Solved scCello Environment for non-cluster users

[keyshavmor]

Hi everyone,

With the message I am attaching a file for creating a Conda environment that should easily work on a Linux environment and Nvidia RTX 3090. Please give it a try and let me know if you face any issues.

I thank @KatarinaYuan for providing a comprehensive YAML file that would work on a cluster setup and I adapted it for a non-cluster system. I request the authors of the repository to include my environment file for the repository users to create an environment to use the code without delay.

I also paste the packages here:

name: scCello
channels:

• defaults
  dependencies:
• _libgcc_mutex=0.1=main
• _openmp_mutex=5.1=1_gnu
• bzip2=1.0.8=h5eee18b_6
• ca-certificates=2025.7.15=h06a4308_0
• expat=2.7.1=h6a678d5_0
• ld_impl_linux-64=2.40=h12ee557_0
• libffi=3.4.4=h6a678d5_1
• libgcc-ng=11.2.0=h1234567_1
• libgomp=11.2.0=h1234567_1
• libstdcxx-ng=11.2.0=h1234567_1
• libuuid=1.41.5=h5eee18b_0
• libxcb=1.17.0=h9b100fa_0
• ncurses=6.5=h7934f7d_0
• openssl=3.0.17=h5eee18b_0
• pip=25.2=pyhc872135_0
• pthread-stubs=0.3=h0ce48e5_1
• python=3.10.18=h1a3bd86_0
• readline=8.3=hc2a1206_0
• setuptools=78.1.1=py310h06a4308_0
• sqlite=3.50.2=hb25bd0a_1
• tk=8.6.15=h54e0aa7_0
• wheel=0.45.1=py310h06a4308_0
• xorg-libx11=1.8.12=h9b100fa_1
• xorg-libxau=1.0.12=h9b100fa_0
• xorg-libxdmcp=1.1.5=h9b100fa_0
• xorg-xorgproto=2024.1=h5eee18b_1
• xz=5.6.4=h5eee18b_1
• zlib=1.2.13=h5eee18b_1
• pip:
  • accelerate==1.10.1
  • aiohappyeyeballs==2.6.1
  • aiohttp==3.12.15
  • aiosignal==1.4.0
  • anndata==0.11.4
  • annotated-types==0.7.0
  • array-api-compat==1.12.0
  • asttokens==3.0.0
  • async-timeout==5.0.1
  • attrs==25.3.0
  • beautifulsoup4==4.13.5
  • cachetools==6.2.0
  • certifi==2025.8.3
  • charset-normalizer==3.4.3
  • click==8.2.1
  • cloudpickle==3.1.1
  • contourpy==1.3.2
  • cuda-bindings==12.9.2
  • cuda-pathfinder==1.2.2
  • cuda-python==12.9.2
  • cudf-cu12==25.8.0
  • cugraph-cu12==25.8.0
  • cuml-cu12==25.8.0
  • cupy-cuda12x==13.6.0
  • cuvs-cu12==25.8.0
  • cycler==0.12.1
  • dask==2025.7.0
  • dask-cuda==25.8.0
  • dask-cudf-cu12==25.8.0
  • datasets==4.0.0
  • decorator==5.2.1
  • deprecated==1.2.18
  • dill==0.3.8
  • distributed==2025.7.0
  • distributed-ucxx-cu12==0.45.1
  • easydict==1.13
  • exceptiongroup==1.3.0
  • executing==2.2.1
  • fastrlock==0.8.3
  • filelock==3.19.1
  • fonttools==4.59.2
  • frozenlist==1.7.0
  • fsspec==2024.12.0
  • gdown==5.2.0
  • gitdb==4.0.12
  • gitpython==3.1.45
  • h5py==3.13.0
  • hf-xet==1.1.9
  • hickle==5.0.3
  • huggingface-hub==0.34.4
  • idna==3.10
  • igraph==0.11.9
  • importlib-metadata==8.7.0
  • ipdb==0.13.13
  • ipython==8.37.0
  • isodate==0.7.2
  • jedi==0.19.2
  • jinja2==3.1.6
  • joblib==1.5.2
  • kiwisolver==1.4.9
  • legacy-api-wrap==1.4.1
  • leidenalg==0.10.2
  • libcudf-cu12==25.8.0
  • libcugraph-cu12==25.8.0
  • libcuml-cu12==25.8.0
  • libcuvs-cu12==25.8.0
  • libkvikio-cu12==25.8.0
  • libraft-cu12==25.8.0
  • librmm-cu12==25.8.0
  • libucx-cu12==1.18.1
  • libucxx-cu12==0.45.1
  • lightning-utilities==0.15.2
  • llvmlite==0.44.0
  • locket==1.0.0
  • markdown-it-py==4.0.0
  • markupsafe==3.0.2
  • matplotlib==3.10.6
  • matplotlib-inline==0.1.7
  • mdurl==0.1.2
  • mpmath==1.3.0
  • msgpack==1.1.1
  • multidict==6.6.4
  • multiprocess==0.70.16
  • natsort==8.4.0
  • networkx==3.4.2
  • numba==0.61.2
  • numba-cuda==0.14.1
  • numpy==2.2.6
  • nvidia-cublas-cu12==12.4.5.8
  • nvidia-cuda-cccl-cu12==12.9.27
  • nvidia-cuda-cupti-cu12==12.4.127
  • nvidia-cuda-nvcc-cu12==12.9.86
  • nvidia-cuda-nvrtc-cu12==12.4.127
  • nvidia-cuda-runtime-cu12==12.4.127
  • nvidia-cudnn-cu12==9.1.0.70
  • nvidia-cufft-cu12==11.2.1.3
  • nvidia-curand-cu12==10.3.5.147
  • nvidia-cusolver-cu12==11.6.1.9
  • nvidia-cusparse-cu12==12.3.1.170
  • nvidia-cusparselt-cu12==0.6.2
  • nvidia-ml-py==12.575.51
  • nvidia-nccl-cu12==2.21.5
  • nvidia-nvjitlink-cu12==12.4.127
  • nvidia-nvtx-cu12==12.4.127
  • nvtx==0.2.13
  • packaging==25.0
  • pandas==2.3.2
  • parso==0.8.5
  • partd==1.4.2
  • patsy==1.0.1
  • pexpect==4.9.0
  • pillow==11.3.0
  • platformdirs==4.4.0
  • prompt-toolkit==3.0.52
  • propcache==0.3.2
  • protobuf==6.32.0
  • psutil==7.0.0
  • ptyprocess==0.7.0
  • pure-eval==0.2.3
  • pyarrow==19.0.1
  • pydantic==2.11.7
  • pydantic-core==2.33.2
  • pydot==4.0.1
  • pygments==2.19.2
  • pylibcudf-cu12==25.8.0
  • pylibcugraph-cu12==25.8.0
  • pylibraft-cu12==25.8.0
  • pynndescent==0.5.13
  • pynvjitlink-cu12==0.7.0
  • pynvml==12.0.0
  • pyparsing==3.2.3
  • pysocks==1.7.1
  • python-dateutil==2.9.0.post0
  • pytz==2025.2
  • pyyaml==6.0.2
  • raft-dask-cu12==25.8.0
  • rapids-dask-dependency==25.8.0
  • rapids-logger==0.1.1
  • rdflib==7.1.4
  • regex==2025.9.1
  • requests==2.32.5
  • rich==14.1.0
  • rmm-cu12==25.8.0
  • safetensors==0.6.2
  • scanpy==1.11.0
  • scib==1.1.7
  • scikit-learn==1.5.2
  • scikit-misc==0.5.1
  • scipy==1.15.3
  • seaborn==0.13.2
  • sentry-sdk==2.37.0
  • session-info2==0.2.1
  • six==1.17.0
  • smmap==5.0.2
  • sortedcontainers==2.4.0
  • soupsieve==2.8
  • stack-data==0.6.3
  • statsmodels==0.14.5
  • sympy==1.13.1
  • tblib==3.1.0
  • texttable==1.7.0
  • threadpoolctl==3.6.0
  • tokenizers==0.21.4
  • tomli==2.2.1
  • toolz==1.0.0
  • torch==2.6.0
  • torchmetrics==1.7.0
  • tornado==6.5.2
  • tqdm==4.67.1
  • traitlets==5.14.3
  • transformers==4.50.3
  • treelite==4.4.1
  • triton==3.2.0
  • typing-extensions==4.15.0
  • typing-inspection==0.4.1
  • tzdata==2025.2
  • ucx-py-cu12==0.45.0
  • ucxx-cu12==0.45.1
  • umap-learn==0.5.7
  • urllib3==2.5.0
  • wandb==0.21.3
  • wcwidth==0.2.13
  • wrapt==1.17.3
  • xxhash==3.5.0
  • yarl==1.20.1
  • zict==3.0.0
  • zipp==3.23.0
    prefix: /home/mandalorian/anaconda3/envs/scCello

scCello.yaml