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Upgrade AmberTools to version 26 #52

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

Upgrade AmberTools to version 26 #52

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56b5848
Upgrade AmberTools to version 26 and streamline Dockerfile
jimboid Jul 29, 2026
04cf8b6
Remove build-args from Docker build step
jimboid Jul 29, 2026
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4 changes: 1 addition & 3 deletions .github/workflows/build.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -53,9 +53,7 @@ jobs:
- name: Build and push by digest
if: github.event_name == 'pull_request'
uses: docker/build-push-action@v7.3.0
with:
build-args: |
AMBERTOOLS_DL=${{ secrets.AMBERTOOLS_DL }}
with:
file: ./docker/Dockerfile
platforms: ${{ matrix.platform }}
labels: ${{ steps.meta.outputs.labels }}
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30 changes: 4 additions & 26 deletions docker/Dockerfile
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Expand Up @@ -4,37 +4,15 @@ FROM ghcr.io/ccpbiosim/jupyterhub-base:$BASE_IMAGE

LABEL maintainer="James Gebbie-Rayet <james.gebbie@stfc.ac.uk>"

ARG AMBERTOOLS_DL=null
ARG AMBERTOOLS_VER=25

# Install workshop deps
RUN mamba install -c conda-forge bioconda::blast openmm numpy=2.2 matplotlib scipy -y
RUN pip install git+https://github.com/CharlieLaughton/Alphafix.git
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
ARG AMBERTOOLS_VER=26.0

# Switch to jovyan user.
USER $NB_USER
WORKDIR $HOME

# Add the exec to the path.
ENV AMBERHOME=/opt/conda
# Install workshop deps
RUN mamba install -c conda-forge bioconda::blast openmm numpy=2.2 matplotlib scipy ambertools=$AMBERTOOLS_VER
RUN pip install git+https://github.com/CharlieLaughton/Alphafix.git

RUN mkdir blastp
WORKDIR /home/jovyan/blastp
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