Protein2PAM/environment.yml at main · Profluent-AI/Protein2PAM · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
name: protein2pam
channels:
  - conda-forge
  - bioconda
  - nvidia
  - pytorch
  - senyan.dev
dependencies:
  - conda-forge::pip
  - conda-forge::python=3.8.*
  - conda-forge::setuptools
  - nvidia::cuda-cudart=11.8.89=0
  - nvidia::cuda-cupti=11.8.87=0
  - nvidia::cuda-libraries=11.8.0=0
  - nvidia::cuda-nvrtc=11.8.89=0
  - nvidia::cuda-nvtx=11.8.86=0
  - nvidia::cuda-runtime=11.8.0=0
  - conda-forge::cudatoolkit=11.8.0=h37601d7_11
  - senyan.dev::cudatoolkit-dev=11.8.0=h1fa729e_6
  - pytorch::pytorch=2.0.1=py3.8_cuda11.8_cudnn8.7.0_0
  - pytorch::pytorch-cuda=11.8=h7e8668a_5
  - pytorch::pytorch-mutex=1.0=cuda
  - pytorch::torchaudio=2.0.2=py38_cu118
  - pytorch::torchtriton=2.0.0=py38
  - pytorch::torchvision=0.15.2=py38_cu118
  - bioconda::mmseqs2
  - bioconda::kalign2==2.04
  - conda-forge::openmm=7.5.1
  - conda-forge::pdbfixer
  - conda-forge::biotite=0.35.0=py38h26c90d9_1
  - pip:
      # General python deps
      - black
      - flake8
      - isort
      - jupyter
      - matplotlib
      - numpy>=1.20.0
      - pandas
      - seaborn>=0.12.0
      - scikit-learn
      - scipy
      - tqdm
      - pre-commit
      - logomaker>=0.8
      - fair-esm>=2.0.0
      # Deep learning deps
      - accelerate>=0.21.0
      - bitsandbytes>=0.41.1
      - einops>=0.6.0
      - tensorboard
      - transformers>=4.30
      - tokenizers
      - pynvml
      - torch
      - Levenshtein
      - sparse
      # GCP deps
      - dvc[gs]
      - scmrepo>=0.1.15  # avoids a bug in DVC
      - google-cloud-storage
      # Bio-related deps
      - biopython>=1.79
      - tmscoring>=0.4
      - iminuit<2
      - pyhmmer
      # Flask API deps
      - flask
      - gunicorn
      - Flask-Cors