diff --git a/docker/Dockerfile b/docker/Dockerfile index 558ed43..773985f 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -6,14 +6,18 @@ LABEL maintainer="James Gebbie-Rayet " ARG TARGETPLATFORM ARG AMBERTOOLS_DL=null -ARG AMBERTOOLS_VER=25 +ARG AMBERTOOLS_VER=26 # Switch to jovyan user. USER $NB_USER WORKDIR $HOME +# Add key locations to the env. +ENV AMBERHOME=/opt/conda +ENV WHAM_HOME=/opt/wham + # Install workshop deps -RUN mamba install nglview pandas numpy matplotlib scipy -y +RUN mamba install nglview pandas numpy matplotlib scipy numba gemmi bioconda::bio rich freesasa scikit-learn sympy networkx -y WORKDIR /tmp RUN wget --no-verbose $AMBERTOOLS_DL/ambertools$AMBERTOOLS_VER.tar.bz2 && \ @@ -23,11 +27,13 @@ RUN wget --no-verbose $AMBERTOOLS_DL/ambertools$AMBERTOOLS_VER.tar.bz2 && \ WORKDIR /tmp/ambertools_src RUN ./update_amber --update +#WORKDIR /tmp/ambertools_src/AmberTools/src/pytraj +#RUN python setup.py --cythonize RUN mkdir /tmp/build WORKDIR /tmp/build RUN cmake /tmp/ambertools_src -DCMAKE_INSTALL_PREFIX=/opt/conda -DPYTHON_EXECUTABLE=/opt/conda/bin/python -DUSE_CONDA_LIBS=TRUE -DBUILD_PYTHON=TRUE -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=TRUE -DDOWNLOAD_MINICONDA=FALSE -DCOMPILER=MANUAL -DBUILD_GUI=FALSE -DCOMPILER=GNU -DOPENMP=TRUE -DCUDA=FALSE -DMPI=FALSE -DUSE_FFT=True -DBUILD_DEPRECATED=False -DBUILD_INDEV=False -DBUILD_PERL=True -DOPTIMIZE=True -RUN make -j8 +RUN make RUN make install # Cleanup. @@ -49,10 +55,6 @@ RUN cd /opt && \ USER $NB_USER WORKDIR $HOME -# Add the exec to the path. -ENV AMBERHOME=/opt/conda -ENV WHAM_HOME=/opt/wham - # Add all of the workshop files to the home directory COPY --chown=1000:100 . . RUN rm -rf AUTHORS LICENSE _config.yml README.md docker .git .github