introduce neurodocker based generation of images

Dockerfile

@@ -1,36 +1,180 @@
-FROM alpine:3.8
-
-RUN apk add --no-cache python3 && \
-    python3 -m ensurepip && \
-    rm -r /usr/lib/python*/ensurepip && \
-    pip3 install --upgrade pip setuptools && \
-    if [ ! -e /usr/bin/pip ]; then ln -s pip3 /usr/bin/pip ; fi && \
-    if [[ ! -e /usr/bin/python ]]; then ln -sf /usr/bin/python3 /usr/bin/python; fi && \
-    rm -r /root/.cache
-
-RUN apk add --no-cache libpng freetype libstdc++ openblas libxml2 libxslt && \
-	apk add --no-cache --virtual .build-deps \
-	    g++ gfortran file binutils \
-	    openblas-dev \
-	    python3-dev \
-	    gcc \
-	    build-base \
-	    libpng-dev \
-	    musl-dev \
-	    freetype-dev \
-	    libxml2-dev \
-	    libxslt-dev && \
-	ln -s /usr/include/locale.h /usr/include/xlocale.h \
-	&& pip3 install numpy \
-	&& pip3 install scipy==1.3.3 \
-	&& pip3 install pandas \
-	&& pip3 install matplotlib \
-	&& pip3 install joblib \
-	&& pip3 install rsHRF \
-	&& rm -r /root/.cache \
-	&& find /usr/lib/python3.*/ -name 'tests' -exec rm -r '{}' + \
-	&& find /usr/lib/python3.*/site-packages/ -name '*.so' -print -exec sh -c 'file "{}" | grep -q "not stripped" && strip -s "{}"' \; \
-	&& rm /usr/include/xlocale.h \
-	&& apk del .build-deps
-
-ENTRYPOINT ["rsHRF"]
+# Your version: 0.6.0 Latest version: 0.7.0
+# Generated by Neurodocker version 0.6.0
+# Timestamp: 2020-04-21 18:20:36 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 neurodebian
+
+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' >> "$ND_ENTRYPOINT"; \
+    fi \
+    && chmod -R 777 /neurodocker && chmod a+s /neurodocker
+
+ENTRYPOINT ["/neurodocker/startup.sh"]
+
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           libpng \
+           freetype \
+           libstdc++ \
+           openblas \
+           libxml2 \
+           libxslt \
+           g++ \
+           gfortran \
+           file \
+           binutils \
+           openblas-dev \
+           python3-dev \
+           gcc \
+           build-base \
+           libpng-dev \
+           musl-dev \
+           freetype-dev \
+           libxml2-dev \
+           libxslt-dev \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN test "$(getent passwd rshrf)" || useradd --no-user-group --create-home --shell /bin/bash rshrf
+USER rshrf
+
+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 "$conda_installer" \
+    && conda update -yq -nbase conda \
+    && conda config --system --prepend channels conda-forge \
+    && conda config --system --set auto_update_conda false \
+    && conda config --system --set show_channel_urls true \
+    && sync && conda clean --all && sync \
+    && conda create -y -q --name rshrf \
+    && conda install -y -q --name rshrf \
+           "python=3.7" \
+           "pandas" \
+           "scipy==1.3.3" \
+           "numpy" \
+           "matplotlib" \
+           "joblib" \
+    && sync && conda clean --all && sync \
+    && bash -c "source activate rshrf \
+    &&   pip install --no-cache-dir  \
+             "rsHRF"" \
+    && rm -rf ~/.cache/pip/* \
+    && sync \
+    && sed -i '$isource activate rshrf' $ND_ENTRYPOINT
+
+RUN mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py
+
+ENTRYPOINT ["/neurodocker/startup.sh"]
+
+WORKDIR /home/rshrf
+
+CMD ["rshrf"]
+
+RUN echo '{ \
+    \n  "pkg_manager": "apt", \
+    \n  "instructions": [ \
+    \n    [ \
+    \n      "base", \
+    \n      "neurodebian" \
+    \n    ], \
+    \n    [ \
+    \n      "install", \
+    \n      [ \
+    \n        "libpng", \
+    \n        "freetype", \
+    \n        "libstdc++", \
+    \n        "openblas", \
+    \n        "libxml2", \
+    \n        "libxslt", \
+    \n        "g++", \
+    \n        "gfortran", \
+    \n        "file", \
+    \n        "binutils", \
+    \n        "openblas-dev", \
+    \n        "python3-dev", \
+    \n        "gcc", \
+    \n        "build-base", \
+    \n        "libpng-dev", \
+    \n        "musl-dev", \
+    \n        "freetype-dev", \
+    \n        "libxml2-dev", \
+    \n        "libxslt-dev" \
+    \n      ] \
+    \n    ], \
+    \n    [ \
+    \n      "user", \
+    \n      "rshrf" \
+    \n    ], \
+    \n    [ \
+    \n      "miniconda", \
+    \n      { \
+    \n        "conda_install": [ \
+    \n          "python=3.7", \
+    \n          "pandas", \
+    \n          "scipy==1.3.3", \
+    \n          "numpy", \
+    \n          "matplotlib", \
+    \n          "joblib" \
+    \n        ], \
+    \n        "pip_install": [ \
+    \n          "rsHRF" \
+    \n        ], \
+    \n        "create_env": "rshrf", \
+    \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      "/home/rshrf" \
+    \n    ], \
+    \n    [ \
+    \n      "cmd", \
+    \n      [ \
+    \n        "rshrf" \
+    \n      ] \
+    \n    ] \
+    \n  ] \
+    \n}' > /neurodocker/neurodocker_specs.json

Singularity

@@ -0,0 +1,181 @@
+# Your version: 0.6.0 Latest version: 0.7.0
+# Generated by Neurodocker version 0.6.0
+# Timestamp: 2020-04-21 18:20:37 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: neurodebian
+
+%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' >> "$ND_ENTRYPOINT";
+fi
+chmod -R 777 /neurodocker && chmod a+s /neurodocker
+
+apt-get update -qq
+apt-get install -y -q --no-install-recommends \
+    libpng \
+    freetype \
+    libstdc++ \
+    openblas \
+    libxml2 \
+    libxslt \
+    g++ \
+    gfortran \
+    file \
+    binutils \
+    openblas-dev \
+    python3-dev \
+    gcc \
+    build-base \
+    libpng-dev \
+    musl-dev \
+    freetype-dev \
+    libxml2-dev \
+    libxslt-dev
+apt-get clean
+rm -rf /var/lib/apt/lists/*
+
+test "$(getent passwd rshrf)" || useradd --no-user-group --create-home --shell /bin/bash rshrf
+su - rshrf
+
+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 rshrf
+conda install -y -q --name rshrf \
+    "python=3.7" \
+    "pandas" \
+    "scipy==1.3.3" \
+    "numpy" \
+    "matplotlib" \
+    "joblib"
+sync && conda clean --all && sync
+bash -c "source activate rshrf
+  pip install --no-cache-dir  \
+      "rsHRF""
+rm -rf ~/.cache/pip/*
+sync
+sed -i '$isource activate rshrf' $ND_ENTRYPOINT
+
+
+mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py
+
+cd /home/rshrf
+
+echo '{
+\n  "pkg_manager": "apt",
+\n  "instructions": [
+\n    [
+\n      "base",
+\n      "neurodebian"
+\n    ],
+\n    [
+\n      "_header",
+\n      {
+\n        "version": "generic",
+\n        "method": "custom"
+\n      }
+\n    ],
+\n    [
+\n      "install",
+\n      [
+\n        "libpng",
+\n        "freetype",
+\n        "libstdc++",
+\n        "openblas",
+\n        "libxml2",
+\n        "libxslt",
+\n        "g++",
+\n        "gfortran",
+\n        "file",
+\n        "binutils",
+\n        "openblas-dev",
+\n        "python3-dev",
+\n        "gcc",
+\n        "build-base",
+\n        "libpng-dev",
+\n        "musl-dev",
+\n        "freetype-dev",
+\n        "libxml2-dev",
+\n        "libxslt-dev"
+\n      ]
+\n    ],
+\n    [
+\n      "user",
+\n      "rshrf"
+\n    ],
+\n    [
+\n      "miniconda",
+\n      {
+\n        "conda_install": [
+\n          "python=3.7",
+\n          "pandas",
+\n          "scipy==1.3.3",
+\n          "numpy",
+\n          "matplotlib",
+\n          "joblib"
+\n        ],
+\n        "pip_install": [
+\n          "rsHRF"
+\n        ],
+\n        "create_env": "rshrf",
+\n        "activate": true
+\n      }
+\n    ],
+\n    [
+\n      "run",
+\n      "mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \\\"0.0.0.0\\\" > ~/.jupyter/jupyter_notebook_config.py"
+\n    ],
+\n    [
+\n      "entrypoint",
+\n      "/neurodocker/startup.sh"
+\n    ],
+\n    [
+\n      "workdir",
+\n      "/home/rshrf"
+\n    ]
+\n  ]
+\n}' > /neurodocker/neurodocker_specs.json
+
+%environment
+export LANG="en_US.UTF-8"
+export LC_ALL="en_US.UTF-8"
+export ND_ENTRYPOINT="/neurodocker/startup.sh"
+export CONDA_DIR="/opt/miniconda-latest"
+export PATH="/opt/miniconda-latest/bin:$PATH"
+
+%runscript
+/neurodocker/startup.sh