diff --git a/docker/Dockerfile b/docker/Dockerfile index 558ed43..ee02a6f 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -5,41 +5,23 @@ FROM ghcr.io/ccpbiosim/jupyterhub-base:$BASE_IMAGE 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 $HOME # Install workshop deps -RUN mamba install nglview pandas numpy matplotlib scipy -y +RUN mamba install nglview pandas numpy matplotlib scipy ambertools=$AMBERTOOLS_VER -y WORKDIR /tmp -RUN wget --no-verbose $AMBERTOOLS_DL/ambertools$AMBERTOOLS_VER.tar.bz2 && \ - tar xjf ambertools$AMBERTOOLS_VER.tar.bz2 && \ - rm ambertools$AMBERTOOLS_VER.tar.bz2 && \ - mv ambertools${AMBERTOOLS_VER}_src ambertools_src - -WORKDIR /tmp/ambertools_src -RUN ./update_amber --update -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 install - -# Cleanup. -RUN rm -r /tmp/ambertools_src /tmp/build - # Install Wham. USER root RUN cd /opt && \ mkdir wham && \ - wget http://membrane.urmc.rochester.edu/sites/default/files/wham/wham-release-2.0.11.tgz && \ - tar xvf wham-release-2.0.11.tgz -C wham --strip-components=1 && \ - rm wham-release-2.0.11.tgz && \ + wget https://github.com/agrossfield/wham/archive/refs/tags/v2.1.1.tar.gz && \ + tar xvf v2.1.1.tar.gz -C wham --strip-components=1 && \ + rm v2.1.1.tar.gz && \ cd wham/wham && \ make clean && \ make &&\ @@ -50,7 +32,6 @@ USER $NB_USER WORKDIR $HOME # Add the exec to the path. -ENV AMBERHOME=/opt/conda ENV WHAM_HOME=/opt/wham # Add all of the workshop files to the home directory @@ -61,7 +42,6 @@ RUN if [ "$TARGETPLATFORM" = "linux/arm64" ]; then \ sed -i 's%trajin rc0.00/md1ps.nc%trajin rc-0.00/md1ps.nc%' /home/jovyan/data/make_us_trj.in; \ fi - # Copy lab workspace COPY --chown=1000:100 docker/default-37a8.jupyterlab-workspace /home/jovyan/.jupyter/lab/workspaces/default-37a8.jupyterlab-workspace