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Update AmberTools version and installation process #53

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Merged
jimboid merged 2 commits into from
Jul 29, 2026
Merged

Update AmberTools version and installation process #53

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994c6bf
Update AmberTools version and installation process
jimboid Jul 29, 2026
440a4b2
Update Wham installation to version 2.1.1
jimboid Jul 29, 2026
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30 changes: 5 additions & 25 deletions docker/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -5,41 +5,23 @@ FROM ghcr.io/ccpbiosim/jupyterhub-base:$BASE_IMAGE
LABEL maintainer="James Gebbie-Rayet <james.gebbie@stfc.ac.uk>"

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 &&\
Expand All @@ -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
Expand All @@ -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

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