#345 start to investigate system install with Conda

conda/setup_conda

@@ -0,0 +1,173 @@
+#!/bin/bash
+
+set -e
+set -x
+
+casaconda="$1"
+if [ -z "$casaconda" ]; then
+    echo "Missing destination directory"
+    exit 1
+fi
+
+# Install Miniforge
+
+miniforge=$(mktemp --suffix .sh)
+wget -O "$miniforge" https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
+sh "$miniforge" -b -p "$casaconda"
+rm "$miniforge"
+conda="$casaconda/bin/conda"
+
+"$conda" update conda -y
+
+build_dependencies=(
+    # General build dependencies (notably useful for pip-compiled packages)
+    gcc
+    gxx
+    git
+    cmake
+    # libc-dev
+    # libpython3-dev
+    make
+    patch
+    pkg-config
+
+    # Build dependencies of MESA's libGL
+ #   #! byacc
+ #   flex
+ #   #! was libxcb-randr0-dev
+ #   libxrandr-devel
+ #   llvmdev #? was llvm-dev
+ #   meson
+ #   mako
+    mesa
+
+    # Build dependencies of MIRCen's fork of openslide
+    autoconf
+    automake
+    libtool
+    pkg-config  # needed for autoreconf
+    openjpeg #? was libopenjp2-7-dev
+    libtiff #? was libtiff-dev
+    cairo-devel-cos6-x86_64 #? was libcairo2-dev
+    gdk-pixbuf #? was libgdk-pixbuf2.0-dev
+    glib2-devel-cos6-x86_64 #? was libglib2.0-dev
+    libxml2-devel-cos6-x86_64 #? was libxml2-dev
+    jxrlib #? was libjxr-dev
+
+
+    # Build dependencies of SIP/PyQt
+#    libqt5svg5-dev  # qtconsole needs PyQt5.QtSvg
+#    libqt5opengl5-dev
+#    qttools5-dev
+#    qtmultimedia5-dev
+#    libqt5webchannel5-dev
+#    libqt5webkit5-dev
+#    libqt5webview5-dev
+#    libqt5x11extras5-dev
+#    libqt5xmlpatterns5-dev
+#    qtwebengine5-dev  # for PyQt
+
+    # Build dependencies of libminc
+    hdf5 #? was libhdf5-dev
+    libnetcdf #? was libnetcdf-dev
+
+    # Build dependencies for draco
+    draco
+#    eigen #? was libeigen3-dev
+
+    pyqt
+)
+"$conda" install -y ${build_dependencies[@]}
+
+export PATH="$casaconda/bin:$PATH"
+export LD_LIBRARY_PATH="$casaconda/lib:$LD_LIBRARY_PATH"
+
+# MIRCen's fork of openslide with support for CZI format
+#
+tmp=$(mktemp -d)
+
+cd "$tmp"
+wget https://github.com/uclouvain/openjpeg/archive/refs/tags/v2.5.0.tar.gz
+tar xf v2.5.0.tar.gz
+cd openjpeg-2.5.0
+mkdir build
+cd build
+cmake .. -DCMAKE_BUILD_TYPE=Release "-DCMAKE_INSTALL_PREFIX=$casaconda"
+make
+make install
+cp libopenjp2.pc $casaconda/lib/pkgconfig/
+
+cd "$tmp"
+git clone --depth=1 https://github.com/MIRCen/openslide.git
+cd openslide
+autoreconf --install
+./configure --prefix="$casaconda"
+make -j$(nproc)
+make install
+
+# reinstall libminc 4.0.0 because newer versions can't properly read freesurfer
+# .mgz files
+cd "$tmp"
+git clone https://github.com/BIC-MNI/libminc.git --single-branch --branch libminc-2-3-00
+cd libminc
+cmake . -DBUILD_TESTING=OFF -DCMAKE_BUILD_TYPE=Release -DLIBMINC_BUILD_SHARED_LIBS=ON -DLIBMINC_MINC1_SUPPORT=ON "-DCMAKE_INSTALL_PREFIX=$casaconda"
+make -j$(nproc)
+make install
+cd ..
+rm -rf libminc
+
+rm -Rf "$tmp"
+
+
+#
+#  Dev environment
+#
+
+# Documentation building
+documentation_building_packages=(
+    doxygen
+    ghostscript
+    graphviz
+    nbconvert #? was jupyter-nbconvert
+    pandoc
+    sphinx
+    sphinx-gallery
+    #! texlive-latex-base
+    #! texlive-latex-extra  # needed by doxygen to render LaTeX formulas
+    #! texlive-fonts-recommended
+    wkhtmltopdf
+)
+
+brainvisa_standard_dev_dependencies=(
+    #! libasound2-dev
+    libblitz #? was libblitz0-dev
+    boost-cpp #? was libboost-dev
+    #! libboost-filesystem-dev
+    #! libboost-system-dev
+    dcmtk #? was libdcmtk-dev
+    libexpat #? was libexpat1-dev
+    #! libgl1-mesa-dev
+    libglib #? was libglib2.0-dev
+    libglu #? was libglu1-mesa-dev
+    libjpeg-turbo #? was libjpeg-dev
+    #! libminc-dev
+    netcdf4 #? was libnetcdf-dev
+    #! libomp-dev  # OpenMP with the clang compiler
+    #! libopenjp2-7-dev
+    libpng #? was libpng-dev
+    #! libqt5x11extras5-dev
+    #! libqwt-qt5-dev
+    libsigcpp #? was libsigc++-2.0-dev
+    #! libspnav-dev
+    libsvm #? was libsvm-dev
+    libtiff #? was libtiff-dev
+    #! libvtk9-dev
+    #! libvtk9-qt-dev
+    libxml2 #? was libxml2-dev
+    #! qttools5-dev
+    #! qtmultimedia5-dev
+    #! qttools5-dev-tools
+    #! zlib1g-dev
+)
+
+"$conda" install -y ${documentation_building_packages[@]} ${brainvisa_standard_dev_dependencies[@]}