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env.yml
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env.yml
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name: symdesign
channels:
- conda-forge
- defaults
- pytorch
- nvidia
- bioconda
dependencies:
- python=3.9 # =3.10
- numpy
- pandas
- scikit-learn
- scipy
- numba
- sqlalchemy=1.4 # Remove to 2.0 once finished with warnings
- mysqlclient
- alembic
- psutil
- pytorch
- torchvision
- torchaudio
- cudatoolkit=11.3
- hhsuite
- requests
- biopython<=1.81
- matplotlib
- tqdm
- proglog
- flametree
# Alphafold
- cudnn # ==8.0.4
- jax==0.4.2 # jax/jaxlib 0.4.4 broke jnp.asarray() for me ...
- jaxlib==0.4.2
- cuda-nvcc=11.3 # Used to ensure same version as cudatoolkit
- hmmer
- kalign2
# - openmm=7.5.1 # version causes conflicts, alphafold needs to update to 8.0.0 to be compatible without versions
- openmm=7.7.0
- pdbfixer
- pip
- pip:
- absl-py==1.0.0
- chex==0.0.7
- dm-haiku==0.0.9
- dm-tree==0.1.6
- immutabledict==2.0.0
- ml-collections==0.1.0
- tensorflow-cpu==2.11.0
- pdbecif
- dnachisel