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Added environment.yaml for conda environments and def file for creating singularity/apptainer image #358

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Added environment.yaml for conda environments and def file for creating singularity/apptainer image #358

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183 changes: 183 additions & 0 deletions apps/protein_folding/helixfold3/environment.yaml
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name: helixfold
channels:
- nvidia
- bioconda
- conda-forge
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- aria2=1.23.0=0
- binutils=2.43=h4852527_2
- binutils_impl_linux-64=2.43=h4bf12b8_2
- binutils_linux-64=2.43=h4852527_2
- bzip2=1.0.8=h4bc722e_7
- c-ares=1.11.0=h470a237_1
- c-compiler=1.8.0=h2b85faf_1
- ca-certificates=2024.8.30=hbcca054_0
- cairo=1.18.0=hebfffa5_3
- cuda-cccl=12.0.90=0
- cuda-command-line-tools=12.0.0=0
- cuda-compiler=12.0.0=h6459364_1
- cuda-cudart=12.0.107=0
- cuda-cudart-dev=12.0.107=0
- cuda-cuobjdump=12.0.76=0
- cuda-cupti=12.4.127=0
- cuda-cuxxfilt=12.0.76=0
- cuda-driver-dev=12.0.107=0
- cuda-gdb=12.4.127=0
- cuda-libraries=12.0.0=ha770c72_1
- cuda-libraries-dev=12.0.0=ha770c72_1
- cuda-nsight=12.0.78=0
- cuda-nvcc=12.0.76=0
- cuda-nvdisasm=12.4.127=0
- cuda-nvml-dev=12.0.76=0
- cuda-nvprof=12.4.127=0
- cuda-nvprune=12.0.76=0
- cuda-nvrtc=12.0.76=0
- cuda-nvrtc-dev=12.0.76=0
- cuda-nvtx=12.4.127=0
- cuda-nvvp=12.0.90=0
- cuda-opencl=12.0.76=0
- cuda-opencl-dev=12.0.76=0
- cuda-profiler-api=12.0.76=0
- cuda-sanitizer-api=12.4.127=0
- cuda-toolkit=12.0.0=ha804496_1
- cuda-tools=12.0.0=ha770c72_0
- cuda-visual-tools=12.0.0=ha770c72_0
- cudatoolkit=11.8.0=h4ba93d1_13
- cudnn=8.4.0.27=hed8a83a_1
- cxx-compiler=1.8.0=h1a2810e_1
- font-ttf-dejavu-sans-mono=2.37=hab24e00_0
- font-ttf-inconsolata=3.000=h77eed37_0
- font-ttf-source-code-pro=2.038=h77eed37_0
- font-ttf-ubuntu=0.83=h77eed37_3
- fontconfig=2.15.0=h7e30c49_1
- fonts-conda-ecosystem=1=0
- fonts-conda-forge=1=0
- freetype=2.12.1=h267a509_2
- gcc=13.3.0=h9576a4e_1
- gcc_impl_linux-64=13.3.0=hfea6d02_1
- gcc_linux-64=13.3.0=hc28eda2_5
- gds-tools=1.5.0.59=0
- gxx=13.3.0=h9576a4e_1
- gxx_impl_linux-64=13.3.0=hdbfa832_1
- gxx_linux-64=13.3.0=h6834431_5
- hhsuite=3.3.0=py39pl5321h0dd7abe_13
- hmmer=3.3.2=hdbdd923_4
- icu=75.1=he02047a_0
- kalign2=2.04=h031d066_7
- kernel-headers_linux-64=3.10.0=he073ed8_18
- ld_impl_linux-64=2.43=h712a8e2_2
- libcublas=12.0.1.189=0
- libcublas-dev=12.0.1.189=0
- libcufft=11.0.0.21=0
- libcufft-dev=11.0.0.21=0
- libcufile=1.5.0.59=0
- libcufile-dev=1.5.0.59=0
- libcurand=10.3.1.50=0
- libcurand-dev=10.3.1.50=0
- libcusolver=11.4.2.57=0
- libcusolver-dev=11.4.2.57=0
- libcusparse=12.0.0.76=0
- libcusparse-dev=12.0.0.76=0
- libexpat=2.6.4=h5888daf_0
- libffi=3.4.2=h7f98852_5
- libgcc=14.2.0=h77fa898_1
- libgcc-devel_linux-64=13.3.0=h84ea5a7_101
- libgcc-ng=14.2.0=h69a702a_1
- libglib=2.82.2=h2ff4ddf_0
- libgomp=14.2.0=h77fa898_1
- libiconv=1.17=hd590300_2
- libnpp=12.0.0.30=0
- libnpp-dev=12.0.0.30=0
- libnsl=2.0.1=hd590300_0
- libnvjitlink=12.0.76=0
- libnvjitlink-dev=12.0.76=0
- libnvjpeg=12.0.0.28=0
- libnvjpeg-dev=12.0.0.28=0
- libpng=1.6.44=hadc24fc_0
- libsanitizer=13.3.0=heb74ff8_1
- libsqlite=3.47.0=hadc24fc_1
- libssh2=1.10.0=haa6b8db_3
- libstdcxx=14.2.0=hc0a3c3a_1
- libstdcxx-devel_linux-64=13.3.0=h84ea5a7_101
- libstdcxx-ng=14.2.0=h4852527_1
- libuuid=2.38.1=h0b41bf4_0
- libxcb=1.17.0=h8a09558_0
- libxcrypt=4.4.36=hd590300_1
- libxml2=2.13.4=hb346dea_2
- libzlib=1.3.1=hb9d3cd8_2
- nccl=2.14.3.1=h0800d71_0
- ncurses=6.5=he02047a_1
- nsight-compute=2022.4.0.15=0
- openbabel=3.1.1=py39h2d01fe1_9
- openssl=1.1.1w=hd590300_0
- pcre2=10.44=hba22ea6_2
- perl=5.32.1=7_hd590300_perl5
- pip=24.3.1=pyh8b19718_0
- pixman=0.43.2=h59595ed_0
- pthread-stubs=0.4=hb9d3cd8_1002
- python=3.9.15=h47a2c10_0_cpython
- python_abi=3.9=5_cp39
- readline=8.2=h8228510_1
- setuptools=75.3.0=pyhd8ed1ab_0
- sqlite=3.47.0=h9eae976_1
- sysroot_linux-64=2.17=h4a8ded7_18
- tk=8.6.13=noxft_h4845f30_101
- tzdata=2024b=hc8b5060_0
- wheel=0.45.0=pyhd8ed1ab_0
- xorg-libice=1.1.1=hb9d3cd8_1
- xorg-libsm=1.2.4=he73a12e_1
- xorg-libx11=1.8.10=h4f16b4b_0
- xorg-libxau=1.0.11=hb9d3cd8_1
- xorg-libxdmcp=1.1.5=hb9d3cd8_0
- xorg-libxext=1.3.6=hb9d3cd8_0
- xorg-libxrender=0.9.11=hb9d3cd8_1
- xorg-xorgproto=2024.1=hb9d3cd8_1
- xz=5.2.6=h166bdaf_0
- zlib=1.3.1=hb9d3cd8_2
- pip:
- absl-py==0.13.0
- anyio==4.6.2.post1
- astor==0.8.1
- biopython==1.79
- certifi==2024.8.30
- charset-normalizer==3.4.0
- chex==0.0.7
- contextlib2==21.6.0
- decorator==5.1.1
- dm-haiku==0.0.4
- dm-tree==0.1.6
- docker==5.0.0
- exceptiongroup==1.2.2
- h11==0.14.0
- httpcore==1.0.6
- httpx==0.27.2
- idna==3.10
- immutabledict==2.0.0
- jax==0.2.14
- jaxlib==0.4.30
- ml-collections==0.1.0
- ml-dtypes==0.5.0
- numpy==1.24.4
- opt-einsum==3.3.0
- paddlepaddle-gpu==2.6.1
- pandas==1.3.4
- pillow==11.0.0
- posebusters==0.3.1
- protobuf==5.28.3
- python-dateutil==2.9.0.post0
- pytz==2024.2
- pyyaml==6.0.2
- rdkit==2024.3.6
- rdkit-pypi==2022.9.5
- requests==2.32.3
- scipy==1.9.0
- six==1.16.0
- sniffio==1.3.1
- tabulate==0.9.0
- toolz==1.0.0
- typing-extensions==4.12.2
- urllib3==2.2.3
- websocket-client==1.8.0
prefix: /opt/miniforge/envs/helixfold
37 changes: 37 additions & 0 deletions apps/protein_folding/helixfold3/helixfold3.def
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Bootstrap: docker
From: nvidia/cuda:12.6.0-cudnn-devel-ubuntu24.04

%labels
Author [email protected]
Version 1.0.0

%post
apt update && DEBIAN_FRONTEND=noninteractive apt install --no-install-recommends -y wget git

wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh"
bash Miniforge3-Linux-x86_64.sh -b -p /opt/miniforge
rm Miniforge3-Linux-x86_64.sh
export PATH="/opt/miniforge/bin:$PATH"

git clone --single-branch --branch dev --depth 1 --no-checkout https://github.com/PaddlePaddle/PaddleHelix.git app/helixfold3
cd app/helixfold3
git sparse-checkout init --cone
git sparse-checkout set apps/protein_folding/helixfold3
git checkout dev
mv apps/protein_folding/helixfold3/* .
rm -rf apps
mamba env create -f environment.yaml

apt autoremove -y && apt remove --purge -y wget git && apt clean -y
rm -rf /var/lib/apt/lists/* /root/.cache *.tar.gz
mamba clean --all --force-pkgs-dirs -y

%environment
export PATH="/app/helixfold3:/opt/miniforge/bin:/opt/miniforge/envs/helixfold/bin:$PATH"
export PYTHONPATH="/app/helixfold3:$PYTHONPATH"
export PYTHON_BIN="/opt/miniforge/envs/helixfold/bin/python3.9"
export ENV_BIN="/opt/miniforge/envs/helixfold/bin"
export OBABEL_BIN="/opt/miniforge/envs/helixfold/bin"

%runscript
mamba run --name helixfold "$@"