Create dockerimage.yml

.github/workflows/dockerimage.yml

@@ -0,0 +1,21 @@
+name: Docker Image CI
+
+on: [push]
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Build the Docker image
+      run: docker build . --file Dockerfile --tag loadedubuntu:${GITHUB_REF#refs/heads/}
+    - name: Dockerize
+      if: success()
+      uses: manusa/actions-publish-docker@v1.1.2
+      with:
+        name: rcourt/loadedubuntu
+        username: ${{ secrets.DOCKER_HUB_USER }}
+        password: ${{ secrets.DOCKER_HUB_PASSWORD }}

Dockerfile

@@ -1,35 +1,82 @@
-FROM ubuntu
+FROM ubuntu:20.04
 
+ENV DEBIAN_FRONTEND=noninteractive
 VOLUME input
 VOLUME output
 VOLUME template
 
-#cmtk
-RUN apt-get -qq -y update \ 
-&& apt-get -qq -y install locales cmtk python python-pip python-dev ipython build-essential git nano autoconf nasm zip automake autoconf m4 libtool bison cmake flex xvfb imagej bc sec libpq-dev python3.7\
-&& pip install --upgrade virtualenv \
-&& pip install --upgrade pip
-
-#python image support
-RUN pip install pynrrd
-RUN pip install h5py
-
-#python neo4j support
-RUN pip install requests
-RUN pip install psycopg2
-RUN pip install neo4j
+# Install base dependencies
+RUN apt-get update && apt-get install -y \
+    software-properties-common \
+    && add-apt-repository -y ppa:deadsnakes/ppa \
+    && apt-get update \
+    && apt-get install -y \
+    locales \
+    cmtk \
+    build-essential \
+    git \
+    nano \
+    autoconf \
+    nasm \
+    zip \
+    automake \
+    m4 \
+    libtool \
+    bison \
+    cmake \
+    flex \
+    xvfb \
+    imagej \
+    bc \
+    sec \
+    libpq-dev \
+    python3.10 \
+    python3.10-dev \
+    python3.10-distutils \
+    python3-pip \
+    wget \
+    curl \
+    libdirectfb-dev \
+    libjpeg-dev \
+    zlib1g-dev \
+    libsdl-gfx1.2-dev \
+    libsdl1.2-dev \
+    libasound2-dev \
+    pkg-config \
+    libpci-dev \
+    dh-autoreconf \
+    csh \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set Python 3.10 as default
+RUN update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.10 1 \
+    && update-alternatives --set python3 /usr/bin/python3.10
+
+# Install pip for Python 3.10
+RUN curl -sS https://bootstrap.pypa.io/get-pip.py | python3.10
+
+# Python image support
+RUN python3.10 -m pip install pynrrd h5py
+
+# Environment variables
+ENV MA=/opt/MouseAtlas
+ENV PATH=/opt/MouseAtlas/bin:$PATH
+ENV LD_LIBRARY_PATH=/opt/MouseAtlas/lib:$LD_LIBRARY_PATH
+ENV LD_RUN_PATH=/opt/MouseAtlas/lib:$LD_RUN_PATH
 
-#woolz
-RUN apt-get -y install build-essential gcc make wget libdirectfb-dev libjpeg-dev zlib1g-dev libsdl-gfx1.2-dev gcc libsdl1.2-dev libasound2-dev  pkg-config libpci-dev dh-autoreconf csh
+# Woolz dependencies
+RUN apt-get -y install build-essential gcc make wget libdirectfb-dev libjpeg-dev zlib1g-dev libsdl-gfx1.2-dev gcc libsdl1.2-dev libasound2-dev pkg-config libpci-dev dh-autoreconf csh
 
 ENV MA=/opt/MouseAtlas
-RUN export PATH=/root/anaconda3/bin:/opt/VFB_neo4j/src:/opt/MouseAtlas/bin:$PATH
+ENV PATH=/opt/MouseAtlas/bin:$PATH
 ENV LD_LIBRARY_PATH=/opt/MouseAtlas/lib:$LD_LIBRARY_PATH
 ENV LD_RUN_PATH=/opt/MouseAtlas/lib:$LD_RUN_PATH
 
+# External Dependencies
 RUN cd /tmp/ \
 && git clone https://github.com/ma-tech/External.git
 
+# Install Fcgi
 RUN cd /tmp/External/ \
 && cd Fcgi/ \
 && tar -zxf fcgi-2.4.0.tar.gz \
@@ -39,6 +86,7 @@ RUN cd /tmp/External/ \
 && make \
 && make install
 
+# Install Log4Cpp
 RUN cd /tmp/External/ \
 && cd Log4Cpp \
 && rm -rf log4cpp-1.0 \
@@ -49,6 +97,7 @@ RUN cd /tmp/External/ \
 && make \
 && make install
 
+# Install PNG
 RUN cd /tmp/External/ \
 && cd PNG \
 && rm -rf libpng-1.6.29 \
@@ -58,6 +107,7 @@ RUN cd /tmp/External/ \
 && make \
 && make install
 
+# Install JPEG
 RUN cd /tmp/External/ \
 && cd Jpeg \
 && rm -rf libjpeg-turbo-1.5.1 \
@@ -68,115 +118,84 @@ RUN cd /tmp/External/ \
 && make \
 && make install
 
+# Install Tiff
 RUN cd /tmp/External/ \
 && cd Tiff \
 && rm -rf tiff-4.0.8 \
 && tar -zxf tiff-4.0.8.tar.gz \
 && cd tiff-4.0.8 \
-&& ./configure --prefix=$MA --disable-shared --enable-static --with-pic --with-jpeg-include-dir=$MA/include --with-jpeg-lib-dir==$MA/lib \
+&& ./configure --prefix=$MA --disable-shared --enable-static --with-pic --with-jpeg-include-dir=$MA/include --with-jpeg-lib-dir=$MA/lib \
 && make \
 && make install
 
+# Install NIfTI
 RUN cd /tmp/External/ \
 && cd NIfTI \
 && tar -zxf nifticlib-2.0.0.tar.gz \
 && cmake nifticlib-2.0.0 \
 && make \
 && make install
 
+# Install cJSON
+RUN cd /tmp/ \
+&& git clone https://github.com/DaveGamble/cJSON.git \
+&& cd cJSON \
+&& mkdir build \
+&& cd build \
+&& cmake .. \
+&& make \
+&& make install
+
+# Woolz compilation
 RUN cd /tmp/ \
 && git clone https://github.com/ma-tech/Woolz.git \
 && cd Woolz \
+&& cp -v Readme.md README \
 && mkdir -p m4 \
 && libtoolize \
 && aclocal \
 && automake --add-missing \
 && autoreconf -i --force \
 && ./build.sh \
-&& ./configure --prefix=$MA --enable-optimise --enable-extff --with-jpeg=$MA --with-tiff=$MA --with-nifti=/usr/local/ \
+&& ./configure --prefix=$MA --enable-optimise --enable-extff --with-jpeg=$MA --with-tiff=$MA --with-nifti=/usr/local/ CPPFLAGS="-I/usr/local/include/cjson" LDFLAGS="-L/usr/local/lib" \
 && make \
 && make install
 
-
-# RUN cd /opt/ \
-# && git clone https://github.com/Robbie1977/NRRDtools.git 
-# RUN cd /opt/ \
-# && git clone https://github.com/Robbie1977/SWCtools.git 
-# RUN cd /opt/ \
-# && git clone https://github.com/Robbie1977/Bound.git 
-# RUN cd /opt/ \
-# && git clone https://github.com/Robbie1977/3DwarpScoring.git 
-# RUN cd /opt/ \
-# && git clone https://github.com/Robbie1977/IndexStackConv.git 
-# RUN cd /opt/ \
-# && git clone https://github.com/Robbie1977/3DstackDisplay.git
-# RUN cd /opt/ \
-# && git clone https://github.com/Robbie1977/lsm2nrrd.git
-# RUN cd /opt/ \
-# && git clone https://github.com/Robbie1977/nrrd2raw.git
+# Clone VFB repositories
 RUN cd /opt/ \
-&& git clone https://github.com/VirtualFlyBrain/VFB_neo4j.git
-# RUN cd /opt/ \
-# && git clone https://github.com/VirtualFlyBrain/StackProcessing.git
-# RUN cd /opt/ \
-# && git clone https://github.com/VirtualFlyBrain/StackLoader.git
-# RUN cd /opt/ \
-# && wget https://downloads.imagej.net/fiji/latest/fiji-linux64.zip \
-# && unzip fiji-linux64.zip \
-# && rm fiji-linux64.zip
-
-# ENV FIJI=/opt/Fiji.app/ImageJ-linux64
-
-# RUN mkdir -p /data/ && cd /data/ \
-# && git clone https://github.com/VirtualFlyBrain/DrosAdultVNSdomains.git
-
-# RUN cd /data/ \
-# && git clone https://github.com/VirtualFlyBrain/DrosAdultBRAINdomains.git
-
-# RUN cd /data/ \
-# && git clone https://github.com/VirtualFlyBrain/DrosAdultHalfBRAINdomains.git
-
-
-
-# RUN mkdir -p /disk/data/VFB/IMAGE_DATA/
-# RUN ln -s /opt/StackLoader /disk/data/VFB/IMAGE_DATA/
-# RUN mkdir -p /partition/bocian/VFBTools
-# RUN ln -s /opt/* /partition/bocian/VFBTools/
-# RUN ln -s /VFB /disk/data/VFB/IMAGE_DATA/
-# RUN mkdir -p /disk/data/VFBTools
-# RUN ln -s /opt/Fiji.app /disk/data/VFBTools/
-# RUN mv /disk/data/VFBTools/Fiji.app /disk/data/VFBTools/Fiji
-# RUN ln -s /opt/* /disk/data/VFBTools/
-# RUN ln -s /disk/data/VFBTools/MouseAtlas /disk/data/VFBTools/Woolz2013Full
-# RUN mkdir -p /partition/karenin/VFB/IMAGE_DATA/
-# RUN ln -s /opt/StackLoader /partition/karenin/VFB/IMAGE_DATA/
-# RUN ln -s /VFB /partition/karenin/VFB/IMAGE_DATA/
-# RUN mkdir -p /partition/bocian/VFBTools/python-modules-2.6/bin/
-# RUN echo "#empty" > /partition/bocian/VFBTools/python-modules-2.6/bin/activate
-# RUN ln -s /opt/StackProcessing /disk/data/VFB/IMAGE_DATA/
+    && git clone https://github.com/VirtualFlyBrain/VFB_neo4j.git \
+    && git clone https://github.com/VirtualFlyBrain/curation.git
 
+# Set environment variables
 ENV TZAREA=Europe
 ENV TZCITY=London
-ENV ANACONDAINS=Anaconda3-5.2.0-Linux-x86_64.sh
+ENV ANACONDAINS=Anaconda3-2023.09-0-Linux-x86_64.sh
 ENV JUPYPASS="sha1:7f8e745dd219:b14fb15e0b4bc290a5d109ae97cba5c361b5d139"
 
-#ipython jupyter notebook
-RUN cd /tmp/ && \
-wget https://repo.anaconda.com/archive/${ANACONDAINS} && \
-bash ${ANACONDAINS} -b 
-
-RUN conda install python=3.7 anaconda=custom
-
-#neo4j requirements
-RUN /root/anaconda3/bin/pip install pynrrd
-RUN /root/anaconda3/bin/pip install requests
-RUN /root/anaconda3/bin/pip install psycopg2
-RUN /root/anaconda3/bin/pip install pandas
-RUN /root/anaconda3/bin/pip install catpy
-
+# Install Anaconda
+RUN cd /tmp/ \
+    && wget https://repo.anaconda.com/archive/${ANACONDAINS} \
+    && bash ${ANACONDAINS} -b
+
+# Install Python packages
+RUN python3.10 -m pip install \
+    requests \
+    psycopg2-binary \
+    neo4j \
+    jupyter \
+    ipykernel
+
+# Set up Python 3.10 kernel for Jupyter
+RUN python3.10 -m ipykernel install --name 'python3.10' --display-name 'Python 3.10'
+
+# Install requirements from VFB repositories
+RUN sed 's/^psycopg2$/psycopg2-binary/g' /opt/VFB_neo4j/requirements.txt >> /opt/requirements.txt \
+    && sed 's/^psycopg2$/psycopg2-binary/g' /opt/curation/requirements.txt >> /opt/requirements.txt \
+    && python3.10 -m pip install -r /opt/requirements.txt
+
+# Copy and prepare scripts
 COPY /scripts/* /scripts/
 RUN chmod +x /scripts/*.sh
 
 ENTRYPOINT /scripts/startup.sh
-
 EXPOSE 80

scripts/startup.sh

@@ -1,5 +1,10 @@
 #!/bin/bash
 
-for folder in $(find / | grep '/\.git$') ; do git --git-dir=$folder pull || : ; done;
+/root/anaconda3/bin/jupyter lab --ip='*' --NotebookApp.password="${JUPYPASS}" --no-browser --port 80 --allow-root &
 
-/root/anaconda3/bin/jupyter lab --ip='*' --NotebookApp.password="${JUPYPASS}" --no-browser --port 80 --allow-root
+for folder in $(find /opt/ | grep '/\.git$') ; do echo $folder; cd $folder/../;  git pull || : ; cd ..; sleep 10m; done; 
+
+while true 
+do 
+  sleep 999m
+done