diff --git a/Dockerfile b/Dockerfile index 7adc810..77c6b0e 100644 --- a/Dockerfile +++ b/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/