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Merge pull request #201 from nighres/master
update the docker file
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,216 +1,31 @@ | ||
| # Generated by Neurodocker and Reproenv. | ||
| # Start from the official Debian image | ||
| FROM debian:bullseye | ||
|
|
||
| FROM debian:stable | ||
| RUN apt-get update -qq \ | ||
| && apt-get install -y -q --no-install-recommends \ | ||
| openjdk-17-jdk git wget build-essential software-properties-common libffi-dev \ | ||
| && rm -rf /var/lib/apt/lists/* | ||
| ENV JAVA_HOME="/docker-java-temurin-home" | ||
| ENV JCC_JDK="/docker-java-temurin-home" | ||
| RUN ln -svT "/usr/lib/jvm/java-17-openjdk-$(dpkg --print-architecture)" /docker-java-temurin-home | ||
| ENV CONDA_DIR="/opt/miniconda-latest" \ | ||
| PATH="/opt/miniconda-latest/bin:$PATH" | ||
| RUN apt-get update -qq \ | ||
| && apt-get install -y -q --no-install-recommends \ | ||
| bzip2 \ | ||
| ca-certificates \ | ||
| curl \ | ||
| && rm -rf /var/lib/apt/lists/* \ | ||
| # Install dependencies. | ||
| && export PATH="/opt/miniconda-latest/bin:$PATH" \ | ||
| && echo "Downloading Miniconda installer ..." \ | ||
| && conda_installer="/tmp/miniconda.sh" \ | ||
| && curl -fsSL -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \ | ||
| && bash "$conda_installer" -b -p /opt/miniconda-latest \ | ||
| && rm -f "$conda_installer" \ | ||
| && conda update -yq -nbase conda \ | ||
| # Prefer packages in conda-forge | ||
| && conda config --system --prepend channels conda-forge \ | ||
| # Packages in lower-priority channels not considered if a package with the same | ||
| # name exists in a higher priority channel. Can dramatically speed up installations. | ||
| # Conda recommends this as a default | ||
| # https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html | ||
| && conda config --set channel_priority strict \ | ||
| && conda config --system --set auto_update_conda false \ | ||
| && conda config --system --set show_channel_urls true \ | ||
| # Enable `conda activate` | ||
| && conda init bash \ | ||
| && conda create -y --name nighres \ | ||
| && conda install -y --name nighres \ | ||
| "python=3.9" \ | ||
| "pip" \ | ||
| "JCC" \ | ||
| "Nilearn" \ | ||
| # Clean up | ||
| && sync && conda clean --all --yes && sync \ | ||
| && rm -rf ~/.cache/pip/* | ||
| COPY ["build.sh", \ | ||
| "cbstools-lib-files.sh", \ | ||
| "imcntk-lib-files.sh", \ | ||
| "dependencies_sha.sh", \ | ||
| "setup.py", \ | ||
| "setup.cfg", \ | ||
| "MANIFEST.in", \ | ||
| "README.rst", \ | ||
| "LICENSE", \ | ||
| "/nighres/"] | ||
| COPY ["nighres", \ | ||
| "/nighres/nighres"] | ||
| WORKDIR /nighres | ||
| RUN conda init && . /root/.bashrc && activate nighres && conda info --envs && pip install jcc && ./build.sh && rm -rf cbstools-public imcn-imaging nighresjava/build nighresjava/src | ||
| ENV CONDA_DIR="/opt/miniconda-latest" \ | ||
| PATH="/opt/miniconda-latest/bin:$PATH" | ||
| RUN conda install -y --name nighres \ | ||
| "jupyterlab" \ | ||
| && bash -c "source activate nighres \ | ||
| && python -m pip install --no-cache-dir \ | ||
| "."" \ | ||
| # Clean up | ||
| && sync && conda clean --all --yes && sync \ | ||
| && rm -rf ~/.cache/pip/* | ||
| COPY ["docker/jupyter_notebook_config.py", \ | ||
| "/etc/jupyter"] | ||
| RUN test "$(getent passwd neuro)" \ | ||
| || useradd --no-user-group --create-home --shell /bin/bash neuro | ||
| USER neuro | ||
| WORKDIR /home/neuro | ||
| # Install necessary tools and dependencies | ||
| RUN apt-get update && apt-get install -y --no-install-recommends \ | ||
| ca-certificates \ | ||
| git \ | ||
| build-essential \ | ||
| python3 \ | ||
| python3-pip \ | ||
| python3-dev \ | ||
| libffi-dev \ | ||
| openjdk-17-jdk \ | ||
| wget \ | ||
| && rm -rf /var/lib/apt/lists/* | ||
|
|
||
| # Adjust JAVA_HOME if necessary and create a symbolic link to match JCC's expected JDK path | ||
| ENV JAVA_HOME=/usr/lib/jvm/java-17-openjdk-amd64 | ||
| RUN ln -s $JAVA_HOME /usr/lib/jvm/temurin-17-jdk-amd64 | ||
|
|
||
| # Install JCC | ||
| RUN python3 -m pip install --upgrade pip && \ | ||
| python3 -m pip install jcc | ||
|
|
||
| # Save specification to JSON. | ||
| USER root | ||
| RUN printf '{ \ | ||
| "pkg_manager": "apt", \ | ||
| "existing_users": [ \ | ||
| "root" \ | ||
| ], \ | ||
| "instructions": [ \ | ||
| { \ | ||
| "name": "from_", \ | ||
| "kwds": { \ | ||
| "base_image": "debian:stable" \ | ||
| } \ | ||
| }, \ | ||
| { \ | ||
| "name": "install", \ | ||
| "kwds": { \ | ||
| "pkgs": [ \ | ||
| "openjdk-17-jdk git wget build-essential software-properties-common libffi-dev" \ | ||
| ], \ | ||
| "opts": null \ | ||
| } \ | ||
| }, \ | ||
| { \ | ||
| "name": "run", \ | ||
| "kwds": { \ | ||
| "command": "apt-get update -qq \\\\\\n && apt-get install -y -q --no-install-recommends \\\\\\n openjdk-17-jdk git wget build-essential software-properties-common libffi-dev \\\\\\n && rm -rf /var/lib/apt/lists/*" \ | ||
| } \ | ||
| }, \ | ||
| { \ | ||
| "name": "env", \ | ||
| "kwds": { \ | ||
| "JAVA_HOME": "/docker-java-temurin-home" \ | ||
| } \ | ||
| }, \ | ||
| { \ | ||
| "name": "env", \ | ||
| "kwds": { \ | ||
| "JCC_JDK": "/docker-java-temurin-home" \ | ||
| } \ | ||
| }, \ | ||
| { \ | ||
| "name": "run", \ | ||
| "kwds": { \ | ||
| "command": "ln -svT \\"/usr/lib/jvm/java-17-openjdk-$\(dpkg --print-architecture\)\\" /docker-java-temurin-home" \ | ||
| } \ | ||
| }, \ | ||
| { \ | ||
| "name": "env", \ | ||
| "kwds": { \ | ||
| "CONDA_DIR": "/opt/miniconda-latest", \ | ||
| "PATH": "/opt/miniconda-latest/bin:$PATH" \ | ||
| } \ | ||
| }, \ | ||
| { \ | ||
| "name": "run", \ | ||
| "kwds": { \ | ||
| "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n bzip2 \\\\\\n ca-certificates \\\\\\n curl\\nrm -rf /var/lib/apt/lists/*\\n# Install dependencies.\\nexport PATH=\\"/opt/miniconda-latest/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-latest\\nrm -f \\"$conda_installer\\"\\nconda update -yq -nbase conda\\n# Prefer packages in conda-forge\\nconda config --system --prepend channels conda-forge\\n# Packages in lower-priority channels not considered if a package with the same\\n# name exists in a higher priority channel. Can dramatically speed up installations.\\n# Conda recommends this as a default\\n# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html\\nconda config --set channel_priority strict\\nconda config --system --set auto_update_conda false\\nconda config --system --set show_channel_urls true\\n# Enable `conda activate`\\nconda init bash\\nconda create -y --name nighres\\nconda install -y --name nighres \\\\\\n \\"python=3.9\\" \\\\\\n \\"pip\\" \\\\\\n \\"JCC\\" \\\\\\n \\"Nilearn\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \ | ||
| } \ | ||
| }, \ | ||
| { \ | ||
| "name": "copy", \ | ||
| "kwds": { \ | ||
| "source": [ \ | ||
| "build.sh", \ | ||
| "cbstools-lib-files.sh", \ | ||
| "imcntk-lib-files.sh", \ | ||
| "dependencies_sha.sh", \ | ||
| "setup.py", \ | ||
| "setup.cfg", \ | ||
| "MANIFEST.in", \ | ||
| "README.rst", \ | ||
| "LICENSE", \ | ||
| "/nighres/" \ | ||
| ], \ | ||
| "destination": "/nighres/" \ | ||
| } \ | ||
| }, \ | ||
| { \ | ||
| "name": "copy", \ | ||
| "kwds": { \ | ||
| "source": [ \ | ||
| "nighres", \ | ||
| "/nighres/nighres" \ | ||
| ], \ | ||
| "destination": "/nighres/nighres" \ | ||
| } \ | ||
| }, \ | ||
| { \ | ||
| "name": "workdir", \ | ||
| "kwds": { \ | ||
| "path": "/nighres" \ | ||
| } \ | ||
| }, \ | ||
| { \ | ||
| "name": "run", \ | ||
| "kwds": { \ | ||
| "command": "conda init && . /root/.bashrc && activate nighres && conda info --envs && pip install jcc && ./build.sh && rm -rf cbstools-public imcn-imaging nighresjava/build nighresjava/src" \ | ||
| } \ | ||
| }, \ | ||
| { \ | ||
| "name": "env", \ | ||
| "kwds": { \ | ||
| "CONDA_DIR": "/opt/miniconda-latest", \ | ||
| "PATH": "/opt/miniconda-latest/bin:$PATH" \ | ||
| } \ | ||
| }, \ | ||
| { \ | ||
| "name": "run", \ | ||
| "kwds": { \ | ||
| "command": "conda install -y --name nighres \\\\\\n \\"jupyterlab\\"\\nbash -c \\"source activate nighres\\n python -m pip install --no-cache-dir \\\\\\n \\".\\"\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \ | ||
| } \ | ||
| }, \ | ||
| { \ | ||
| "name": "copy", \ | ||
| "kwds": { \ | ||
| "source": [ \ | ||
| "docker/jupyter_notebook_config.py", \ | ||
| "/etc/jupyter" \ | ||
| ], \ | ||
| "destination": "/etc/jupyter" \ | ||
| } \ | ||
| }, \ | ||
| { \ | ||
| "name": "user", \ | ||
| "kwds": { \ | ||
| "user": "neuro" \ | ||
| } \ | ||
| }, \ | ||
| { \ | ||
| "name": "workdir", \ | ||
| "kwds": { \ | ||
| "path": "/home/neuro" \ | ||
| } \ | ||
| } \ | ||
| ] \ | ||
| }' > /.reproenv.json | ||
| USER neuro | ||
| # End saving to specification to JSON. | ||
| # Clone the nighres repository | ||
| RUN git clone https://github.com/nighres/nighres | ||
|
|
||
| # Change directory into the cloned repository, run the build script, and install nighres | ||
| WORKDIR /nighres | ||
| RUN ./build.sh && \ | ||
| python3 -m pip install . |