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Add Dockerfile and tidy dependencies
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‎apps/protein_folding/helixfold3/Dockerfile‎

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ARG CUDA=12.8.1
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FROM nvidia/cuda:${CUDA}-cudnn-devel-ubuntu22.04
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# FROM directive resets ARGS, so we specify again (the value is retained if
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# previously set).
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ARG CUDA
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LABEL Author="[email protected]" \
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title="helixfold3" \
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description="Docker image containing all software requirements to run helixfold3"
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RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y wget git && \
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wget -q -P /tmp "https://github.com/conda-forge/miniforge/releases/download/24.11.0-0/Miniforge3-$(uname)-$(uname -m).sh" && \
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bash /tmp/Miniforge3-$(uname)-$(uname -m).sh -b -p /conda && \
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git clone --filter=blob:none --no-checkout https://github.com/PaddlePaddle/PaddleHelix.git /app/helixfold3 && \
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cd /app/helixfold3 && \
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git sparse-checkout init --cone && \
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git sparse-checkout set apps/protein_folding/helixfold3 && \
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git checkout dev && \
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mv apps/protein_folding/helixfold3/* . && \
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rm -rf /tmp/Miniforge3-$(uname)-$(uname -m).sh /var/lib/apt/lists/* /root/.cache apps && \
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apt-get remove --purge -y wget git && apt-get autoremove -y && apt-get clean -y
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COPY environment.yaml /app/helixfold3/environment.yaml
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ENV PATH="/conda/bin:$PATH"
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RUN mamba env create --file=/app/helixfold3/environment.yaml && \
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mamba install -y -c bioconda aria2 hmmer==3.3.2 kalign2==2.04 hhsuite==3.3.0 -n helixfold && \
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mamba install -y -c conda-forge openbabel -n helixfold && \
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mamba clean --all --force-pkgs-dirs -y && \
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rm -rf /root/.cache
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ENV PATH="/conda/bin:/app/helixfold3:./maxit_src/bin:/conda/envs/helixfold/bin:$PATH" \
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RCSBROOT="./maxit_src" \
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MAXIT_SRC="./maxit_src" \
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PYTHON_BIN="/conda/envs/helixfold/bin/python3.9" \
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ENV_BIN="/conda/envs/helixfold/bin" \
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OBABEL_BIN="/conda/envs/helixfold/bin"
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ENTRYPOINT ["mamba", "run", "--name", "helixfold"]

‎apps/protein_folding/helixfold3/environment.yaml‎

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name: helixfold
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channels:
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- nvidia
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- bioconda
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- conda-forge
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- bioconda
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- nvidia
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- biocore
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dependencies:
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- _libgcc_mutex=0.1=conda_forge
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- _openmp_mutex=4.5=2_gnu
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- aria2=1.23.0=0
10-
- binutils=2.43=h4852527_2
11-
- binutils_impl_linux-64=2.43=h4bf12b8_2
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- binutils_linux-64=2.43=h4852527_2
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- bzip2=1.0.8=h4bc722e_7
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- c-ares=1.11.0=h470a237_1
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- c-compiler=1.8.0=h2b85faf_1
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- ca-certificates=2024.8.30=hbcca054_0
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- cairo=1.18.0=hebfffa5_3
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- cuda-cccl=12.0.90=0
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- cuda-command-line-tools=12.0.0=0
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- cuda-compiler=12.0.0=h6459364_1
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- cuda-cudart=12.0.107=0
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- cuda-cudart-dev=12.0.107=0
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- cuda-cuobjdump=12.0.76=0
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- cuda-cupti=12.4.127=0
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- cuda-cuxxfilt=12.0.76=0
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- cuda-driver-dev=12.0.107=0
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- cuda-gdb=12.4.127=0
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- cuda-libraries=12.0.0=ha770c72_1
29-
- cuda-libraries-dev=12.0.0=ha770c72_1
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- cuda-nsight=12.0.78=0
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- cuda-nvcc=12.0.76=0
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- cuda-nvdisasm=12.4.127=0
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- cuda-nvml-dev=12.0.76=0
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- cuda-nvprof=12.4.127=0
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- cuda-nvprune=12.0.76=0
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- cuda-nvrtc=12.0.76=0
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- cuda-nvrtc-dev=12.0.76=0
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- cuda-nvtx=12.4.127=0
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- cuda-nvvp=12.0.90=0
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- cuda-opencl=12.0.76=0
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- cuda-opencl-dev=12.0.76=0
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- cuda-profiler-api=12.0.76=0
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- cuda-sanitizer-api=12.4.127=0
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- cuda-toolkit=12.0.0=ha804496_1
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- cuda-tools=12.0.0=ha770c72_0
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- cuda-visual-tools=12.0.0=ha770c72_0
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- cudatoolkit=11.8.0=h4ba93d1_13
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- cudnn=8.4.0.27=hed8a83a_1
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- cxx-compiler=1.8.0=h1a2810e_1
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- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
51-
- font-ttf-inconsolata=3.000=h77eed37_0
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- font-ttf-source-code-pro=2.038=h77eed37_0
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- font-ttf-ubuntu=0.83=h77eed37_3
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- fontconfig=2.15.0=h7e30c49_1
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- fonts-conda-ecosystem=1=0
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- fonts-conda-forge=1=0
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- freetype=2.12.1=h267a509_2
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- gcc=13.3.0=h9576a4e_1
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- gcc_impl_linux-64=13.3.0=hfea6d02_1
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- gcc_linux-64=13.3.0=hc28eda2_5
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- gds-tools=1.5.0.59=0
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- gxx=13.3.0=h9576a4e_1
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- gxx_impl_linux-64=13.3.0=hdbfa832_1
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- gxx_linux-64=13.3.0=h6834431_5
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- hhsuite=3.3.0=py39pl5321h0dd7abe_13
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- hmmer=3.3.2=hdbdd923_4
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- icu=75.1=he02047a_0
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- kalign2=2.04=h031d066_7
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- kernel-headers_linux-64=3.10.0=he073ed8_18
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- ld_impl_linux-64=2.43=h712a8e2_2
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- libcublas=12.0.1.189=0
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- libcublas-dev=12.0.1.189=0
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- libcufft=11.0.0.21=0
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- libcufft-dev=11.0.0.21=0
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- libcufile=1.5.0.59=0
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- libcufile-dev=1.5.0.59=0
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- libcurand=10.3.1.50=0
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- libcurand-dev=10.3.1.50=0
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- libcusolver=11.4.2.57=0
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- libcusolver-dev=11.4.2.57=0
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- libcusparse=12.0.0.76=0
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- libcusparse-dev=12.0.0.76=0
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- libexpat=2.6.4=h5888daf_0
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- libffi=3.4.2=h7f98852_5
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- libgcc=14.2.0=h77fa898_1
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- libgcc-devel_linux-64=13.3.0=h84ea5a7_101
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- libgcc-ng=14.2.0=h69a702a_1
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- libglib=2.82.2=h2ff4ddf_0
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- libgomp=14.2.0=h77fa898_1
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- libiconv=1.17=hd590300_2
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- libnpp=12.0.0.30=0
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- libnpp-dev=12.0.0.30=0
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- libnsl=2.0.1=hd590300_0
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- libnvjitlink=12.0.76=0
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- libnvjitlink-dev=12.0.76=0
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- libnvjpeg=12.0.0.28=0
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- libnvjpeg-dev=12.0.0.28=0
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- libpng=1.6.44=hadc24fc_0
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- libsanitizer=13.3.0=heb74ff8_1
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- libsqlite=3.47.0=hadc24fc_1
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- libssh2=1.10.0=haa6b8db_3
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- libstdcxx=14.2.0=hc0a3c3a_1
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- libstdcxx-devel_linux-64=13.3.0=h84ea5a7_101
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- libstdcxx-ng=14.2.0=h4852527_1
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- libuuid=2.38.1=h0b41bf4_0
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- libxcb=1.17.0=h8a09558_0
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- libxcrypt=4.4.36=hd590300_1
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- libxml2=2.13.4=hb346dea_2
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- libzlib=1.3.1=hb9d3cd8_2
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- nccl=2.14.3.1=h0800d71_0
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- ncurses=6.5=he02047a_1
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- nsight-compute=2022.4.0.15=0
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- openbabel=3.1.1=py39h2d01fe1_9
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- openssl=1.1.1w=hd590300_0
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- pcre2=10.44=hba22ea6_2
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- perl=5.32.1=7_hd590300_perl5
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- pip=24.3.1=pyh8b19718_0
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- pixman=0.43.2=h59595ed_0
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- pthread-stubs=0.4=hb9d3cd8_1002
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- python=3.9.15=h47a2c10_0_cpython
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- python_abi=3.9=5_cp39
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- readline=8.2=h8228510_1
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- setuptools=75.3.0=pyhd8ed1ab_0
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- sqlite=3.47.0=h9eae976_1
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- sysroot_linux-64=2.17=h4a8ded7_18
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- tk=8.6.13=noxft_h4845f30_101
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- tzdata=2024b=hc8b5060_0
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- wheel=0.45.0=pyhd8ed1ab_0
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- xorg-libice=1.1.1=hb9d3cd8_1
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- xorg-libsm=1.2.4=he73a12e_1
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- xorg-libx11=1.8.10=h4f16b4b_0
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- xorg-libxau=1.0.11=hb9d3cd8_1
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- xorg-libxdmcp=1.1.5=hb9d3cd8_0
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- xorg-libxext=1.3.6=hb9d3cd8_0
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- xorg-libxrender=0.9.11=hb9d3cd8_1
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- xorg-xorgproto=2024.1=hb9d3cd8_1
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- xz=5.2.6=h166bdaf_0
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- zlib=1.3.1=hb9d3cd8_2
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- python=3.9
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- cuda-toolkit=12.0
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- cudnn=8.4.0
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- nccl=2.14
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- libgcc=14.2.0
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- libgomp=14.2.0
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- pip=25.0.1
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- aria2=1.37.0
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- hmmer=3.4
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- kalign2=2.04
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- hhsuite=3.3.0
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- openbabel=3.1.1
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- pip:
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- paddlepaddle-gpu==2.6.1 -f https://www.paddlepaddle.org.cn/whl/linux/mkl/avx/stable.html
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- absl-py==0.13.0
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- anyio==4.6.2.post1
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- astor==0.8.1
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- biopython==1.79
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- certifi==2024.8.30
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- charset-normalizer==3.4.0
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- chex==0.0.7
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- contextlib2==21.6.0
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- decorator==5.1.1
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- dm-haiku==0.0.4
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- dm-tree==0.1.6
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- docker==5.0.0
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- exceptiongroup==1.2.2
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- h11==0.14.0
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- httpcore==1.0.6
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- httpx==0.27.2
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- idna==3.10
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- immutabledict==2.0.0
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- jax==0.2.14
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- jaxlib==0.4.30
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- ml-collections==0.1.0
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- ml-dtypes==0.5.0
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- numpy==1.24.4
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- opt-einsum==3.3.0
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- paddlepaddle-gpu==2.6.1
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- pandas==1.3.4
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- pillow==11.0.0
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- posebusters==0.3.1
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- protobuf==5.28.3
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- python-dateutil==2.9.0.post0
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- pytz==2024.2
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- pyyaml==6.0.2
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- rdkit==2024.3.6
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- rdkit-pypi==2022.9.5
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- requests==2.32.3
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- scipy==1.9.0
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- six==1.16.0
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- sniffio==1.3.1
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- tabulate==0.9.0
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- toolz==1.0.0
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- typing-extensions==4.12.2
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- urllib3==2.2.3
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- websocket-client==1.8.0
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prefix: /opt/miniforge/envs/helixfold
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- rdkit-pypi==2022.9.5
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- posebusters==0.3.6

‎apps/protein_folding/helixfold3/helixfold3.def‎

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Bootstrap: docker
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From: nvidia/cuda:12.6.0-cudnn-devel-ubuntu24.04
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From: nvidia/cuda:12.8.1-cudnn-devel-ubuntu22.04
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%labels
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Author [email protected]
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Version 1.0.0
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title="helixfold3"
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description="Docker image containing all software requirements to run helixfold3"
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%files
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environment.yaml /app/helixfold3/environment.yaml
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%post
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apt update && DEBIAN_FRONTEND=noninteractive apt install --no-install-recommends -y wget git
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wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh"
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bash Miniforge3-Linux-x86_64.sh -b -p /opt/miniforge
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rm Miniforge3-Linux-x86_64.sh
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export PATH="/opt/miniforge/bin:$PATH"
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wget -q -P /tmp "https://github.com/conda-forge/miniforge/releases/download/24.11.0-0/Miniforge3-$(uname)-$(uname -m).sh"
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bash /tmp/Miniforge3-$(uname)-$(uname -m).sh -b -p /conda
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rm /tmp/Miniforge3-$(uname)-$(uname -m).sh
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export PATH="/conda/bin:$PATH"
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git clone --single-branch --branch dev --depth 1 --no-checkout https://github.com/PaddlePaddle/PaddleHelix.git app/helixfold3
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cd app/helixfold3
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git clone --filter=blob:none --no-checkout https://github.com/PaddlePaddle/PaddleHelix.git /app/helixfold3
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cd /app/helixfold3
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git sparse-checkout init --cone
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git sparse-checkout set apps/protein_folding/helixfold3
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git checkout dev
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mv apps/protein_folding/helixfold3/* .
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rm -rf apps
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mamba env create -f environment.yaml
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mamba env create --file=/app/helixfold3/environment.yaml
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mamba install -y -c bioconda aria2 hmmer==3.3.2 kalign2==2.04 hhsuite==3.3.0 -n helixfold
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mamba install -y -c conda-forge openbabel -n helixfold
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apt autoremove -y && apt remove --purge -y wget git && apt clean -y
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rm -rf /var/lib/apt/lists/* /root/.cache *.tar.gz
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mamba clean --all --force-pkgs-dirs -y
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%environment
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export PATH="/app/helixfold3:/opt/miniforge/bin:/opt/miniforge/envs/helixfold/bin:$PATH"
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export PYTHONPATH="/app/helixfold3:$PYTHONPATH"
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export PYTHON_BIN="/opt/miniforge/envs/helixfold/bin/python3.9"
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export ENV_BIN="/opt/miniforge/envs/helixfold/bin"
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export OBABEL_BIN="/opt/miniforge/envs/helixfold/bin"
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export PATH="/conda/bin:/app/helixfold3:./maxit_src/bin:/conda/envs/helixfold/bin:$PATH"
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export RCSBROOT="./maxit_src"
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export MAXIT_SRC="./maxit_src"
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export PYTHON_BIN="/conda/envs/helixfold/bin/python3.9"
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export ENV_BIN="/conda/envs/helixfold/bin"
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export OBABEL_BIN="/conda/envs/helixfold/bin"
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3643
%runscript
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mamba run --name helixfold "$@"

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