Skip to content

Update AMBERTOOLS version to 26 #37

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
jimboid wants to merge 8 commits into
base: main
Choose a base branch
from
Open

Update AMBERTOOLS version to 26 #37

Changes from all commits
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
e0f97c2
Update AMBERTOOLS version to 26
jimboid May 1, 2026
2d8926e
Add additional dependencies to Dockerfile
jimboid May 1, 2026
8e97a76
Update package installation in Dockerfile
jimboid May 1, 2026
1f5603c
Add sympy and networkx to workshop dependencies
jimboid May 1, 2026
926c78f
Update Dockerfile
jimboid May 1, 2026
f95cc15
Update Dockerfile to build PyTraj with Cython
jimboid Jun 2, 2026
2fe1b8f
Set environment variables for Amber and WHAM paths
jimboid Jun 2, 2026
0d38e96
Disable pytraj build in Dockerfile
jimboid Jun 2, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 9 additions & 7 deletions docker/Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,18 @@ 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

# 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 && \
Expand All @@ -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.
Expand All @@ -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
Expand Down
Loading