From d746b220b4be6b304839ab1a0a1d04797f5795c7 Mon Sep 17 00:00:00 2001 From: Ali Khan Date: Sat, 28 Sep 2024 08:41:55 -0400 Subject: [PATCH] Add pyvips, remove fiji (#2) - Pyvips used for tif reading of z-stacks in spimprep - fiji removed since replaced by bigstitcher-spark - ome-zarr added to pyproject instead of just dockerfile (was a workaround) --- Dockerfile | 31 ++---------- poetry.lock | 125 ++++++++++++++++++++++++++++++++++++++++++++++++- pyproject.toml | 2 + 3 files changed, 130 insertions(+), 28 deletions(-) diff --git a/Dockerfile b/Dockerfile index 07dab5a..a0458dc 100644 --- a/Dockerfile +++ b/Dockerfile @@ -35,8 +35,8 @@ ENV LANG C.UTF-8 ENV JAVA_HOME=/usr/lib/jvm/java-1.8.0-amazon-corretto -#install maven hdf5-tools deps, 7zip (for zarr zipstore archiving) -RUN apt-get update && apt-get install -y maven hdf5-tools libblosc-dev p7zip-full libxtst-dev && mkdir -p /opt/bin +#install maven hdf5-tools deps, 7zip (for zarr zipstore archiving), libvips +RUN apt-get update && apt-get install -y maven hdf5-tools libblosc-dev p7zip-full libxtst-dev libvips-dev && mkdir -p /opt/bin ENV PATH $PATH:/opt/bin @@ -50,28 +50,6 @@ RUN cd /opt/BigStitcher-Spark && ./install -t 32 -m 128 ENV PATH $PATH:/opt/BigStitcher-Spark -# Install Fiji. -RUN mkdir /opt/fiji \ - && cd /opt/fiji \ - && wget -q https://downloads.imagej.net/fiji/archive/20240208-1017/fiji-nojre.zip \ - && unzip fiji-nojre.zip \ - && rm fiji-nojre.zip - -# Add fiji to the PATH -ENV PATH $PATH:/opt/fiji/Fiji.app - - -# Update URLs use https -RUN ImageJ-linux64 --update edit-update-site ImageJ https://update.imagej.net/ \ - && ImageJ-linux64 --update edit-update-site Fiji https://update.fiji.sc/ \ - && ImageJ-linux64 --update edit-update-site Java-8 https://sites.imagej.net/Java-8/ - - -#install bigstitcher -RUN ImageJ-linux64 --update add-update-site BigStitcher https://sites.imagej.net/BigStitcher/ \ - && ImageJ-linux64 --update refresh-update-sites \ - && ImageJ-linux64 --update update \ - && ImageJ-linux64 --update list # Stage: itksnap (built with Ubuntu16.04 - glibc 2.23) FROM khanlab/itksnap:main as itksnap @@ -83,10 +61,9 @@ FROM python as runtime COPY --from=itksnap /opt/itksnap-mini/* /opt/bin -#install pythondeps (including ome-zarr separately, having issues with including it in pyproject - also use master branch -#to get latest fixes for omero metadata) +#install pythondeps COPY . /opt/pythondeps -RUN pip install --no-cache-dir /opt/pythondeps && pip install --no-cache-dir git+https://github.com/ome/ome-zarr-py@master +RUN pip install --no-cache-dir /opt/pythondeps ENTRYPOINT ["/bin/bash", "-l", "-c"] diff --git a/poetry.lock b/poetry.lock index e389e67..1db2bb4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -389,6 +389,86 @@ files = [ {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"}, ] +[[package]] +name = "cffi" +version = "1.17.1" +description = "Foreign Function Interface for Python calling C 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