Merge pull request #22 from BIOP/biop-desktop-012

biop-desktop-0.1.2

Author: romainGuiet

docker/Dockerfile-ms

@@ -15,7 +15,7 @@ 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=0.0.1
+ARG INKSCAPE_VERSION=0.1.0
 ARG OMNI_VERSION=1.0.7-dev2
 ARG BRAINRENDER_VERSION=0.0.3
 
@@ -191,7 +191,7 @@ COPY --from=cellprofiler-image /home/biop/Desktop/cellprofiler.desktop /home/bio
 
 #################################################################
 # Add the inkscape-imagej-panel extension for inskcape
-COPY --from=inkscape-image /home/biop/.config/inkscape/extensions/  /home/biop/.config/inkscape/extensions/ 
+COPY --from=inkscape-image /home/biop/.config/inkscape/  /home/biop/.config/inkscape/
 
 #################################################################
 # Install omnipose

docker/inkscape/Dockerfile-inkscape

@@ -1,5 +1,6 @@
-ARG BASE_IMAGE=0.0.3
-FROM biop-vnc-base:${BASE_IMAGE}
+ARG BASE_IMAGE=0.1.0
+ARG ALIAS=biop/
+FROM ${ALIAS}biop-vnc-base:${BASE_IMAGE}
 
 USER root
 
@@ -17,6 +18,11 @@ RUN unzip inkscape-imagej-panel-master.zip \
     && rm -rf 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
+COPY inkscape/preferences.xml /home/biop/.config/inkscape/preferences.xml
+
 RUN chown -R biop:biop /home/biop/ \
     && chmod -R a+rwx /home/biop/    
 
@@ -25,4 +31,4 @@ RUN chown -R biop:biop /home/biop/ \
 USER biop
 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"]