From f965bacd9a00c968852f711f772f7cb02eb1d19f Mon Sep 17 00:00:00 2001 From: Tong Yu Date: Tue, 15 Oct 2024 09:16:03 +0200 Subject: [PATCH] Add files via upload --- requirements.txt | 270 +++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 270 insertions(+) create mode 100644 requirements.txt diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..00d9cda --- /dev/null +++ b/requirements.txt @@ -0,0 +1,270 @@ +absl-py==1.1.0 +accelerate==0.24.1 +aiohttp==3.8.3 +aiosignal==1.3.1 +alembic==1.11.0 +anndata==0.8.0 +antlr4-python3-runtime==4.9.3 +argcomplete==2.0.0 +argh==0.26.2 +arrow==1.2.2 +asciitree==0.3.3 +astunparse==1.6.3 +async-timeout==4.0.2 +attrs==21.4.0 +axial-positional-embedding==0.2.1 +banal==1.0.6 +beautifulsoup4==4.12.2 +binaryornot==0.4.4 +bio==1.3.9 +bioframe==0.7.2 +biopython==1.79 +biothings-client==0.2.6 +boto3==1.28.73 +botocore==1.31.73 +Brotli==1.1.0 +brotlipy @ file:///home/conda/feedstock_root/build_artifacts/brotlipy_1648854164373/work +cachetools==5.2.0 +catboost==1.1.1 +certifi==2022.12.7 +cffi @ file:///tmp/abs_98z5h56wf8/croots/recipe/cffi_1659598650955/work +chardet==4.0.0 +charset-normalizer @ file:///home/conda/feedstock_root/build_artifacts/charset-normalizer_1661170624537/work +click==8.1.3 +cmake==3.26.3 +colorama @ file:///home/conda/feedstock_root/build_artifacts/colorama_1666700638685/work +colorlog==6.6.0 +contourpy==1.0.6 +cookiecutter==2.1.1 +cryptography @ file:///home/conda/feedstock_root/build_artifacts/cryptography_1637687020823/work +cycler==0.11.0 +Cython==0.29.30 +dataset==1.6.0 +datasets==2.12.0 +deprecation==2.1.0 +dill==0.3.6 +dm-haiku==0.0.10 +docker-pycreds==0.4.0 +einops==0.8.0 +etils==0.8.0 +evoaug==1.0.6 +fasteners==0.19 +feather-format==0.4.1 +filelock==3.14.0 +fire==0.4.0 +flash-attn==1.0.9 +FLASH-pytorch==0.1.9 +flatbuffers==1.12 +flopth==0.1.5 +fonttools==4.38.0 +frozenlist==1.3.3 +fsspec==2024.6.0 +future @ file:///home/conda/feedstock_root/build_artifacts/future_1673596611778/work +gast==0.4.0 +gdown==4.7.1 +genomic-benchmarks==0.0.9 +gffutils==0.11.0 +gitdb==4.0.9 +GitPython==3.1.27 +google-auth==2.8.0 +google-auth-oauthlib==0.4.6 +google-pasta==0.2.0 +googleapis-common-protos==1.56.4 +gpn @ git+https://github.com/songlab-cal/gpn.git@05b23c54c572813810c094b31031901f7109575b +graphviz==0.20.1 +greenlet==2.0.2 +grpcio==1.46.3 +h2o @ file:///home/conda/feedstock_root/build_artifacts/h2o-py_1673012261920/work +h5py==3.7.0 +hickle==5.0.2 +huggingface-hub==0.18.0 +hydra-core==1.3.1 +idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1663625384323/work +importlib-metadata==4.11.4 +importlib-resources==5.9.0 +inflate64==1.0.0 +jax==0.4.19 +jaxlib==0.4.19+cuda11.cudnn86 +Jinja2==3.1.4 +jinja2-time==0.2.0 +jmespath==1.0.1 +jmp==0.0.4 +joblib==1.3.2 +keras==2.9.0 +Keras-Preprocessing==1.1.2 +kipoi==0.8.5 +kipoi-conda==0.3.1 +kipoi-utils==0.7.6 +kipoiseq==0.7.1 +kiwisolver==1.4.4 +libclang==14.0.1 +lightgbm==3.3.5 +lightning-utilities==0.6.0.post0 +linformer==0.2.1 +lit==16.0.5 +llvmlite==0.39.1 +local-attention==1.4.4 +Mako==1.2.4 +mamba-ssm==2.0.3 +Markdown==3.3.7 +MarkupSafe==2.1.5 +matplotlib==3.6.2 +Mega-pytorch==0.0.15 +ml-dtypes==0.3.1 +mpmath==1.3.0 +multidict==6.0.4 +multiprocess==0.70.14 +multivolumefile==0.2.3 +mygene==3.2.2 +natsort==8.1.0 +ncls==0.0.65 +networkx==3.2.1 +ninja==1.11.1 +nucleotide-transformer @ file:///cluster/home/tonyu/VE_Pretraining/nucleotide-transformer +numba==0.56.4 +numcodecs==0.12.1 +numpy==1.23.5 +nvidia-cublas-cu11==11.10.3.66 +nvidia-cublas-cu12==12.1.3.1 +nvidia-cuda-cupti-cu11==11.7.101 +nvidia-cuda-cupti-cu12==12.1.105 +nvidia-cuda-nvcc-cu11==11.8.89 +nvidia-cuda-nvrtc-cu11==11.7.99 +nvidia-cuda-nvrtc-cu12==12.1.105 +nvidia-cuda-runtime-cu11==11.7.99 +nvidia-cuda-runtime-cu12==12.1.105 +nvidia-cudnn-cu11==8.5.0.96 +nvidia-cudnn-cu12==8.9.2.26 +nvidia-cufft-cu11==10.9.0.58 +nvidia-cufft-cu12==11.0.2.54 +nvidia-curand-cu11==10.2.10.91 +nvidia-curand-cu12==10.3.2.106 +nvidia-cusolver-cu11==11.4.0.1 +nvidia-cusolver-cu12==11.4.5.107 +nvidia-cusparse-cu11==11.7.4.91 +nvidia-cusparse-cu12==12.1.0.106 +nvidia-nccl-cu11==2.14.3 +nvidia-nccl-cu12==2.20.5 +nvidia-nvjitlink-cu12==12.5.40 +nvidia-nvtx-cu11==11.7.91 +nvidia-nvtx-cu12==12.1.105 +nystrom-attention==0.0.11 +oauthlib==3.2.0 +omegaconf==2.3.0 +opt-einsum==3.3.0 +packaging==21.3 +pandarallel==1.6.5 +pandas==1.4.2 +pathtools==0.1.2 +patsy==0.5.3 +peft==0.6.1 +performer-pytorch==1.1.4 +Pillow==9.1.1 +plotly==5.13.1 +product-key-memory==0.1.10 +promise==2.3 +protobuf==3.20.1 +psutil==5.9.1 +ptflops==0.7.1.2 +ptwt==0.1.9 +py7zr==0.21.0 +pyarrow==12.0.0 +pyasn1==0.4.8 +pyasn1-modules==0.2.8 +pybcj==1.0.2 +pyBigWig==0.3.23 +pycox==0.2.3 +pycparser @ file:///home/conda/feedstock_root/build_artifacts/pycparser_1636257122734/work +pycryptodomex==3.20.0 +pyfaidx==0.7.0 +pynndescent==0.5.8 +pyOpenSSL @ file:///home/conda/feedstock_root/build_artifacts/pyopenssl_1608055815057/work +pyparsing==3.0.9 +pyppmd==1.1.0 +pyranges==0.0.117 +pyrle==0.0.35 +pysam==0.21.0 +PySocks @ file:///home/conda/feedstock_root/build_artifacts/pysocks_1648857263093/work +python-dateutil==2.8.2 +python-slugify==6.1.2 +pytorch-fast-transformers==0.4.0 +pytorch-lightning==1.9.0 +pytorch-metric-learning==2.6.0 +pytorch-tabnet==4.0 +pytz==2022.1 +PyWavelets==1.6.0 +PyYAML==6.0 +pyzstd==0.16.0 +reformer-pytorch==1.4.4 +regex==2022.10.31 +related==0.7.2 +requests @ file:///home/conda/feedstock_root/build_artifacts/requests_1673863902341/work +requests-oauthlib==1.3.1 +responses==0.18.0 +rotary-embedding-torch==0.3.3 +rsa==4.8 +s3transfer==0.7.0 +safetensors==0.4.0 +scanpy==1.9.1 +scikit-learn==1.1.1 +scipy==1.11.3 +seaborn==0.12.1 +sentry-sdk==1.5.12 +session-info==1.0.0 +setproctitle==1.2.3 +shortuuid==1.0.9 +simplejson==3.17.6 +six @ file:///home/conda/feedstock_root/build_artifacts/six_1620240208055/work 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file:///home/conda/feedstock_root/build_artifacts/urllib3_1673452138552/work +wandb==0.13.0 +Werkzeug==2.1.2 +wrapt==1.14.1 +xgboost==1.7.4 +xxhash==3.2.0 +yarl==1.8.2 +zarr==2.18.2 +zipp==3.8.0 +zstandard==0.23.0