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Dockerfile_fiji
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Dockerfile_fiji
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FROM ubuntu:focal
RUN apt-get -qq update \
&& apt-get -qq install --no-install-recommends --yes \
wget \
bzip2 \
ca-certificates \
curl \
unzip \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
#Get imagej
RUN wget --quiet https://downloads.imagej.net/fiji/latest/fiji-linux64.zip -P /tmp/ \
&& unzip /tmp/fiji-linux64.zip -d /opt/ \
&& rm /tmp/fiji-linux64.zip
ENV PATH /opt/Fiji.app:$PATH
# Install BigStitcher
RUN ImageJ-linux64 --headless --update add-update-site BigStitcher https://sites.imagej.net/BigStitcher/ \
&& ImageJ-linux64 --headless --update update
# Install BaSiC_Mod
RUN wget --quiet https://github.com/VasylVaskivskyi/BaSiC_Mod/releases/download/v1.0/BaSiC_Mod_v10.zip -P /tmp/ \
&& unzip /tmp/BaSiC_Mod_v10.zip -d /tmp/ \
&& mv /tmp/BaSiC_Mod_v10/BaSiC_Mod.jar /opt/Fiji.app/plugins/ \
&& mv /tmp/BaSiC_Mod_v10/dependencies/* /opt/Fiji.app/jars/. \
&& rm -r /tmp/BaSiC_Mod_v10 \
&& rm /tmp/BaSiC_Mod_v10.zip \
&& rm /opt/Fiji.app/jars/jtransforms-2.4.jar \
&& rm /opt/Fiji.app/jars/netlib-java-0.9.3-renjin-patched-2.jar \
&& ImageJ-linux64 --headless --update update
FROM ubuntu:focal
RUN apt-get -qq update \
&& apt-get -qq install --no-install-recommends --yes \
wget \
bzip2 \
ca-certificates \
curl \
unzip \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
#Get imagej
RUN wget --quiet https://downloads.imagej.net/fiji/latest/fiji-linux64.zip -P /tmp/ \
&& unzip /tmp/fiji-linux64.zip -d /opt/ \
&& rm /tmp/fiji-linux64.zip
ENV PATH /opt/Fiji.app:$PATH
# Install BigStitcher
RUN ImageJ-linux64 --headless --update add-update-site BigStitcher https://sites.imagej.net/BigStitcher/ \
&& ImageJ-linux64 --headless --update update
# Install BaSiC_Mod
RUN wget --quiet https://github.com/hubmapconsortium/BaSiC_Mod/releases/download/v1.0/BaSiC_Mod_v10.zip -P /tmp/ \
&& unzip /tmp/BaSiC_Mod_v10.zip -d /tmp/ \
&& mv /tmp/BaSiC_Mod_v10/BaSiC_Mod.jar /opt/Fiji.app/plugins/ \
&& mv /tmp/BaSiC_Mod_v10/dependencies/* /opt/Fiji.app/jars/. \
&& rm -r /tmp/BaSiC_Mod_v10 \
&& rm /tmp/BaSiC_Mod_v10.zip \
&& rm /opt/Fiji.app/jars/jtransforms-2.4.jar \
&& rm /opt/Fiji.app/jars/netlib-java-0.9.3-renjin-patched-2.jar \
&& ImageJ-linux64 --headless --update update