The workshop in the version held at MIFOBIO 2018

Dockerfile

@@ -9,33 +9,33 @@ COPY --chown=1000:100 docker/logo-32x32.png docker/logo-64x64.png .local/share/j
 COPY --chown=1000:100 docker/python2-kernel.json .local/share/jupyter/kernels/python2/kernel.json
 
 # Cell Profiler (add to the Python2 environment)
-ADD docker/environment-python2-cellprofiler.yml .setup/
-RUN conda env update -n python2 -q -f .setup/environment-python2-cellprofiler.yml
+#ADD docker/environment-python2-cellprofiler.yml .setup/
+#RUN conda env update -n python2 -q -f .setup/environment-python2-cellprofiler.yml
 # CellProfiler has to be installed in a separate step because it requires
 # the JAVA_HOME environment variable set in the updated environment
-ARG CELLPROFILER_VERSION=v3.1.3
-RUN bash -c "source activate python2 && pip install git+https://github.com/CellProfiler/CellProfiler.git@$CELLPROFILER_VERSION"
+#ARG CELLPROFILER_VERSION=v3.1.3
+#RUN bash -c "source activate python2 && pip install git+https://github.com/CellProfiler/CellProfiler.git@$CELLPROFILER_VERSION"
 
 # R-kernel and R-OMERO prerequisites
-ADD docker/environment-r-omero.yml .setup/
-RUN conda env update -n r-omero -q -f .setup/environment-r-omero.yml && \
-    /opt/conda/envs/r-omero/bin/Rscript -e "IRkernel::installspec(displayname='OMERO R')"
+ADD docker/environment-r.yml .setup/
+RUN conda env update -n R -q -f .setup/environment-r.yml && \
+    /opt/conda/envs/R/bin/Rscript -e "IRkernel::installspec(displayname='R')"
 
 USER root
-RUN mkdir /opt/romero /opt/omero && \
-    fix-permissions /opt/romero /opt/omero
+RUN mkdir /opt/R /opt/omero && \
+    fix-permissions /opt/R /opt/omero
 # R requires these two packages at runtime
 RUN apt-get install -y -q \
     libxrender1 \
     libsm6
 USER $NB_UID
 
 # install rOMERO
-ENV _JAVA_OPTIONS="-Xss2560k -Xmx2g"
-ARG ROMERO_VERSION=v0.4.2
-RUN cd /opt/romero && \
-    curl -sf https://raw.githubusercontent.com/ome/rOMERO-gateway/$ROMERO_VERSION/install.R --output install.R && \
-    bash -c "source activate r-omero && Rscript install.R --version=$ROMERO_VERSION --quiet"
+#ENV _JAVA_OPTIONS="-Xss2560k -Xmx2g"
+#ARG ROMERO_VERSION=v0.4.2
+#RUN cd /opt/romero && \
+#    curl -sf https://raw.githubusercontent.com/ome/rOMERO-gateway/$ROMERO_VERSION/install.R --output install.R && \
+#    bash -c "source activate r-omero && Rscript install.R --version=$ROMERO_VERSION --quiet"
 
 # OMERO full CLI
 # This currently uses the python2 environment, should we move it to its own?

docker/environment-python2-omero.yml

@@ -1,5 +1,12 @@
 name: python2
 channels:
 - bioconda
+- conda-forge
 dependencies:
-- python-omero
+- python-omero=5.4.7
+- pip=10.*
+- scikit-image
+- scipy
+- matplotlib
+- pip:
+  - centrosome

docker/environment-r.yml

@@ -0,0 +1,11 @@
+channels:
+- bioconda
+- conda-forge
+- defaults
+dependencies:
+- r-base
+- r-devtools
+- r-irdisplay
+- r-irkernel
+- r-tidyverse
+prefix: /opt/conda/envs/R

exercises/02-Introduction_Omero_PartI.ipynb

@@ -136,7 +136,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython2",
-   "version": "2.7.3"
+   "version": "2.7.14"
   }
  },
  "nbformat": 4,

exercises/06-cell_analysis.ipynb

@@ -516,7 +516,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython2",
-   "version": "2.7.3"
+   "version": "2.7.14"
   }
  },
  "nbformat": 4,

exercises/07-statistical_analysis.ipynb

@@ -177,7 +177,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "OMERO R",
+   "display_name": "R",
    "language": "R",
    "name": "ir"
   },