Updated dev env

env/dev.Dockerfile

@@ -1,21 +1,30 @@
-FROM gitpod/workspace-python:2023-02-27-14-39-56
+FROM gitpod/workspace-full-vnc:2023-08-09-14-26-44
 
-# Install Java and OpenCV
+# Install Java, OpenCV, and QT5
 RUN sudo apt-get update && \
-    sudo apt-get install -y openjdk-13-jre python3-opencv && \
+    sudo apt-get install -y openjdk-19-jre \
+        python3-opencv \
+        qtbase5-dev \
+        qtchooser \
+        qt5-qmake \
+        qtbase5-dev-tools && \
     sudo rm -rf /var/lib/apt/lists/*
 
-# Additional packages for Roadie scripts
+# Python packages for Napari and Roadie
 RUN pip install --no-cache-dir \
+  "napari[all]" \
   threadpoolctl \
-  sklearn \
+  scikit-learn \
   pandas \
   tifffile \
   zarr \
   scikit-image \
   ome_types \
   palom
 
+# Let pyjnius find that JRE without the full JDK installed
+ENV JAVA_HOME=/usr/lib/jvm/java-19-openjdk-amd64
+
 # Install Nextflow
 RUN curl -s https://get.nextflow.io | bash && \
     sudo mv nextflow /usr/bin
@@ -24,5 +33,5 @@ RUN curl -s https://get.nextflow.io | bash && \
 RUN sudo mkdir -p /data && \
     sudo chown gitpod:gitpod /data && \
     cd /workspace && \
-    nextflow run labsyspharm/mcmicro/exemplar.nf --name exemplar-001 && \
+    nextflow run labsyspharm/mcmicro/exemplar.nf --name exemplar-001 --path /data && \
     rm -rf work