Updated Dockerfile

Dockerfile

@@ -6,8 +6,7 @@ RUN apt-get update && apt-get install -y build-essential
 
 RUN apt-get install -y python3 python3-pip vim
 
-RUN pip3 install jupyterlab numpy scipy matplotlib seaborn pandas sklearn scikit-image \
-        jupyter_contrib_nbextensions jupyter_nbextensions_configurator jupyterthemes
+RUN pip3 install jupyterlab numpy scipy matplotlib seaborn pandas sklearn scikit-image
 
 RUN pip3 install -Iv six==1.12.0
 
@@ -17,15 +16,18 @@ RUN julia -e 'using Pkg; Pkg.add("IJulia"); Pkg.build(); using IJulia;'
 
 ## Julia Baysor envitonment
 
-RUN julia -e 'using Pkg; Pkg.add("PackageCompiler")'
+RUN julia -e 'using Pkg; Pkg.add(Pkg.PackageSpec(;name="PackageCompiler", version="2.0.6"))'
 RUN julia -e 'using Pkg; Pkg.add(PackageSpec(url="https://github.com/hms-dbmi/Baysor.git")); Pkg.build();'
 
 RUN julia -e 'import Baysor, Pkg; Pkg.activate(dirname(dirname(pathof(Baysor)))); Pkg.instantiate();'
-RUN julia -e 'using PackageCompiler; import Baysor, Pkg; Pkg.activate(dirname(dirname(pathof(Baysor)))); create_sysimage(:Baysor; precompile_execution_file="$(dirname(pathof(Baysor)))/../bin/precompile.jl", replace_default=true, cpu_target="generic")'
+RUN julia -e 'using PackageCompiler; import Baysor, Pkg; Pkg.activate(dirname(dirname(pathof(Baysor)))); \
+    create_sysimage(:Baysor; precompile_execution_file="$(dirname(pathof(Baysor)))/../bin/precompile.jl", sysimage_path="/root/BaysorSysimage.so")'
 
 RUN \
-    printf "#!/usr/bin/env julia\n\nimport Baysor\nBaysor.run_cli()" >> /bin/baysor && \
+      printf "#!/usr/local/julia/bin/julia --sysimage=/root/BaysorSysimage.so\n\nimport Baysor\nBaysor.run_cli()" >> /bin/baysor && \
     chmod +x /bin/baysor
 
+RUN baysor --help
+
 ENTRYPOINT ["/bin/bash"]
 WORKDIR /root/