diff --git a/dockerfiles/Dockerfile_nfcore-proteinfold_rosettafold_all_atom b/dockerfiles/Dockerfile_nfcore-proteinfold_rosettafold_all_atom index d477b94..8f5f3b9 100644 --- a/dockerfiles/Dockerfile_nfcore-proteinfold_rosettafold_all_atom +++ b/dockerfiles/Dockerfile_nfcore-proteinfold_rosettafold_all_atom @@ -6,20 +6,20 @@ LABEL Author="j.caley@unsw.edu.au" \ description="Docker image containing all software requirements to run the RUN_ROSETTAFOLD_ALL_ATOM module using the nf-core/proteinfold pipeline" ENV PYTHONPATH="/app/RoseTTAFold-All-Atom:$PYTHONPATH" \ - PATH="/opt/miniforge/bin:/app/RoseTTAFold-All-Atom:$PATH" \ + PATH="/conda/bin:/app/RoseTTAFold-All-Atom:$PATH" \ DGLBACKEND="pytorch" RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y wget git && \ wget -q -P /tmp "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" && \ - bash /tmp/Miniforge3-$(uname)-$(uname -m).sh && \ - rm /tmp/Miniforge3-Linux-x86_64.sh && \ - export PATH="/opt/miniforge/bin:$PATH" && \ + bash /tmp/Miniforge3-$(uname)-$(uname -m).sh -b -p /conda && \ + rm /tmp/Miniforge3-$(uname)-$(uname -m).sh && \ + export PATH="/conda/bin:$PATH" && \ git clone --single-branch --depth 1 https://github.com/Australian-Structural-Biology-Computing/RoseTTAFold-All-Atom.git /app/RoseTTAFold-All-Atom && \ cd /app/RoseTTAFold-All-Atom && \ - mamba env create -f environment.yaml && \ + mamba env create --file=environment.yaml && \ mamba run -n RFAA \ 'python rf2aa/SE3Transformer/setup.py install && \ bash install_dependencies.sh' && \ @@ -35,4 +35,4 @@ RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install --no-instal rm -rf /var/lib/apt/lists/* /root/.cache *.tar.gz && \ mamba clean --all --force-pkgs-dirs -y -ENTRYPOINT ["mamba", "run", "--name", "RFAA", "python", "-m", "rf2aa.run_inference", "--config-name"] +ENTRYPOINT ["/conda/bin/mamba", "run", "--name", "RFAA", "python", "-m", "rf2aa.run_inference", "--config-name"]