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napari_viewer.def
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Bootstrap: docker
From: python:3.8.8
%post
# Install the OpenGL and XCB libraries to run napari
apt-get -y update
apt-get install -y libgles2-mesa-dev \
mesa-utils \
libx11-xcb-perl \
libxcb-composite0 \
libxcb-damage0 \
libxcb-doc \
libxcb-dpms0 \
libxcb-dri2-0 \
libxcb-dri3-0 \
libxcb-glx0 \
libxcb-present0 \
libxcb-randr0 \
libxcb-record0 \
libxcb-render0 \
libxcb-res0 \
libxcb-screensaver0 \
libxcb-shape0 \
libxcb-shm0 \
libxcb-sync1 \
libxcb-xf86dri0 \
libxcb-xfixes0 \
libxcb-xinerama0 \
libxcb-xinput0 \
libxcb-xkb1 \
libxcb-xtest0 \
libxcb-xv0 \
libxcb-xvmc0 \
libxcb1 \
libxcb-imdkit0 \
libxcb-util0 \
libxcb-cursor0 \
libxcb-image0 \
libxcb-keysyms1 \
libxcb-render-util0 \
libxcb-ewmh2 \
libxcb-icccm4 \
libxcb-xrm0 \
libxkbcommon-x11-0 \
libxkbcommon0 \
libxkbfile1 \
libdbus-1-3 \
git
pip install --upgrade pip
pip install blosc
pip install zarr
pip install napari[all]
pip install requests
pip install aiohttp
pip install fsspec
pip install s3fs
pip install ome-zarr
pip install napari-ome-zarr
ln -sf /usr/lib/x86_64-linux-gnu/libxcb-util.so.0.0.0 /usr/lib/x86_64-linux-gnu/libxcb-util.so.1.0.0
ln -sf /usr/lib/x86_64-linux-gnu/libxcb-util.so.0.0.0 /usr/lib/x86_64-linux-gnu/libxcb-util.so.1.0
ln -sf /usr/lib/x86_64-linux-gnu/libxcb-util.so.0.0.0 /usr/lib/x86_64-linux-gnu/libxcb-util.so.1
cd /usr/local/
git clone https://github.com/TheJacksonLaboratory/HCS_visualization_tools.git
%runscript
ZARR_PATH=$1
if [ $# -lt 2 ]; then
GROUP="0"
else
GROUP=$2
fi
exec python /usr/local/HCS_visualization_tools/src/napari_viewer.py -z $ZARR_PATH -g $GROUP