diff --git a/environment.yml b/environment.yml new file mode 100644 index 0000000..e88da69 --- /dev/null +++ b/environment.yml @@ -0,0 +1,293 @@ +name: monica +channels: + - conda-forge + - defaults +dependencies: + - _libgcc_mutex=0.1=main + - _openmp_mutex=5.1=1_gnu + - brotlipy=0.7.0=py39hb9d737c_1004 + - ca-certificates=2022.12.7=ha878542_0 + - certifi=2022.12.7=pyhd8ed1ab_0 + - cffi=1.15.1=py39h74dc2b5_0 + - colorama=0.4.6=pyhd8ed1ab_0 + - cryptography=3.4.8=py39h95dcef6_1 + - h2o-py=3.38.0.4=pyhd8ed1ab_0 + - ld_impl_linux-64=2.38=h1181459_1 + - libblas=3.9.0=15_linux64_openblas + - libcblas=3.9.0=15_linux64_openblas + - libffi=3.3=he6710b0_2 + - libgcc-ng=11.2.0=h1234567_1 + - libgfortran-ng=12.2.0=h69a702a_19 + - libgfortran5=12.2.0=h337968e_19 + - libgomp=11.2.0=h1234567_1 + - liblapack=3.9.0=15_linux64_openblas + - libopenblas=0.3.20=pthreads_h78a6416_0 + - libstdcxx-ng=11.2.0=h1234567_1 + - ncurses=6.3=h7f8727e_2 + - openjdk=8.0.332=h166bdaf_0 + - openssl=1.1.1t=h7f8727e_0 + - pip=21.2.4=py39h06a4308_0 + - pycparser=2.21=pyhd8ed1ab_0 + - pyopenssl=20.0.1=pyhd8ed1ab_0 + - pysocks=1.7.1=py39hf3d152e_5 + - python=3.9.12=h12debd9_1 + - python_abi=3.9=2_cp39 + - readline=8.1.2=h7f8727e_1 + - setuptools=61.2.0=py39h06a4308_0 + - six=1.16.0=pyh6c4a22f_0 + - sqlite=3.38.3=hc218d9a_0 + - tk=8.6.12=h1ccaba5_0 + - tzdata=2022a=hda174b7_0 + - wheel=0.37.1=pyhd3eb1b0_0 + - xz=5.2.5=h7f8727e_1 + - zlib=1.2.12=h7f8727e_2 + - pip: + - 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 + - cachetools==5.2.0 + - catboost==1.1.1 + - chardet==4.0.0 + - charset-normalizer==2.0.12 + - click==8.1.3 + - cmake==3.26.3 + - colorlog==6.6.0 + - contourpy==1.0.6 + - cookiecutter==2.1.1 + - 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==0.6.0 + - etils==0.8.0 + - evoaug==1.0.6 + - fasteners==0.19 + - feather-format==0.4.1 + - filelock==3.8.2 + - 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==2023.10.0 + - future==0.18.2 + - 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==0.5 + - greenlet==2.0.2 + - grpcio==1.46.3 + - h5py==3.7.0 + - hickle==5.0.2 + - huggingface-hub==0.18.0 + - hydra-core==1.3.1 + - idna==3.3 + - 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==3.1.2 + - 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==2.1.1 + - 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==2.8.8 + - ninja==1.11.1 + - nucleotide-transformer==0.0.1 + - numba==0.56.4 + - numcodecs==0.12.1 + - numpy==1.23.5 + - nvidia-cublas-cu11==11.10.3.66 + - nvidia-cuda-cupti-cu11==11.7.101 + - nvidia-cuda-nvcc-cu11==11.8.89 + - nvidia-cuda-nvrtc-cu11==11.7.99 + - nvidia-cuda-runtime-cu11==11.7.99 + - nvidia-cudnn-cu11==8.5.0.96 + - nvidia-cufft-cu11==10.9.0.58 + - nvidia-curand-cu11==10.2.10.91 + - nvidia-cusolver-cu11==11.4.0.1 + - nvidia-cusparse-cu11==11.7.4.91 + - nvidia-nccl-cu11==2.14.3 + - nvidia-nvtx-cu11==11.7.91 + - 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 + - pycryptodomex==3.20.0 + - pyfaidx==0.7.0 + - pynndescent==0.5.8 + - pyparsing==3.0.9 + - pyppmd==1.1.0 + - pyranges==0.0.117 + - pyrle==0.0.35 + - pysam==0.21.0 + - python-dateutil==2.8.2 + - python-graphviz==0.20.1 + - 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==2.28.0 + - 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 + - sklearn==0.0 + - smmap==5.0.0 + - sorted-nearest==0.0.37 + - soupsieve==2.4.1 + - sparsemax==0.1.9 + - sqlalchemy==1.4.48 + - statsmodels==0.13.5 + - stdlib-list==0.8.0 + - sympy==1.12 + - tabulate==0.8.9 + - tenacity==8.2.2 + - tensorboard==2.9.1 + - tensorboard-data-server==0.6.1 + - tensorboard-plugin-wit==1.8.1 + - tensorflow==2.9.1 + - tensorflow-datasets==4.6.0 + - tensorflow-estimator==2.9.0 + - tensorflow-hub==0.13.0 + - tensorflow-io-gcs-filesystem==0.26.0 + - tensorflow-metadata==1.10.0 + - tensorly==0.8.0 + - termcolor==1.1.0 + - text-unidecode==1.3 + - texttable==1.7.0 + - threadpoolctl==3.1.0 + - timm==0.6.12 + - tinydb==4.7.0 + - tokenizers==0.13.2 + - toml==0.10.2 + - torch==1.13.1 + - torchaudio==0.13.1 + - torchdata==0.6.1 + - torcheval==0.0.7 + - torchinfo==1.8.0 + - torchmetrics==0.11.0 + - torchtext==0.15.2 + - torchtuples==0.2.2 + - torchvision==0.14.1 + - tqdm==4.64.0 + - transformers==4.29.2 + - triton==2.0.0 + - typing-extensions==4.2.0 + - umap-learn==0.5.3 + - urllib3==1.26.9 + - 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 +prefix: /cluster/home/tonyu/.conda/envs/monica