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# - Run as non-root user
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# - Julia is already set up, with the setup-julia.bash command
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set -exuo pipefail
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# Install base Julia packages
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julia -e '
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import Pkg;
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Pkg.update();
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Pkg.add([
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"HDF5",
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"IJulia"
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]);
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Pkg.precompile();
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'
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# Move the kernelspec out to the system share location. Avoids
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# problems with runtime UID change not taking effect properly on the
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# .local folder in the jovyan home dir. move kernelspec out of home
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mv "${HOME}/.local/share/jupyter/kernels/julia"* "${CONDA_DIR}/share/jupyter/kernels/"
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chmod -R go+rx "${CONDA_DIR}/share/jupyter"
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rm -rf "${HOME}/.local"
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fix-permissions "${JULIA_PKGDIR}" "${CONDA_DIR}/share/jupyter"
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39
minimal-notebook/setup-scripts/setup-julia.bash
Executable file
39
minimal-notebook/setup-scripts/setup-julia.bash
Executable file
@@ -0,0 +1,39 @@
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#!/bin/bash
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set -exuo pipefail
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# Requirements:
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# - This script is run as the root user
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# - The JULIA_PKGDIR environment variable is set
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# Default julia version to install if env var is not set
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# Check https://julialang.org/downloads/
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JULIA_VERSION="${JULIA_VERSION:-1.9.1}"
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# Figure out what architecture we are installing in
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JULIA_ARCH=$(uname -m)
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JULIA_SHORT_ARCH="${JULIA_ARCH}"
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if [ "${JULIA_SHORT_ARCH}" == "x86_64" ]; then
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JULIA_SHORT_ARCH="x64"
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fi
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# Figure out Julia Installer URL
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JULIA_INSTALLER="julia-${JULIA_VERSION}-linux-${JULIA_ARCH}.tar.gz"
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JULIA_MAJOR_MINOR=$(echo "${JULIA_VERSION}" | cut -d. -f 1,2)
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# Download and install Julia
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cd /tmp
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mkdir "/opt/julia-${JULIA_VERSION}"
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wget --progress=dot:giga "https://julialang-s3.julialang.org/bin/linux/${JULIA_SHORT_ARCH}/${JULIA_MAJOR_MINOR}/${JULIA_INSTALLER}"
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tar xzf "${JULIA_INSTALLER}" -C "/opt/julia-${JULIA_VERSION}" --strip-components=1
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rm "${JULIA_INSTALLER}"
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# Link Julia installed version to /usr/local/bin, so julia launches it
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ln -fs /opt/julia-*/bin/julia /usr/local/bin/julia
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# Tell Julia where conda libraries are
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mkdir -p /etc/julia
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echo "push!(Libdl.DL_LOAD_PATH, \"${CONDA_DIR}/lib\")" >> /etc/julia/juliarc.jl
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# Create JULIA_PKGDIR, where user libraries are installed
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mkdir "${JULIA_PKGDIR}"
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chown "${NB_USER}" "${JULIA_PKGDIR}"
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fix-permissions "${JULIA_PKGDIR}"
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