From 56b5848dafb7f76bb9f20905c255d4f3c623b434 Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Wed, 29 Jul 2026 16:27:53 +0100 Subject: [PATCH 1/2] Upgrade AmberTools to version 26 and streamline Dockerfile Updated AmberTools version and simplified installation steps. --- docker/Dockerfile | 30 ++++-------------------------- 1 file changed, 4 insertions(+), 26 deletions(-) diff --git a/docker/Dockerfile b/docker/Dockerfile index ed777a4..aebde81 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -4,37 +4,15 @@ FROM ghcr.io/ccpbiosim/jupyterhub-base:$BASE_IMAGE LABEL maintainer="James Gebbie-Rayet " -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 From 04cf8b6142be45b2e5ef962caf5e86cfedad0cfe Mon Sep 17 00:00:00 2001 From: James Gebbie-Rayet Date: Wed, 29 Jul 2026 16:28:50 +0100 Subject: [PATCH 2/2] Remove build-args from Docker build step Removed build-args from the build and push step in the workflow. --- .github/workflows/build.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml index 4ba0d38..784967f 100644 --- a/.github/workflows/build.yaml +++ b/.github/workflows/build.yaml @@ -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 }}