Initial draft virtualization

Dockerfile

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+# Your version: 0.6.0 Latest version: 0.6.0
+# Generated by Neurodocker version 0.6.0
+# Timestamp: 2020-02-19 19:32:31 UTC
+# 
+# Thank you for using Neurodocker. If you discover any issues
+# or ways to improve this software, please submit an issue or
+# pull request on our GitHub repository:
+# 
+#     https://github.com/kaczmarj/neurodocker
+
+FROM ubuntu:latest
+
+ARG DEBIAN_FRONTEND="noninteractive"
+
+ENV LANG="en_US.UTF-8" \
+    LC_ALL="en_US.UTF-8" \
+    ND_ENTRYPOINT="/neurodocker/startup.sh"
+RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
+    && apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           apt-utils \
+           bzip2 \
+           ca-certificates \
+           curl \
+           locales \
+           unzip \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
+    && dpkg-reconfigure --frontend=noninteractive locales \
+    && update-locale LANG="en_US.UTF-8" \
+    && chmod 777 /opt && chmod a+s /opt \
+    && mkdir -p /neurodocker \
+    && if [ ! -f "$ND_ENTRYPOINT" ]; then \
+         echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
+    &&   echo 'set -e' >> "$ND_ENTRYPOINT" \
+    &&   echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
+    &&   echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
+    fi \
+    && chmod -R 777 /neurodocker && chmod a+s /neurodocker
+
+ENTRYPOINT ["/neurodocker/startup.sh"]
+
+RUN bash -c 'apt-get update'
+
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           git \
+           libsm6 \
+           libxext6 \
+           libgl1-mesa-dev \
+           libvtk6.3 \
+           xvfb \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+USER root
+
+RUN bash -c 'curl https://raw.githubusercontent.com/PeerHerholz/BrainSpace/initial_draft_virtualization/requirements.txt > requirements.txt && chmod 777 requirements.txt'
+
+RUN test "$(getent passwd brainspace)" || useradd --no-user-group --create-home --shell /bin/bash brainspace
+USER brainspace
+
+ENV CONDA_DIR="/opt/miniconda-latest" \
+    PATH="/opt/miniconda-latest/bin:$PATH"
+RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
+    && echo "Downloading Miniconda installer ..." \
+    && conda_installer="/tmp/miniconda.sh" \
+    && curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
+    && bash "$conda_installer" -b -p /opt/miniconda-latest \
+    && rm -f "$conda_installer" \
+    && conda update -yq -nbase conda \
+    && conda config --system --prepend channels conda-forge \
+    && conda config --system --set auto_update_conda false \
+    && conda config --system --set show_channel_urls true \
+    && sync && conda clean --all && sync \
+    && conda create -y -q --name brainspace \
+    && conda install -y -q --name brainspace \
+           "python=3.7" \
+           "panel" \
+           "pyqt" \
+           "pyvista" \
+           "notebook" \
+           "ipython" \
+    && sync && conda clean --all && sync \
+    && bash -c "source activate brainspace \
+    &&   pip install --no-cache-dir  \
+             "-r" \
+             "requirements.txt" \
+             "git+https://github.com/PeerHerholz/BrainSpace.git@notebook_binder_support" \
+             "xvfbwrapper" \
+             "ipywidgets" \
+             "ipyevents" \
+             "jupytext" \
+             "seaborn"" \
+    && rm -rf ~/.cache/pip/* \
+    && sync \
+    && sed -i '$isource activate brainspace' $ND_ENTRYPOINT
+
+RUN mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py
+
+ENTRYPOINT ["/neurodocker/startup.sh"]
+
+WORKDIR /opt/miniconda-latest/envs/brainspace/lib/python3.7/site-packages/brainspace/examples
+
+RUN sed -i '$ijupytext --set-formats ipynb,py *.py && rm *.ipynb' $ND_ENTRYPOINT
+
+CMD ["jupyter", "notebook"]
+
+RUN echo '{ \
+    \n  "pkg_manager": "apt", \
+    \n  "instructions": [ \
+    \n    [ \
+    \n      "base", \
+    \n      "ubuntu:latest" \
+    \n    ], \
+    \n    [ \
+    \n      "run_bash", \
+    \n      "apt-get update" \
+    \n    ], \
+    \n    [ \
+    \n      "install", \
+    \n      [ \
+    \n        "git", \
+    \n        "libsm6", \
+    \n        "libxext6", \
+    \n        "libgl1-mesa-dev", \
+    \n        "libvtk6.3", \
+    \n        "xvfb" \
+    \n      ] \
+    \n    ], \
+    \n    [ \
+    \n      "user", \
+    \n      "root" \
+    \n    ], \
+    \n    [ \
+    \n      "run_bash", \
+    \n      "curl https://raw.githubusercontent.com/PeerHerholz/BrainSpace/initial_draft_virtualization/requirements.txt > requirements.txt && chmod 777 requirements.txt" \
+    \n    ], \
+    \n    [ \
+    \n      "user", \
+    \n      "brainspace" \
+    \n    ], \
+    \n    [ \
+    \n      "miniconda", \
+    \n      { \
+    \n        "conda_install": [ \
+    \n          "python=3.7", \
+    \n          "panel", \
+    \n          "pyqt", \
+    \n          "pyvista", \
+    \n          "notebook", \
+    \n          "ipython" \
+    \n        ], \
+    \n        "pip_install": [ \
+    \n          "-r", \
+    \n          "requirements.txt", \
+    \n          "git+https://github.com/PeerHerholz/BrainSpace.git@notebook_binder_support", \
+    \n          "xvfbwrapper", \
+    \n          "ipywidgets", \
+    \n          "ipyevents", \
+    \n          "jupytext", \
+    \n          "seaborn" \
+    \n        ], \
+    \n        "create_env": "brainspace", \
+    \n        "activate": true \
+    \n      } \
+    \n    ], \
+    \n    [ \
+    \n      "run", \
+    \n      "mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \\\"0.0.0.0\\\" > ~/.jupyter/jupyter_notebook_config.py" \
+    \n    ], \
+    \n    [ \
+    \n      "entrypoint", \
+    \n      "/neurodocker/startup.sh" \
+    \n    ], \
+    \n    [ \
+    \n      "workdir", \
+    \n      "/opt/miniconda-latest/envs/brainspace/lib/python3.7/site-packages/brainspace/examples" \
+    \n    ], \
+    \n    [ \
+    \n      "add_to_entrypoint", \
+    \n      "jupytext --set-formats ipynb,py *.py && rm *.ipynb" \
+    \n    ], \
+    \n    [ \
+    \n      "cmd", \
+    \n      [ \
+    \n        "jupyter", \
+    \n        "notebook" \
+    \n      ] \
+    \n    ] \
+    \n  ] \
+    \n}' > /neurodocker/neurodocker_specs.json

Singularity

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+# Your version: 0.6.0 Latest version: 0.6.0
+# Generated by Neurodocker version 0.6.0
+# Timestamp: 2020-02-19 19:32:33 UTC
+# 
+# Thank you for using Neurodocker. If you discover any issues
+# or ways to improve this software, please submit an issue or
+# pull request on our GitHub repository:
+# 
+#     https://github.com/kaczmarj/neurodocker
+
+Bootstrap: docker
+From: ubuntu:latest
+
+%post
+export ND_ENTRYPOINT="/neurodocker/startup.sh"
+apt-get update -qq
+apt-get install -y -q --no-install-recommends \
+    apt-utils \
+    bzip2 \
+    ca-certificates \
+    curl \
+    locales \
+    unzip
+apt-get clean
+rm -rf /var/lib/apt/lists/*
+sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen
+dpkg-reconfigure --frontend=noninteractive locales
+update-locale LANG="en_US.UTF-8"
+chmod 777 /opt && chmod a+s /opt
+mkdir -p /neurodocker
+if [ ! -f "$ND_ENTRYPOINT" ]; then
+  echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT"
+  echo 'set -e' >> "$ND_ENTRYPOINT"
+  echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT"
+  echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT";
+fi
+chmod -R 777 /neurodocker && chmod a+s /neurodocker
+
+bash -c 'apt-get update'
+
+apt-get update -qq
+apt-get install -y -q --no-install-recommends \
+    git \
+    libsm6 \
+    libxext6 \
+    libgl1-mesa-dev \
+    libvtk6.3 \
+    xvfb
+apt-get clean
+rm -rf /var/lib/apt/lists/*
+
+su - root
+
+bash -c 'curl https://raw.githubusercontent.com/PeerHerholz/BrainSpace/initial_draft_virtualization/requirements.txt > requirements.txt && chmod 777 requirements.txt'
+
+test "$(getent passwd brainspace)" || useradd --no-user-group --create-home --shell /bin/bash brainspace
+su - brainspace
+
+export PATH="/opt/miniconda-latest/bin:$PATH"
+echo "Downloading Miniconda installer ..."
+conda_installer="/tmp/miniconda.sh"
+curl -fsSL --retry 5 -o "$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
+conda config --system --prepend channels conda-forge
+conda config --system --set auto_update_conda false
+conda config --system --set show_channel_urls true
+sync && conda clean --all && sync
+conda create -y -q --name brainspace
+conda install -y -q --name brainspace \
+    "python=3.7" \
+    "panel" \
+    "pyqt" \
+    "pyvista" \
+    "notebook" \
+    "ipython"
+sync && conda clean --all && sync
+bash -c "source activate brainspace
+  pip install --no-cache-dir  \
+      "-r" \
+      "requirements.txt" \
+      "git+https://github.com/PeerHerholz/BrainSpace.git@notebook_binder_support" \
+      "xvfbwrapper" \
+      "ipywidgets" \
+      "ipyevents" \
+      "jupytext" \
+      "seaborn""
+rm -rf ~/.cache/pip/*
+sync
+sed -i '$isource activate brainspace' $ND_ENTRYPOINT
+
+
+mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py
+
+cd /opt/miniconda-latest/envs/brainspace/lib/python3.7/site-packages/brainspace/examples
+
+sed -i '$ijupytext --set-formats ipynb,py *.py && rm *.ipynb' $ND_ENTRYPOINT
+
+echo '{
+\n  "pkg_manager": "apt",
+\n  "instructions": [
+\n    [
+\n      "base",
+\n      "ubuntu:latest"
+\n    ],
+\n    [
+\n      "_header",
+\n      {
+\n        "version": "generic",
+\n        "method": "custom"
+\n      }
+\n    ],
+\n    [
+\n      "run_bash",
+\n      "apt-get update"
+\n    ],
+\n    [
+\n      "install",
+\n      [
+\n        "git",
+\n        "libsm6",
+\n        "libxext6",
+\n        "libgl1-mesa-dev",
+\n        "libvtk6.3",
+\n        "xvfb"
+\n      ]
+\n    ],
+\n    [
+\n      "user",
+\n      "root"
+\n    ],
+\n    [
+\n      "run_bash",
+\n      "curl https://raw.githubusercontent.com/PeerHerholz/BrainSpace/initial_draft_virtualization/requirements.txt > requirements.txt && chmod 777 requirements.txt"
+\n    ],
+\n    [
+\n      "user",
+\n      "brainspace"
+\n    ],
+\n    [
+\n      "miniconda",
+\n      {
+\n        "conda_install": [
+\n          "python=3.7",
+\n          "panel",
+\n          "pyqt",
+\n          "pyvista",
+\n          "notebook",
+\n          "ipython"
+\n        ],
+\n        "pip_install": [
+\n          "-r",
+\n          "requirements.txt",
+\n          "git+https://github.com/PeerHerholz/BrainSpace.git@notebook_binder_support",
+\n          "xvfbwrapper",
+\n          "ipywidgets",
+\n          "ipyevents",
+\n          "jupytext",
+\n          "seaborn"
+\n        ],
+\n        "create_env": "brainspace",
+\n        "activate": true
+\n      }
+\n    ],
+\n    [
+\n      "run",
+\n      "mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \\\"0.0.0.0\\\" > ~/.jupyter/jupyter_notebook_config.py"
+\n    ],
+\n    [
+\n      "entrypoint",
+\n      "/neurodocker/startup.sh"
+\n    ],
+\n    [
+\n      "workdir",
+\n      "/opt/miniconda-latest/envs/brainspace/lib/python3.7/site-packages/brainspace/examples"
+\n    ],
+\n    [
+\n      "add_to_entrypoint",
+\n      "jupytext --set-formats ipynb,py *.py && rm *.ipynb"
+\n    ]
+\n  ]
+\n}' > /neurodocker/neurodocker_specs.json
+
+%environment
+export LANG="en_US.UTF-8"
+export LC_ALL="en_US.UTF-8"
+export ND_ENTRYPOINT="/neurodocker/startup.sh"
+export CONDA_DIR="/opt/miniconda-latest"
+export PATH="/opt/miniconda-latest/bin:$PATH"
+
+%runscript
+/neurodocker/startup.sh