From ff9bfa3aeb01199e48fb529fc88aeb30fb102be6 Mon Sep 17 00:00:00 2001 From: Ali Khan Date: Wed, 18 Sep 2024 22:36:21 -0400 Subject: [PATCH] add back n5-utils etc, is needed for bigstitcher --- Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index e79b604..df2fa16 100644 --- a/Dockerfile +++ b/Dockerfile @@ -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