Merge pull request #23 from BIOP/v0.1.4

modify Dockerfile-inkscape and Dockerfile-ms

Author: romainGuiet

docker/Dockerfile-ms

@@ -15,25 +15,25 @@ ARG EM_VERSION=1.1.0
 ARG STARDIST_VERSION=0.8.5
 ARG ABBA_VERSION=0.8.0-01
 ARG CELLPROFILER_VERSION=4.2.6
-ARG INKSCAPE_VERSION=0.1.0
+ARG INKSCAPE_VERSION=0.1.2
 ARG OMNI_VERSION=1.0.7-dev2
 ARG BRAINRENDER_VERSION=0.0.3
 
-FROM ${ALIAS}biop-qupath:${QUPATH_VERSION} as qupath-image
-FROM ${ALIAS}biop-ilastik:${ILASTIK_VERSION} as ilastik-image
-FROM ${ALIAS}biop-fiji:${FIJI_VERSION} as fiji-image
-FROM ${ALIAS}biop-cellpose:${CELLPOSE_VERSION} as cellpose-image
-FROM ${ALIAS}biop-devbio:${DEVBIO_VERSION} as devbio-image
-FROM ${ALIAS}biop-samapi:${SAMAPI_VERSION} as samapi-image
-FROM ${ALIAS}biop-empanada:${EM_VERSION} as empanada-image
-FROM ${ALIAS}biop-stardist:${STARDIST_VERSION} as stardist-image
-FROM ${ALIAS}biop-abba:${ABBA_VERSION} as abba-image
-FROM ${ALIAS}biop-cellprofiler:${CELLPROFILER_VERSION} as cellprofiler-image
-FROM ${ALIAS}biop-inkscape:${INKSCAPE_VERSION} as inkscape-image
-FROM ${ALIAS}biop-omni:${OMNI_VERSION} as omnipose-image
-FROM ${ALIAS}biop-brainrender:${BRAINRENDER_VERSION} as brainrender-image
-
-FROM ${ALIAS}biop-vnc-base:${BASE_IMAGE} as base
+FROM ${ALIAS}biop-qupath:${QUPATH_VERSION} AS qupath-image
+FROM ${ALIAS}biop-ilastik:${ILASTIK_VERSION} AS ilastik-image
+FROM ${ALIAS}biop-fiji:${FIJI_VERSION} AS fiji-image
+FROM ${ALIAS}biop-cellpose:${CELLPOSE_VERSION} AS cellpose-image
+FROM ${ALIAS}biop-devbio:${DEVBIO_VERSION} AS devbio-image
+FROM ${ALIAS}biop-samapi:${SAMAPI_VERSION} AS samapi-image
+FROM ${ALIAS}biop-empanada:${EM_VERSION} AS empanada-image
+FROM ${ALIAS}biop-stardist:${STARDIST_VERSION} AS stardist-image
+FROM ${ALIAS}biop-abba:${ABBA_VERSION} AS abba-image
+FROM ${ALIAS}biop-cellprofiler:${CELLPROFILER_VERSION} AS cellprofiler-image
+FROM ${ALIAS}biop-inkscape:${INKSCAPE_VERSION} AS inkscape-image
+FROM ${ALIAS}biop-omni:${OMNI_VERSION} AS omnipose-image
+FROM ${ALIAS}biop-brainrender:${BRAINRENDER_VERSION} AS brainrender-image
+
+FROM ${ALIAS}biop-vnc-base:${BASE_IMAGE} AS base
 
 USER root
 
@@ -206,6 +206,23 @@ COPY --from=omnipose-image /opt/conda/envs/omnipose/ /opt/conda/envs/omnipose/
 # To make the different conda env available in jupyter
 COPY jupyter/kernels/ /home/biop/.local/share/jupyter/kernels/
 
+
+
+#################################################################
+# TODO : put back with inkscape installation
+# replace inkscape from base with the one from the inkscape-image (newer)
+RUN sudo apt-get update -y \
+    && sudo apt-get install software-properties-common -y \
+    && sudo apt-get update -y \
+    && sudo add-apt-repository ppa:inkscape.dev/stable \
+    && sudo apt-get update -y \
+    && sudo apt-get install inkscape -y
+
+# Install Inkscape extension
+# and the inkscape_modules environment
+# get a "docker: Error response from daemon: max depth exceeded."
+#COPY --from=inkscape-image /opt/conda/envs/inkscape_modules/ /opt/conda/envs/inkscape_modules/ 
+
 #################################################################
 # final chown and chmod
 RUN chown -R biop:biop /home/biop/ \
@@ -214,8 +231,7 @@ RUN chown -R biop:biop /home/biop/ \
 #################################################################
 # Container start
 USER biop
+RUN conda init
 WORKDIR /home/biop
 ENTRYPOINT ["/usr/local/bin/jupyter"]
-CMD ["lab", "--allow-root", "--ip=*", "--port=8888", "--no-browser", "--NotebookApp.token=''", "--NotebookApp.allow_origin='*'", "--notebook-dir=/home/biop"]
-
-
+CMD ["lab", "--allow-root", "--ip=*", "--port=8888", "--no-browser", "--NotebookApp.token=''", "--NotebookApp.allow_origin='*'", "--notebook-dir=/home/biop"]

docker/inkscape/Dockerfile-inkscape

@@ -7,6 +7,10 @@ USER root
 #################################################################
 # Install Inkscape extension 
 RUN sudo apt-get update -y \
+    && sudo apt-get install software-properties-common -y \
+    && sudo apt-get update -y \
+    && sudo add-apt-repository ppa:inkscape.dev/stable \
+    && sudo apt-get update -y \
     && sudo apt-get install inkscape -y 
 
 #################################################################
@@ -19,10 +23,29 @@ RUN unzip inkscape-imagej-panel-master.zip \
     && rm -rf inkscape-imagej-panel-master/
 
 #################################################################
-# Inkscape preferences with path to ImageJ, devbio conda env already set up
-# won't work ofr this image that does not have devbio nor Fiji
+# Inkscape preferences with path to ImageJ, inkscape conda env already set up
+# won't work ofr this image that does not have inkscape nor Fiji
 COPY inkscape/preferences.xml /home/biop/.config/inkscape/preferences.xml
 
+
+#################################################################
+# Install SimpInkScr extension
+# RUN cd $HOME/.config/inkscape/extensions/ && git clone https://github.com/spakin/SimpInkScr.git
+RUN wget https://github.com/spakin/SimpInkScr/releases/download/v5.0.0/simple_inkscape_scripting.zip
+RUN unzip simple_inkscape_scripting.zip \
+    && cp -r simple_inkscape_scripting/* /home/biop/.config/inkscape/extensions/ \
+    && rm -rf simple_inkscape_scripting.zip \
+    && rm -rf simple_inkscape_scripting/
+
+##############################################################################
+# install inkscape_modules environment
+COPY inkscape/env_inkscape.yml /tmp/env_inkscape.yml
+RUN conda env update -n inkscape_modules -f /tmp/env_inkscape.yml \
+    && conda clean --all -f -y \
+    && conda env export -n "biop" \
+     && rm /tmp/env_inkscape.yml
+
+
 RUN chown -R biop:biop /home/biop/ \
     && chmod -R a+rwx /home/biop/