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add back n5-utils etc, is needed for bigstitcher
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akhanf committed Sep 19, 2024
1 parent abc8d4d commit ff9bfa3
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6 changes: 3 additions & 3 deletions Dockerfile
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Expand Up @@ -36,12 +36,12 @@ 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 && mkdir -p /opt/bin
RUN apt-get update && apt-get install -y maven hdf5-tools libblosc-dev p7zip-full && mkdir -p /opt/bin

#ENV PATH $PATH:/opt/bin
ENV PATH $PATH:/opt/bin

#install n5-utils
#RUN cd /opt && git clone https://github.com/saalfeldlab/n5-utils && cd n5-utils && ./install /opt/bin
RUN cd /opt && git clone https://github.com/saalfeldlab/n5-utils && cd n5-utils && ./install /opt/bin

#install bigstitcher-spark, and customize launcher to include args for mem and cpu
#RUN cd /opt && git clone https://github.com/akhanf/BigStitcher-Spark.git && cd BigStitcher-Spark && ./install -t 32 -m 128 && cp -v affine-fusion /opt/bin && cp -v target/BigStitcher-Spark-0.0.2-SNAPSHOT.jar /opt/bin
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