Commit 3242f2b0 authored by Romain Guiet's avatar Romain Guiet
Browse files

Update Dockerfile with elastix, p7zip, qupath_ext , fiji-ABBA

parent 75796db7
Pipeline #352646 passed with stage
in 22 minutes and 5 seconds
...@@ -61,6 +61,7 @@ RUN ${fiji} ${addCommand} "3D ImageJ Suite" "https://sites.imagej.net/Tboudier/" ...@@ -61,6 +61,7 @@ RUN ${fiji} ${addCommand} "3D ImageJ Suite" "https://sites.imagej.net/Tboudier/"
RUN ${fiji} ${addCommand} "IJPB-plugins" "https://sites.imagej.net/IJPB-plugins/" RUN ${fiji} ${addCommand} "IJPB-plugins" "https://sites.imagej.net/IJPB-plugins/"
RUN ${fiji} ${addCommand} "CSBDeep" "https://sites.imagej.net/CSBDeep/" RUN ${fiji} ${addCommand} "CSBDeep" "https://sites.imagej.net/CSBDeep/"
RUN ${fiji} ${addCommand} "StarDist" "https://sites.imagej.net/StarDist/" RUN ${fiji} ${addCommand} "StarDist" "https://sites.imagej.net/StarDist/"
RUN ${fiji} ${addCommand} "ABBA" "https://biop.epfl.ch/Fiji-ABBA/"
RUN ${fiji} ${updateCommand} RUN ${fiji} ${updateCommand}
...@@ -88,14 +89,35 @@ COPY qupath.desktop /home/jovyan/Desktop/ ...@@ -88,14 +89,35 @@ COPY qupath.desktop /home/jovyan/Desktop/
RUN chmod +x /home/jovyan/Desktop/qupath.desktop RUN chmod +x /home/jovyan/Desktop/qupath.desktop
# adds QuPath extensions # adds QuPath extensions
env QP_EXT_DIR /home/jovyan/Desktop/QuPath_Common_Data/extensions/ ENV QP_EXT_DIR /home/jovyan/Desktop/QuPath_Common_Data/extensions/
RUN mkdir -p ${QP_EXT_DIR} RUN mkdir -p ${QP_EXT_DIR}
RUN wget -q https://github.com/qupath/qupath-extension-omero/releases/download/v0.3.0/qupath-extension-omero-0.3.0.jar RUN wget -q https://github.com/qupath/qupath-extension-omero/releases/download/v0.3.0/qupath-extension-omero-0.3.0.jar
RUN mv qupath-extension-omero-0.3.0.jar ${QP_EXT_DIR} \ RUN mv qupath-extension-omero-0.3.0.jar ${QP_EXT_DIR} \
&& chmod -R a+rwX ${QP_EXT_DIR} \ && chmod -R a+rwX ${QP_EXT_DIR} \
&& chmod -R a+rwX ${QP_EXT_DIR}qupath-extension-omero-0.3.0.jar && chmod -R a+rwX ${QP_EXT_DIR}qupath-extension-omero-0.3.0.jar
ENV qp_warpy_version 0.2.0
RUN wget -q https://github.com/BIOP/qupath-extension-warpy/releases/download/${qp_warpy_version}/qupath-extension-warpy-${qp_warpy_version}.zip
RUN mv qupath-extension-warpy-${qp_warpy_version}.zip ${QP_EXT_DIR} \
&& chmod -R a+rwX ${QP_EXT_DIR} \
&& chmod -R a+rwX ${QP_EXT_DIR}qupath-extension-warpy-${qp_warpy_version}.zip
ENV qp_abba_version 0.1.1
RUN wget -q https://github.com/BIOP/qupath-extension-abba/releases/download/${qp_abba_version}/qupath-extension-abba-${qp_abba_version}.zip
RUN mv qupath-extension-abba-${qp_abba_version}.zip ${QP_EXT_DIR} \
&& chmod -R a+rwX ${QP_EXT_DIR} \
&& chmod -R a+rwX ${QP_EXT_DIR}qupath-extension-abba-${qp_abba_version}.zip
RUN apt-get update && \
apt install -y p7zip-full
ENV elastix_version 5.0.1
RUN wget https://github.com/SuperElastix/elastix/releases/download/${elastix_version}/elastix-${elastix_version}-linux.tar.bz2 \
&& tar -xjvf elastix-${elastix_version}-linux.tar.bz2 -C /opt/ \
&& rm elastix-${elastix_version}-linux.tar.bz2 \
&& chmod -R a+rwX /opt/elastix-${elastix_version}-linux
USER ${NB_USER} USER ${NB_USER}
......
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