From 2d5fd0c120d43a9d6459cb3e46b52f02e895b0ca Mon Sep 17 00:00:00 2001
From: Rob Court <robbie.court@gmail.com>
Date: Thu, 17 Oct 2024 17:40:58 +0100
Subject: [PATCH] fix for cJSON.h

---
 Dockerfile | 41 +++++++++++++++++++++++++++++++----------
 1 file changed, 31 insertions(+), 10 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index c960dd4..57786f8 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -4,34 +4,46 @@ VOLUME input
 VOLUME output
 VOLUME template
 
-#cmtk
+# Base dependencies
 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 maven python3 python3-pip \
 && pip install --upgrade virtualenv \
 && pip install --upgrade pip
 
-#python image support
+# Python image support
 RUN pip install pynrrd
 RUN pip install h5py
 
 RUN pip3 install pynrrd h5py requests psycopg2 neo4j==1.7.6
 
-#python neo4j support
+# Python neo4j support
 RUN pip install requests
 RUN pip install psycopg2
 RUN pip install neo4j==1.7.6
 
-#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
+
+# Install cJSON
+RUN cd /tmp/ \
+&& git clone https://github.com/DaveGamble/cJSON.git \
+&& cd cJSON \
+&& mkdir build \
+&& cd build \
+&& cmake .. \
+&& make \
+&& make install
 
 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
 
+# 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 \
@@ -41,6 +53,7 @@ RUN cd /tmp/External/ \
 && make \
 && make install
 
+# Install Log4Cpp
 RUN cd /tmp/External/ \
 && cd Log4Cpp \
 && rm -rf log4cpp-1.0 \
@@ -51,6 +64,7 @@ RUN cd /tmp/External/ \
 && make \
 && make install
 
+# Install PNG
 RUN cd /tmp/External/ \
 && cd PNG \
 && rm -rf libpng-1.6.29 \
@@ -60,6 +74,7 @@ RUN cd /tmp/External/ \
 && make \
 && make install
 
+# Install JPEG
 RUN cd /tmp/External/ \
 && cd Jpeg \
 && rm -rf libjpeg-turbo-1.5.1 \
@@ -70,6 +85,7 @@ RUN cd /tmp/External/ \
 && make \
 && make install
 
+# Install Tiff
 RUN cd /tmp/External/ \
 && cd Tiff \
 && rm -rf tiff-4.0.8 \
@@ -79,6 +95,7 @@ RUN cd /tmp/External/ \
 && make \
 && make install
 
+# Install NIfTI
 RUN cd /tmp/External/ \
 && cd NIfTI \
 && tar -zxf nifticlib-2.0.0.tar.gz \
@@ -86,6 +103,7 @@ RUN cd /tmp/External/ \
 && make \
 && make install
 
+# Woolz compilation
 RUN cd /tmp/ \
 && git clone https://github.com/ma-tech/Woolz.git \
 && cd Woolz \
@@ -100,7 +118,7 @@ RUN cd /tmp/ \
 && make \
 && make install
 
-
+# Additional tools installation
 RUN cd /opt/ \
 && git clone https://github.com/Robbie1977/NRRDtools.git 
 RUN cd /opt/ \
@@ -132,15 +150,12 @@ 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
 
-
-
+# Various symlinks
 RUN mkdir -p /disk/data/VFB/IMAGE_DATA/
 RUN ln -s /opt/StackLoader /disk/data/VFB/IMAGE_DATA/
 RUN mkdir -p /partition/bocian/VFBTools
@@ -158,6 +173,7 @@ 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/
 
+# Install JGO and other tools
 RUN cd /opt/ && \
 git clone https://github.com/scijava/jgo && \
 cd /bin && \
@@ -168,15 +184,18 @@ cd template-building && \
 git checkout v0.1.0 && \
 mvn -Dimagej.app.directory=$FIJI clean compile install
 
+# Copy scripts and set permissions
 COPY /scripts/* /scripts/
 RUN chmod +x /scripts/*.sh
 
+# Environment variables for scripts
 ENV woolzDir=/usr/lib/cmtk/bin/
 ENV dirName=/opt/StackLoader/PutAlignedFilesInHere/
 ENV fijiBin=/opt/Fiji.app/ImageJ-linux64
 ENV sriptDir=/opt/StackProcessing/scripts/
 ENV imageDir=/IMAGE_DATA/VFB/i/
 
+# Install ImageMagick
 RUN cd /opt/ && \
 wget https://www.imagemagick.org/archive/ImageMagick.tar.gz && \
 tar xvzf ImageMagick.tar.gz && \
@@ -187,6 +206,8 @@ make install && \
 ldconfig /usr/local/lib && \
 magick -version
 
+# Set the entry point
 ENTRYPOINT /scripts/startup.sh
 
+# Expose port 80
 EXPOSE 80