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Initial commit: FlowDock pipeline configured for WES execution
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This commit is contained in:
Olamide Isreal
2026-03-16 15:23:29 +01:00
commit a3ffec6a07
116 changed files with 16139 additions and 0 deletions
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environments/flowdock_environment_docker.yaml Normal file
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name: flowdock
channels:
- pyg
- pytorch
- nvidia
- defaults
- conda-forge
dependencies:
- mendeleev=0.20.1=pymin39_ha308f57_3
- networkx=3.4.2=pyh267e887_2
- python=3.10.16=he725a3c_1_cpython
- pytorch=2.2.1=py3.10_cuda11.8_cudnn8.7.0_0
- pytorch-cuda=11.8=h7e8668a_6
- pytorch-mutex=1.0=cuda
- pytorch-scatter=2.1.2=py310_torch_2.2.0_cu118
- rdkit=2024.09.6=py310hcd13295_0
- scikit-learn=1.6.1=py310h27f47ee_0
- scipy=1.15.2=py310h1d65ade_0
- torchaudio=2.2.1=py310_cu118
- torchtriton=2.2.0=py310
- torchvision=0.17.1=py310_cu118
- tqdm=4.67.1=pyhd8ed1ab_1
- pip:
- beartype==0.20.0
- biopandas==0.5.1
- biopython==1.79
- biotite==1.1.0
- git+https://github.com/NVIDIA/dllogger.git@0540a43971f4a8a16693a9de9de73c1072020769
- dm-tree==0.1.9
- einops==0.8.1
- fair-esm==2.0.0
- fairscale==0.4.13
- gemmi==0.7.0
- hydra-colorlog==1.2.0
- hydra-core==1.3.2
- hydra-optuna-sweeper==1.2.0
- lightning==2.5.0.post0
- lightning-utilities==0.14.1
- lovely-numpy==0.2.13
- lovely-tensors==0.1.18
- ml-collections==1.0.0
- msgpack==1.1.0
- msgpack-numpy==0.4.8
- numpy==1.26.4
- omegaconf==2.3.0
- git+https://github.com/amorehead/openfold.git@fe1275099639bf7e617e09ef24d6af778647dd64
- pandas==2.2.3
- plinder==0.2.24
- plotly==6.0.0
- posebusters==0.2.13
# - prody==2.4.1 # NOTE: we must `pip` install Prody to skip its NumPy dependency
- pytorch-lightning==2.5.0.post0
- git+https://github.com/facebookresearch/pytorch3d.git@3da7703c5ac10039645966deddffe8db52eab8c5
- rich==13.9.4
- rootutils==1.0.7
- seaborn==0.13.2
- torchmetrics==1.6.3
- wandb==0.19.8