Solved scCello Environment for non-cluster users #6
Description
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