# Enviroment.yml file? scvi installation problems

**URL:** <https://discourse.scverse.org/t/enviroment-yml-file-scvi-installation-problems/1803>\
**Category:** scvi-tools\
**Created:** [October 9, 2023, 7:13pm UTC](https://discourse.scverse.org/t/enviroment-yml-file-scvi-installation-problems/1803 "2023-10-09T19:13:33Z")\
**Posts on this page:** 9\
**Page:** 1

<div class="post-metadata">

**Author:** ![jagraz](https://avatars.discourse-cdn.com/v4/letter/j/e99b99/32.png) [@jagraz](https://discourse.scverse.org/u/jagraz)\
**Post date:** [October 9, 2023, 7:13pm UTC](https://discourse.scverse.org/t/enviroment-yml-file-scvi-installation-problems/1803/1 "2023-10-09T19:13:33Z")

</div>

Hi,  
I’m having trouble installing the scvi-tools. Anyone care to share an enviroment.yml file?  
Installs successfully, but fails during imports (ex pandas, pydantic). Below is my enviroment.yml file  
Thank you

name: single-cell  
channels:

- anaconda
- pytorch
- bioconda
- conda-forge  
dependencies:
- \_libgcc\_mutex=0.1=conda\_forge
- \_openmp\_mutex=4.5=2\_kmp\_llvm
- adjusttext=0.7.3.1=py\_1
- aiohttp=3.8.5=py310h2372a71\_0
- aiosignal=1.3.1=pyhd8ed1ab\_0
- airr=1.5.0=pyh7cba7a3\_0
- anndata=0.9.2=pyhd8ed1ab\_0
- annotated-types=0.5.0=pyhd8ed1ab\_0
- arpack=3.8.0=nompi\_h0baa96a\_101
- async-timeout=4.0.3=pyhd8ed1ab\_0
- attrs=23.1.0=pyh71513ae\_1
- awkward=2.4.4=pyhd8ed1ab\_0
- awkward-cpp=24=py310hd41b1e2\_0
- aws-c-auth=0.7.4=hc8144f4\_1
- aws-c-cal=0.6.2=h09139f6\_2
- aws-c-common=0.9.3=hd590300\_0
- aws-c-compression=0.2.17=h184a658\_3
- aws-c-event-stream=0.3.2=hd6ebb48\_1
- aws-c-http=0.7.13=hc690213\_1
- aws-c-io=0.13.32=h63140e9\_5
- aws-c-mqtt=0.9.6=h32970c0\_2
- aws-c-s3=0.3.17=hb5e3142\_3
- aws-c-sdkutils=0.1.12=h184a658\_2
- aws-checksums=0.1.17=h184a658\_2
- aws-crt-cpp=0.23.1=h94c364a\_5
- aws-sdk-cpp=1.11.156=h6600424\_3
- binutils\_impl\_linux-64=2.40=hf600244\_0
- blas=2.116=mkl
- blas-devel=3.9.0=16\_linux64\_mkl
- bokeh=3.2.2=pyhd8ed1ab\_0
- brotli=1.1.0=hd590300\_1
- brotli-bin=1.1.0=hd590300\_1
- brotli-python=1.1.0=py310hc6cd4ac\_1
- bzip2=1.0.8=h7f98852\_4
- c-ares=1.19.1=hd590300\_0
- ca-certificates=2023.7.22=hbcca054\_0
- cached-property=1.5.2=hd8ed1ab\_1
- cached\_property=1.5.2=pyha770c72\_1
- certifi=2023.7.22=pyhd8ed1ab\_0
- charset-normalizer=3.2.0=pyhd8ed1ab\_0
- click=8.1.7=unix\_pyh707e725\_0
- cloudpickle=2.2.1=pyhd8ed1ab\_0
- colorama=0.4.6=pyhd8ed1ab\_0
- contourpy=1.1.1=py310hd41b1e2\_1
- cuda-version=11.7=h67201e3\_2
- cudatoolkit=11.7.1=h4bc3d14\_12
- cudnn=8.8.0.121=h838ba91\_3
- cycler=0.12.0=pyhd8ed1ab\_0
- cytoolz=0.12.2=py310h2372a71\_1
- dask=2023.9.3=pyhd8ed1ab\_0
- dask-core=2023.9.3=pyhd8ed1ab\_0
- dask-image=2023.8.1=pyhd8ed1ab\_0
- distributed=2023.9.3=pyhd8ed1ab\_0
- docrep=0.3.2=pyh44b312d\_0
- entrypoints=0.4=pyhd8ed1ab\_0
- et\_xmlfile=1.1.0=pyhd8ed1ab\_0
- ffmpeg=4.3=hf484d3e\_0
- filelock=3.12.4=pyhd8ed1ab\_0
- fonttools=4.43.0=py310h2372a71\_0
- freetype=2.12.1=h267a509\_2
- frozenlist=1.4.0=py310h2372a71\_1
- fsspec=2023.9.2=pyh1a96a4e\_0
- gcc=13.2.0=h574f8da\_2
- gcc\_impl\_linux-64=13.2.0=h338b0a0\_2
- gflags=2.2.2=he1b5a44\_1004
- glog=0.6.0=h6f12383\_0
- glpk=5.0=h445213a\_0
- gmp=6.2.1=h58526e2\_0
- gmpy2=2.1.2=py310h3ec546c\_1
- gnutls=3.6.13=h85f3911\_1
- h5py=3.9.0=nompi\_py310ha2ad45a\_103
- hdf5=1.14.2=nompi\_h4f84152\_100
- icu=73.2=h59595ed\_0
- idna=3.4=pyhd8ed1ab\_0
- igraph=0.10.7=h66a01bf\_1
- imagecodecs-lite=2019.12.3=py310h1f7b6fc\_7
- importlib-metadata=6.8.0=pyha770c72\_0
- importlib\_metadata=6.8.0=hd8ed1ab\_0
- inflect=7.0.0=pyhd8ed1ab\_0
- jax=0.4.16=pyhd8ed1ab\_0
- jaxlib=0.4.14=cuda112py310hb0456fb\_201
- jinja2=3.1.2=pyhd8ed1ab\_1
- joblib=1.3.2=pyhd8ed1ab\_0
- jpeg=9e=h166bdaf\_2
- kernel-headers\_linux-64=2.6.32=he073ed8\_16
- keyutils=1.6.1=h166bdaf\_0
- kiwisolver=1.4.5=py310hd41b1e2\_1
- krb5=1.21.2=h659d440\_0
- lame=3.100=h166bdaf\_1003
- lazy\_loader=0.3=pyhd8ed1ab\_0
- lcms2=2.15=hfd0df8a\_0
- ld\_impl\_linux-64=2.40=h41732ed\_0
- leidenalg=0.10.1=py310hc6cd4ac\_0
- lerc=4.0.0=h27087fc\_0
- libabseil=20230802.1=cxx17\_h59595ed\_0
- libaec=1.1.1=h59595ed\_0
- libarrow=13.0.0=h1935d02\_5\_cpu
- libblas=3.9.0=16\_linux64\_mkl
- libbrotlicommon=1.1.0=hd590300\_1
- libbrotlidec=1.1.0=hd590300\_1
- libbrotlienc=1.1.0=hd590300\_1
- libcblas=3.9.0=16\_linux64\_mkl
- libcrc32c=1.1.2=h9c3ff4c\_0
- libcurl=8.3.0=hca28451\_0
- libdeflate=1.17=h0b41bf4\_0
- libedit=3.1.20191231=he28a2e2\_2
- libev=4.33=h516909a\_1
- libevent=2.1.12=hf998b51\_1
- libffi=3.4.2=h7f98852\_5
- libgcc-devel\_linux-64=13.2.0=ha9c7c90\_2
- libgcc-ng=13.2.0=h807b86a\_2
- libgfortran-ng=13.2.0=h69a702a\_2
- libgfortran5=13.2.0=ha4646dd\_2
- libgomp=13.2.0=h807b86a\_2
- libgoogle-cloud=2.12.0=h8d7e28b\_2
- libgrpc=1.57.0=ha4d0f93\_1
- libhwloc=2.9.3=default\_h554bfaf\_1009
- libiconv=1.17=h166bdaf\_0
- libjpeg-turbo=2.0.0=h9bf148f\_0
- liblapack=3.9.0=16\_linux64\_mkl
- liblapacke=3.9.0=16\_linux64\_mkl
- libleidenalg=0.11.1=h00ab1b0\_0
- libllvm14=14.0.6=hcd5def8\_4
- libnghttp2=1.52.0=h61bc06f\_0
- libnsl=2.0.0=hd590300\_1
- libnuma=2.0.16=h0b41bf4\_1
- libpng=1.6.39=h753d276\_0
- libprotobuf=4.23.4=hf27288f\_6
- libsanitizer=13.2.0=h7e041cc\_2
- libsqlite=3.43.0=h2797004\_0
- libssh2=1.11.0=h0841786\_0
- libstdcxx-ng=13.2.0=h7e041cc\_2
- libthrift=0.19.0=hb90f79a\_1
- libtiff=4.5.0=h6adf6a1\_2
- libutf8proc=2.8.0=h166bdaf\_0
- libuuid=2.38.1=h0b41bf4\_0
- libwebp-base=1.3.2=hd590300\_0
- libxcb=1.13=h7f98852\_1004
- libxml2=2.11.5=h232c23b\_1
- libzlib=1.2.13=hd590300\_5
- llvm-openmp=15.0.7=h0cdce71\_0
- locket=1.0.0=pyhd8ed1ab\_0
- lz4=4.3.2=py310h350c4a5\_1
- lz4-c=1.9.4=hcb278e6\_0
- markupsafe=2.1.3=py310h2372a71\_1
- matplotlib-base=3.8.0=py310h62c0568\_1
- matplotlib-scalebar=0.8.1=pyhd8ed1ab\_0
- mkl=2022.1.0=h84fe81f\_915
- mkl-devel=2022.1.0=ha770c72\_916
- mkl-include=2022.1.0=h84fe81f\_915
- ml\_dtypes=0.2.0=py310hcc13569\_2
- mpc=1.3.1=hfe3b2da\_0
- mpfr=4.2.0=hb012696\_0
- mpmath=1.3.0=pyhd8ed1ab\_0
- msgpack-python=1.0.6=py310hd41b1e2\_0
- mudata=0.2.3=pyhd8ed1ab\_0
- multidict=6.0.4=py310h1fa729e\_0
- munkres=1.0.7=py\_1
- natsort=8.4.0=pyhd8ed1ab\_0
- nccl=2.19.3.1=h0800d71\_0
- ncurses=6.4=hcb278e6\_0
- nettle=3.6=he412f7d\_0
- networkx=3.1=pyhd8ed1ab\_0
- nose=1.3.7=py\_1006
- numcodecs=0.11.0=py310heca2aa9\_1
- omnipath=1.0.7=pyhd8ed1ab\_0
- openh264=2.1.1=h780b84a\_0
- openjpeg=2.5.0=hfec8fc6\_2
- openpyxl=3.0.10=py310h5eee18b\_0
- openssl=3.1.3=hd590300\_0
- opt-einsum=3.0.0=py\_0
- orc=1.9.0=h52d3b3c\_2
- packaging=23.2=pyhd8ed1ab\_0
- pandas=2.1.1=py310hcc13569\_1
- parasail-python=1.3.4=py310h6cc9453\_0
- partd=1.4.1=pyhd8ed1ab\_0
- patsy=0.5.3=pyhd8ed1ab\_0
- pillow=9.4.0=py310h023d228\_1
- pims=0.6.1=pyhd8ed1ab\_1
- pip=23.2.1=pyhd8ed1ab\_0
- platformdirs=3.11.0=pyhd8ed1ab\_0
- pooch=1.7.0=pyhd8ed1ab\_4
- psutil=5.9.5=py310h2372a71\_1
- pthread-stubs=0.4=h36c2ea0\_1001
- pynndescent=0.5.10=pyh1a96a4e\_0
- pyparsing=3.1.1=pyhd8ed1ab\_0
- pysocks=1.7.1=pyha2e5f31\_6
- python=3.10.12=hd12c33a\_0\_cpython
- python-dateutil=2.8.2=pyhd8ed1ab\_0
- python-igraph=0.10.8=py310h1e3ba49\_1
- python-levenshtein=0.12.0=0
- python-tzdata=2023.3=pyhd8ed1ab\_0
- python\_abi=3.10=4\_cp310
- pytorch=2.1.0=py3.10\_cpu\_0
- pytorch-mutex=1.0=cpu
- pytz=2023.3.post1=pyhd8ed1ab\_0
- pywavelets=1.4.1=py310h1f7b6fc\_1
- pyyaml=6.0.1=py310h2372a71\_1
- rdma-core=28.9=h59595ed\_1
- re2=2023.03.02=h8c504da\_0
- readline=8.2=h8228510\_1
- requests=2.31.0=pyhd8ed1ab\_0
- s2n=1.3.52=h06160fa\_0
- scanpy=1.9.5=pyhd8ed1ab\_0
- scikit-image=0.20.0=py310h9b08913\_1
- scikit-learn=1.3.1=py310h1fdf081\_0
- scirpy=0.13.1=pyhdfd78af\_0
- seaborn=0.13.0=hd8ed1ab\_0
- seaborn-base=0.13.0=pyhd8ed1ab\_0
- session-info=1.0.0=pyhd8ed1ab\_0
- setuptools=68.2.2=pyhd8ed1ab\_0
- six=1.16.0=pyh6c4a22f\_0
- slicerator=1.1.0=pyhd8ed1ab\_0
- snappy=1.1.10=h9fff704\_0
- sortedcontainers=2.4.0=pyhd8ed1ab\_0
- squarify=0.4.3=py\_0
- statsmodels=0.14.0=py310h278f3c1\_1
- sympy=1.12=pypyh9d50eac\_103
- sysroot\_linux-64=2.12=he073ed8\_16
- tblib=2.0.0=pyhd8ed1ab\_0
- texttable=1.7.0=pyhd8ed1ab\_0
- threadpoolctl=3.2.0=pyha21a80b\_0
- tk=8.6.13=h2797004\_0
- toolz=0.12.0=pyhd8ed1ab\_0
- torchaudio=2.1.0=py310\_cpu
- torchvision=0.16.0=py310\_cpu
- tornado=6.3.3=py310h2372a71\_1
- tqdm=4.66.1=pyhd8ed1ab\_0
- typing-extensions=4.8.0=hd8ed1ab\_0
- typing\_extensions=4.8.0=pyha770c72\_0
- tzdata=2023c=h71feb2d\_0
- ucx=1.14.1=h64cca9d\_5
- umap-learn=0.5.4=py310hff52083\_0
- unicodedata2=15.1.0=py310h2372a71\_0
- validators=0.22.0=pyhd8ed1ab\_0
- wheel=0.41.2=pyhd8ed1ab\_0
- wrapt=1.15.0=py310h2372a71\_1
- xarray=2023.9.0=pyhd8ed1ab\_0
- xlrd=1.2.0=pyh9f0ad1d\_1
- xorg-libxau=1.0.11=hd590300\_0
- xorg-libxdmcp=1.1.3=h7f98852\_0
- xyzservices=2023.10.0=pyhd8ed1ab\_0
- xz=5.2.6=h166bdaf\_0
- yaml=0.2.5=h7f98852\_2
- yamlordereddictloader=0.4.0=py\_0
- yarl=1.9.2=py310h2372a71\_0
- zarr=2.16.1=pyhd8ed1ab\_0
- zict=3.0.0=pyhd8ed1ab\_0
- zipp=3.17.0=pyhd8ed1ab\_0
- zlib=1.2.13=hd590300\_5
- zstd=1.5.5=hfc55251\_0
- pip:
  - absl-py==2.0.0
  - accessible-pygments==0.0.4
  - aiobotocore==2.5.4
  - aioitertools==0.11.0
  - alabaster==0.7.13
  - annoy==1.17.3
  - anyio==3.7.1
  - appdirs==1.4.4
  - argon2-cffi==23.1.0
  - argon2-cffi-bindings==21.2.0
  - arrow==1.3.0
  - asciitree==0.3.3
  - asttokens==2.4.0
  - async-lru==2.0.4
  - babel==2.13.0
  - backcall==0.2.0
  - backoff==2.2.1
  - beautifulsoup4==4.12.2
  - biopython==1.81
  - biothings-client==0.3.0
  - black==23.9.1
  - bleach==6.0.0
  - blessed==1.20.0
  - botocore==1.31.17
  - cachetools==5.3.1
  - cell2location==0.1.3
  - cellxgene-census==1.6.0
  - cffi==1.16.0
  - cfgv==3.4.0
  - chex==0.1.7
  - comm==0.1.4
  - contextlib2==21.6.0
  - coverage==7.3.2
  - croniter==1.4.1
  - cython==3.0.2
  - dateutils==0.6.12
  - debugpy==1.8.0
  - decorator==5.1.1
  - deepdiff==6.5.0
  - defusedxml==0.7.1
  - diskcache==5.6.3
  - distlib==0.3.7
  - dm-tree==0.1.8
  - docutils==0.17.1
  - etils==1.5.0
  - exceptiongroup==1.1.3
  - execnet==2.0.2
  - executing==2.0.0
  - fastapi==0.103.2
  - fasteners==0.19
  - fastjsonschema==2.18.1
  - flake8==6.1.0
  - flax==0.7.4
  - fqdn==1.5.1
  - future==0.18.3
  - genomepy==0.16.1
  - google-auth==2.23.2
  - google-auth-oauthlib==1.0.0
  - greenlet==3.0.0
  - grpcio==1.59.0
  - h11==0.14.0
  - huggingface-hub==0.17.3
  - hyperopt==0.2.7
  - hypothesis==6.87.1
  - identify==2.5.30
  - imageio==2.31.5
  - imagesize==1.4.1
  - importlib-resources==6.1.0
  - iniconfig==2.0.0
  - inquirer==3.1.3
  - ipykernel==6.25.2
  - ipython==8.16.1
  - ipython-genutils==0.2.0
  - ipywidgets==8.1.1
  - isoduration==20.11.0
  - itsdangerous==2.1.2
  - jedi==0.19.1
  - jmespath==1.0.1
  - json5==0.9.14
  - jsonpointer==2.4
  - jsonschema==4.19.1
  - jsonschema-specifications==2023.7.1
  - jupyter==1.0.0
  - jupyter-cache==0.6.1
  - jupyter-client==8.3.1
  - jupyter-console==6.6.3
  - jupyter-core==5.3.2
  - jupyter-events==0.7.0
  - jupyter-lsp==2.2.0
  - jupyter-server==2.7.3
  - jupyter-server-terminals==0.4.4
  - jupyterlab==4.0.6
  - jupyterlab-pygments==0.2.2
  - jupyterlab-server==2.25.0
  - jupyterlab-widgets==3.0.9
  - latexcodec==2.0.1
  - lightning==2.0.9.post0
  - lightning-cloud==0.5.39
  - lightning-utilities==0.9.0
  - llvmlite==0.39.1
  - loguru==0.7.2
  - loompy==3.0.7
  - markdown==3.4.4
  - markdown-it-py==2.2.0
  - matplotlib-inline==0.1.6
  - mccabe==0.7.0
  - mdit-py-plugins==0.3.5
  - mdurl==0.1.2
  - mistune==3.0.2
  - mizani==0.9.3
  - ml-collections==0.1.1
  - msgpack==1.0.7
  - multipledispatch==1.0.0
  - muon==0.1.5
  - mygene==3.2.2
  - mypy-extensions==1.0.0
  - mysql-connector-python==8.1.0
  - myst-nb==0.17.2
  - myst-parser==0.18.1
  - nbclient==0.7.4
  - nbconvert==7.8.0
  - nbformat==5.9.2
  - nest-asyncio==1.5.8
  - nodeenv==1.8.0
  - norns==0.1.6
  - notebook==7.0.4
  - notebook-shim==0.2.3
  - numba==0.56.4
  - numpy==1.23.5
  - numpy-groupies==0.10.2
  - numpyro==0.13.2
  - oauthlib==3.2.2
  - opencv-python==4.8.1.78
  - optax==0.1.7
  - orbax-checkpoint==0.4.1
  - ordered-set==4.1.0
  - overrides==7.4.0
  - pandocfilters==1.5.0
  - parso==0.8.3
  - pathspec==0.11.2
  - pexpect==4.8.0
  - pickleshare==0.7.5
  - plotnine==0.12.3
  - plottable==0.1.5
  - pluggy==1.3.0
  - pre-commit==3.4.0
  - prometheus-client==0.17.1
  - prompt-toolkit==3.0.39
  - protobuf==4.21.12
  - ptyprocess==0.7.0
  - pure-eval==0.2.2
  - py4j==0.10.9.7
  - pyarrow==13.0.0
  - pyasn1==0.5.0
  - pyasn1-modules==0.3.0
  - pybtex==0.24.0
  - pybtex-docutils==1.0.3
  - pycodestyle==2.11.0
  - pycparser==2.21
  - pydantic==2.1.1
  - pydantic-core==2.4.0
  - pydata-sphinx-theme==0.14.1
  - pyfaidx==0.7.2.2
  - pyflakes==3.1.0
  - pygments==2.16.1
  - pyjwt==2.8.0
  - pymde==0.1.18
  - pyro-api==0.1.2
  - pyro-ppl==1.8.6
  - pytest==7.4.2
  - pytest-asyncio==0.21.1
  - pytest-cov==4.1.0
  - pytest-xdist==3.3.1
  - python-editor==1.0.4
  - python-json-logger==2.0.7
  - python-multipart==0.0.6
  - pytorch-lightning==2.0.9.post0
  - pyzmq==25.1.1
  - qtconsole==5.4.4
  - qtpy==2.4.0
  - ray==2.7.0
  - readchar==4.0.5
  - referencing==0.30.2
  - requests-oauthlib==1.3.1
  - rfc3339-validator==0.1.4
  - rfc3986-validator==0.1.1
  - rich==13.6.0
  - rpds-py==0.10.3
  - rsa==4.9
  - ruff==0.0.292
  - s3fs==2023.9.2
  - scib-metrics==0.4.0
  - scikit-misc==0.3.0
  - scipy==1.10.1
  - scrublet==0.2.3
  - scvi-tools==1.0.3
  - send2trash==1.8.2
  - sniffio==1.3.0
  - snowballstemmer==2.2.0
  - somacore==1.0.4
  - soupsieve==2.5
  - sparse==0.14.0
  - spatialdata==0.0.1
  - sphinx==5.3.0
  - sphinx-autodoc-typehints==1.23.0
  - sphinx-book-theme==1.0.1
  - sphinx-copybutton==0.5.2
  - sphinx-design==0.5.0
  - sphinx-hoverxref==1.3.0
  - sphinxcontrib-applehelp==1.0.7
  - sphinxcontrib-bibtex==2.6.1
  - sphinxcontrib-devhelp==1.0.5
  - sphinxcontrib-htmlhelp==2.0.4
  - sphinxcontrib-jquery==4.1
  - sphinxcontrib-jsmath==1.0.1
  - sphinxcontrib-qthelp==1.0.6
  - sphinxcontrib-serializinghtml==1.1.9
  - sphinxext-opengraph==0.8.2
  - sqlalchemy==2.0.21
  - squidpy==1.3.0
  - stack-data==0.6.3
  - starlette==0.27.0
  - starsessions==1.3.0
  - stdlib-list==0.9.0
  - tabulate==0.9.0
  - tbb==2021.10.0
  - tensorboard==2.14.1
  - tensorboard-data-server==0.7.1
  - tensorboardx==2.6.2.2
  - tensorstore==0.1.45
  - terminado==0.17.1
  - tifffile==2023.9.26
  - tiledb==0.22.3
  - tiledbsoma==1.4.3
  - tinycss2==1.2.1
  - tomli==2.0.1
  - torchmetrics==1.2.0
  - traitlets==5.11.2
  - types-python-dateutil==2.8.19.14
  - uri-template==1.3.0
  - urllib3==1.26.17
  - uvicorn==0.23.2
  - virtualenv==20.24.5
  - wcwidth==0.2.8
  - webcolors==1.13
  - webencodings==0.5.1
  - websocket-client==1.6.3
  - websockets==11.0.3
  - werkzeug==3.0.0
  - widgetsnbextension==4.0.9

---

<div class="post-metadata">

**Author:** ![martinkim0](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/martinkim0/32/881_2.png) [@martinkim0](https://discourse.scverse.org/u/martinkim0)\
**Post date:** [October 9, 2023, 9:57pm UTC](https://discourse.scverse.org/t/enviroment-yml-file-scvi-installation-problems/1803/2 "2023-10-09T21:57:09Z")

</div>

Hi, could you share the full traceback of the import error you are getting?

---

<div class="post-metadata">

**Author:** ![jagraz](https://avatars.discourse-cdn.com/v4/letter/j/e99b99/32.png) [@jagraz](https://discourse.scverse.org/u/jagraz)\
**Post date:** [October 9, 2023, 11:37pm UTC](https://discourse.scverse.org/t/enviroment-yml-file-scvi-installation-problems/1803/3 "2023-10-09T23:37:34Z")

</div>

Does this help?

(single-cell) jagraz@UPenn:~$ python  
Python 3.10.12 | packaged by conda-forge | (main, Jun 23 2023, 22:40:32) [GCC 12.3.0] on linux  
Type “help”, “copyright”, “credits” or “license” for more information.

> > > import scvi  
> > > Traceback (most recent call last):  
> > > File “”, line 1, in   
> > > File “/home/jagraz/miniforge3/envs/single-cell/lib/python3.10/site-packages/scvi/ **init**.py”, line 8, in   
> > > from .\_settings import settings  
> > > File “/home/jagraz/miniforge3/envs/single-cell/lib/python3.10/site-packages/scvi/\_settings.py”, line 8, in   
> > > from lightning.pytorch import seed\_everything  
> > > File “/home/jagraz/miniforge3/envs/single-cell/lib/python3.10/site-packages/lightning/ **init**.py”, line 17, in   
> > > from lightning.app import storage # noqa: E402  
> > > File “/home/jagraz/miniforge3/envs/single-cell/lib/python3.10/site-packages/lightning/app/ **init**.py”, line 24, in   
> > > from lightning.app import components # noqa: E402, F401  
> > > File “/home/jagraz/miniforge3/envs/single-cell/lib/python3.10/site-packages/lightning/app/components/ **init**.py”, line 1, in   
> > > from lightning.app.components.database.client import DatabaseClient  
> > > File “/home/jagraz/miniforge3/envs/single-cell/lib/python3.10/site-packages/lightning/app/components/database/ **init**.py”, line 1, in   
> > > from lightning.app.components.database.client import DatabaseClient  
> > > File “/home/jagraz/miniforge3/envs/single-cell/lib/python3.10/site-packages/lightning/app/components/database/client.py”, line 22, in   
> > > from lightning.app.components.database.utilities import \_GeneralModel  
> > > File “/home/jagraz/miniforge3/envs/single-cell/lib/python3.10/site-packages/lightning/app/components/database/utilities.py”, line 28, in   
> > > from pydantic.main import ModelMetaclass  
> > > ImportError: cannot import name ‘ModelMetaclass’ from ‘pydantic.main’ (/home/jagraz/miniforge3/envs/single-cell/lib/python3.10/site-packages/pydantic/main.py)

---

<div class="post-metadata">

**Author:** ![martinkim0](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/martinkim0/32/881_2.png) [@martinkim0](https://discourse.scverse.org/u/martinkim0)\
**Post date:** [October 10, 2023, 4:54pm UTC](https://discourse.scverse.org/t/enviroment-yml-file-scvi-installation-problems/1803/4 "2023-10-10T16:54:38Z")

</div>

Hmm this is strange, the error should have been patched in Lightning 2.0.6. I think downgrading pydantic to \<2.0.0 should work for now, could you try that out?

```auto
pip install -U pydantic==1.10.13

```

---

<div class="post-metadata">

**Author:** ![jagraz](https://avatars.discourse-cdn.com/v4/letter/j/e99b99/32.png) [@jagraz](https://discourse.scverse.org/u/jagraz)\
**Post date:** [October 10, 2023, 5:57pm UTC](https://discourse.scverse.org/t/enviroment-yml-file-scvi-installation-problems/1803/5 "2023-10-10T17:57:12Z")

</div>

I get a different error now:  
File “/home/jagraz/miniforge3/envs/scvi-env-p39/lib/python3.9/ctypes/ **init**.py”, line 374, in **init**  
self.\_handle = \_dlopen(self.\_name, mode)  
OSError: libtorch\_cuda.so: cannot open shared object file: No such file or directory

This is my installation sequence, see any issues here?  
conda create -n scvi-env-p39 python=3.9  
conda activate scvi-env-p39  
conda install -c anaconda pip  
conda install pytorch torchvision torchaudio pytorch-cuda=11.7 -c pytorch -c nvidia  
conda install jax jaxlib -c conda-forge  
pip install scvi-tools

---

<div class="post-metadata">

**Author:** ![jagraz](https://avatars.discourse-cdn.com/v4/letter/j/e99b99/32.png) [@jagraz](https://discourse.scverse.org/u/jagraz)\
**Post date:** [October 10, 2023, 5:59pm UTC](https://discourse.scverse.org/t/enviroment-yml-file-scvi-installation-problems/1803/6 "2023-10-10T17:59:35Z")

</div>

Perhaps if you share your python environment using the command below, I could try to duplicate yours  
conda env create -f single-cell-analysis-environment.yml

I’ve tried using python 3.9 and 3.10, but dont seem to work failing with the same error below. Does installing scVI suppose to be difficult? I’m missing something very simple, but can’t pinpoint.  
OSError: libtorch\_cuda.so: cannot open shared object file: No such file or directory

conda list torch  
-# packages in environment at /home/jagraz/miniforge3/envs/scvi-env-p310:  
-#  
-# Name Version Build Channel  
pytorch-cuda 11.7 h778d358\_5 pytorch  
pytorch-lightning 2.0.9.post0 pypi\_0 pypi  
pytorch-mutex 1.0 cuda pytorch  
torchaudio 2.0.0 py310\_cu117 pytorch  
torchmetrics 1.2.0 pypi\_0 pypi  
torchvision 0.15.0 py310\_cu117 pytorch

Using Nvidia RTX A4000

I’ve been fighting this issue for a week. Any suggestions will be greatly appreciated.

---

<div class="post-metadata">

**Author:** ![martinkim0](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/martinkim0/32/881_2.png) [@martinkim0](https://discourse.scverse.org/u/martinkim0)\
**Post date:** [October 10, 2023, 10:44pm UTC](https://discourse.scverse.org/t/enviroment-yml-file-scvi-installation-problems/1803/7 "2023-10-10T22:44:44Z")

</div>

Hi, I’ve pasted my environment packages below:

```auto
name: scvi-tools-dev
channels:
  - pytorch
  - nvidia
  - conda-forge
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_kmp_llvm
  - blas=2.116=mkl
  - blas-devel=3.9.0=16_linux64_mkl
  - brotli-python=1.1.0=py311hb755f60_0
  - bzip2=1.0.8=h7f98852_4
  - ca-certificates=2023.7.22=hbcca054_0
  - certifi=2023.7.22=pyhd8ed1ab_0
  - charset-normalizer=3.2.0=pyhd8ed1ab_0
  - cuda-cudart=11.8.89=0
  - cuda-cupti=11.8.87=0
  - cuda-libraries=11.8.0=0
  - cuda-nvcc=11.8.89=0
  - cuda-nvrtc=11.8.89=0
  - cuda-nvtx=11.8.86=0
  - cuda-runtime=11.8.0=0
  - ffmpeg=4.3=hf484d3e_0
  - filelock=3.12.4=pyhd8ed1ab_0
  - freetype=2.12.1=h267a509_2
  - gmp=6.2.1=h58526e2_0
  - gmpy2=2.1.2=py311h6a5fa03_1
  - gnutls=3.6.13=h85f3911_1
  - icu=73.2=h59595ed_0
  - idna=3.4=pyhd8ed1ab_0
  - jinja2=3.1.2=pyhd8ed1ab_1
  - jpeg=9e=h0b41bf4_3
  - lame=3.100=h166bdaf_1003
  - lcms2=2.15=hfd0df8a_0
  - ld_impl_linux-64=2.40=h41732ed_0
  - lerc=4.0.0=h27087fc_0
  - libblas=3.9.0=16_linux64_mkl
  - libcblas=3.9.0=16_linux64_mkl
  - libcublas=11.11.3.6=0
  - libcufft=10.9.0.58=0
  - libcufile=1.7.2.10=0
  - libcurand=10.3.3.141=0
  - libcusolver=11.4.1.48=0
  - libcusparse=11.7.5.86=0
  - libdeflate=1.17=h0b41bf4_0
  - libexpat=2.5.0=hcb278e6_1
  - libffi=3.4.2=h7f98852_5
  - libgcc-ng=13.2.0=h807b86a_1
  - libgfortran-ng=13.2.0=h69a702a_1
  - libgfortran5=13.2.0=ha4646dd_1
  - libgomp=13.2.0=h807b86a_1
  - libhwloc=2.9.2=default_h554bfaf_1009
  - libiconv=1.17=h166bdaf_0
  - liblapack=3.9.0=16_linux64_mkl
  - liblapacke=3.9.0=16_linux64_mkl
  - libnpp=11.8.0.86=0
  - libnsl=2.0.0=h7f98852_0
  - libnvjpeg=11.9.0.86=0
  - libpng=1.6.39=h753d276_0
  - libsqlite=3.43.0=h2797004_0
  - libstdcxx-ng=13.2.0=h7e041cc_1
  - libtiff=4.5.0=h6adf6a1_2
  - libuuid=2.38.1=h0b41bf4_0
  - libwebp-base=1.3.2=hd590300_0
  - libxcb=1.13=h7f98852_1004
  - libxml2=2.11.5=h232c23b_1
  - libzlib=1.2.13=hd590300_5
  - llvm-openmp=16.0.6=h4dfa4b3_0
  - markupsafe=2.1.3=py311h459d7ec_0
  - mkl=2022.1.0=h84fe81f_915
  - mkl-devel=2022.1.0=ha770c72_916
  - mkl-include=2022.1.0=h84fe81f_915
  - mpc=1.3.1=hfe3b2da_0
  - mpfr=4.2.0=hb012696_0
  - mpmath=1.3.0=pyhd8ed1ab_0
  - ncurses=6.4=hcb278e6_0
  - nettle=3.6=he412f7d_0
  - networkx=3.1=pyhd8ed1ab_0
  - openh264=2.1.1=h780b84a_0
  - openjpeg=2.5.0=hfec8fc6_2
  - openssl=3.1.3=hd590300_0
  - pillow=9.4.0=py311h50def17_1
  - pip=23.2.1=pyhd8ed1ab_0
  - pthread-stubs=0.4=h36c2ea0_1001
  - pysocks=1.7.1=pyha2e5f31_6
  - python=3.11.5=hab00c5b_0_cpython
  - python_abi=3.11=4_cp311
  - pytorch=2.0.1=py3.11_cuda11.8_cudnn8.7.0_0
  - pytorch-cuda=11.8=h7e8668a_5
  - pytorch-mutex=1.0=cuda
  - readline=8.2=h8228510_1
  - requests=2.31.0=pyhd8ed1ab_0
  - setuptools=68.2.2=pyhd8ed1ab_0
  - sympy=1.12=pypyh9d50eac_103
  - tk=8.6.12=h27826a3_0
  - torchaudio=2.0.2=py311_cu118
  - torchtriton=2.0.0=py311
  - torchvision=0.15.2=py311_cu118
  - typing_extensions=4.8.0=pyha770c72_0
  - wheel=0.41.2=pyhd8ed1ab_0
  - xorg-libxau=1.0.11=hd590300_0
  - xorg-libxdmcp=1.1.3=h7f98852_0
  - xz=5.2.6=h166bdaf_0
  - zlib=1.2.13=hd590300_5
  - zstd=1.5.5=hfc55251_0
  - pip:
      - absl-py==2.0.0
      - accessible-pygments==0.0.4
      - aiobotocore==2.5.4
      - aiohttp==3.8.5
      - aioitertools==0.11.0
      - aiosignal==1.3.1
      - alabaster==0.7.13
      - anndata==0.10.1
      - annotated-types==0.5.0
      - anyio==3.7.1
      - appdirs==1.4.4
      - argon2-cffi==23.1.0
      - argon2-cffi-bindings==21.2.0
      - array-api-compat==1.4
      - arrow==1.2.3
      - asttokens==2.4.0
      - async-lru==2.0.4
      - async-timeout==4.0.3
      - attrs==23.1.0
      - babel==2.12.1
      - backcall==0.2.0
      - backoff==2.2.1
      - beautifulsoup4==4.12.2
      - biopython==1.81
      - biothings-client==0.3.0
      - black==23.9.1
      - bleach==6.0.0
      - blessed==1.20.0
      - botocore==1.31.17
      - cachetools==5.3.1
      - cellxgene-census==1.6.0
      - cffi==1.15.1
      - cfgv==3.4.0
      - chex==0.1.7
      - click==8.1.7
      - cloudpickle==2.2.1
      - colorama==0.4.6
      - comm==0.1.4
      - contextlib2==21.6.0
      - contourpy==1.1.1
      - coverage==7.3.1
      - croniter==1.4.1
      - cycler==0.11.0
      - dateutils==0.6.12
      - debugpy==1.8.0
      - decorator==5.1.1
      - deepdiff==6.5.0
      - defusedxml==0.7.1
      - diskcache==5.6.3
      - distlib==0.3.7
      - dm-tree==0.1.8
      - docrep==0.3.2
      - docutils==0.17.1
      - embedding-scvi==0.0.1
      - etils==1.5.0
      - executing==1.2.0
      - fastapi==0.103.1
      - fastjsonschema==2.18.0
      - flake8==6.1.0
      - flax==0.7.4
      - fonttools==4.42.1
      - fqdn==1.5.1
      - frozenlist==1.4.0
      - fsspec==2023.9.1
      - future==0.18.3
      - genomepy==0.16.1
      - google-auth==2.23.0
      - google-auth-oauthlib==1.0.0
      - greenlet==2.0.2
      - grpcio==1.58.0
      - h11==0.14.0
      - h5py==3.9.0
      - huggingface-hub==0.17.2
      - hyperopt==0.2.7
      - identify==2.5.29
      - igraph==0.10.8
      - imagesize==1.4.1
      - importlib-metadata==6.8.0
      - importlib-resources==6.0.1
      - iniconfig==2.0.0
      - inquirer==3.1.3
      - ipykernel==6.25.2
      - ipython==8.15.0
      - ipython-genutils==0.2.0
      - ipywidgets==8.1.1
      - isoduration==20.11.0
      - itsdangerous==2.1.2
      - jax==0.4.16
      - jaxlib==0.4.16+cuda11.cudnn86
      - jedi==0.19.0
      - jmespath==1.0.1
      - joblib==1.3.2
      - json5==0.9.14
      - jsonpointer==2.4
      - jsonschema==4.19.0
      - jsonschema-specifications==2023.7.1
      - jupyter==1.0.0
      - jupyter-cache==0.6.1
      - jupyter-client==8.3.1
      - jupyter-console==6.6.3
      - jupyter-core==5.3.1
      - jupyter-events==0.7.0
      - jupyter-lsp==2.2.0
      - jupyter-server==2.7.3
      - jupyter-server-terminals==0.4.4
      - jupyterlab==4.0.6
      - jupyterlab-pygments==0.2.2
      - jupyterlab-server==2.25.0
      - jupyterlab-widgets==3.0.9
      - kiwisolver==1.4.5
      - latexcodec==2.0.1
      - lightning==2.0.9
      - lightning-cloud==0.5.38
      - lightning-utilities==0.9.0
      - llvmlite==0.40.1
      - loguru==0.7.2
      - loompy==3.0.7
      - markdown==3.4.4
      - markdown-it-py==2.2.0
      - matplotlib==3.8.0
      - matplotlib-inline==0.1.6
      - mccabe==0.7.0
      - mdit-py-plugins==0.3.5
      - mdurl==0.1.2
      - mistune==3.0.1
      - ml-collections==0.1.1
      - ml-dtypes==0.3.0
      - msgpack==1.0.5
      - mudata==0.2.3
      - multidict==6.0.4
      - multipledispatch==1.0.0
      - mygene==3.2.2
      - mypy-extensions==1.0.0
      - mysql-connector-python==8.1.0
      - myst-nb==0.17.2
      - myst-parser==0.18.1
      - natsort==8.4.0
      - nbclient==0.7.4
      - nbconvert==7.8.0
      - nbformat==5.9.2
      - nest-asyncio==1.5.8
      - nodeenv==1.8.0
      - norns==0.1.6
      - nose==1.3.7
      - notebook==7.0.3
      - notebook-shim==0.2.3
      - numba==0.57.0
      - numpy==1.24.4
      - numpy-groupies==0.9.22
      - numpyro==0.13.0
      - nvidia-cublas-cu11==11.11.3.6
      - nvidia-cuda-cupti-cu11==11.8.87
      - nvidia-cuda-nvcc-cu11==11.8.89
      - nvidia-cuda-nvrtc-cu11==11.8.89
      - nvidia-cuda-runtime-cu11==11.8.89
      - nvidia-cudnn-cu11==8.9.4.25
      - nvidia-cufft-cu11==10.9.0.58
      - nvidia-cusolver-cu11==11.4.1.48
      - nvidia-cusparse-cu11==11.7.5.86
      - oauthlib==3.2.2
      - opt-einsum==3.3.0
      - optax==0.1.7
      - orbax-checkpoint==0.3.5
      - ordered-set==4.1.0
      - overrides==7.4.0
      - packaging==23.1
      - pandas==2.1.0
      - pandocfilters==1.5.0
      - parso==0.8.3
      - pathspec==0.11.2
      - patsy==0.5.3
      - pexpect==4.8.0
      - pickleshare==0.7.5
      - platformdirs==3.10.0
      - plottable==0.1.5
      - pluggy==1.3.0
      - pre-commit==3.4.0
      - prometheus-client==0.17.1
      - prompt-toolkit==3.0.39
      - protobuf==4.21.12
      - psutil==5.9.5
      - ptyprocess==0.7.0
      - pure-eval==0.2.2
      - py4j==0.10.9.7
      - pyarrow==13.0.0
      - pyasn1==0.5.0
      - pyasn1-modules==0.3.0
      - pybtex==0.24.0
      - pybtex-docutils==1.0.3
      - pycodestyle==2.11.0
      - pycparser==2.21
      - pydantic==2.1.1
      - pydantic-core==2.4.0
      - pydata-sphinx-theme==0.14.0
      - pyfaidx==0.7.2.1
      - pyflakes==3.1.0
      - pygments==2.16.1
      - pyjwt==2.8.0
      - pymde==0.1.18
      - pynndescent==0.5.10
      - pyparsing==3.1.1
      - pyro-api==0.1.2
      - pyro-ppl==1.8.6
      - pytest==7.4.2
      - pytest-cov==4.1.0
      - python-dateutil==2.8.2
      - python-editor==1.0.4
      - python-json-logger==2.0.7
      - python-multipart==0.0.6
      - pytorch-lightning==2.0.9
      - pytz==2023.3.post1
      - pyyaml==6.0.1
      - pyzmq==25.1.1
      - qtconsole==5.4.4
      - qtpy==2.4.0
      - ray==2.7.0
      - readchar==4.0.5
      - referencing==0.30.2
      - requests-oauthlib==1.3.1
      - rfc3339-validator==0.1.4
      - rfc3986-validator==0.1.1
      - rich==13.5.3
      - rpds-py==0.10.3
      - rsa==4.9
      - ruff==0.0.290
      - s3fs==2023.9.1
      - scanpy==1.9.5
      - scib-metrics==0.4.0
      - scikit-learn==1.3.0
      - scipy==1.10.1
      - scvi-tools==1.0.3
      - seaborn==0.12.2
      - send2trash==1.8.2
      - session-info==1.0.0
      - six==1.16.0
      - sniffio==1.3.0
      - snowballstemmer==2.2.0
      - somacore==1.0.4
      - soupsieve==2.5
      - sparse==0.14.0
      - sphinx==5.3.0
      - sphinx-autodoc-typehints==1.23.0
      - sphinx-book-theme==1.0.1
      - sphinx-copybutton==0.5.2
      - sphinx-design==0.5.0
      - sphinx-hoverxref==1.3.0
      - sphinxcontrib-applehelp==1.0.7
      - sphinxcontrib-bibtex==2.6.1
      - sphinxcontrib-devhelp==1.0.5
      - sphinxcontrib-htmlhelp==2.0.4
      - sphinxcontrib-jquery==4.1
      - sphinxcontrib-jsmath==1.0.1
      - sphinxcontrib-qthelp==1.0.6
      - sphinxcontrib-serializinghtml==1.1.9
      - sphinxext-opengraph==0.8.2
      - sqlalchemy==2.0.21
      - stack-data==0.6.2
      - starlette==0.27.0
      - starsessions==1.3.0
      - statsmodels==0.14.0
      - stdlib-list==0.9.0
      - tabulate==0.9.0
      - tbb==2021.10.0
      - tensorboard==2.14.0
      - tensorboard-data-server==0.7.1
      - tensorboardx==2.6.2.2
      - tensorstore==0.1.43
      - terminado==0.17.1
      - texttable==1.6.7
      - threadpoolctl==3.2.0
      - tiledb==0.22.3
      - tiledbsoma==1.4.3
      - tinycss2==1.2.1
      - toolz==0.12.0
      - torchmetrics==1.1.2
      - tornado==6.3.3
      - tqdm==4.66.1
      - traitlets==5.10.0
      - tzdata==2023.3
      - umap-learn==0.5.4
      - uri-template==1.3.0
      - urllib3==1.26.16
      - uvicorn==0.23.2
      - virtualenv==20.24.5
      - wcwidth==0.2.6
      - webcolors==1.13
      - webencodings==0.5.1
      - websocket-client==1.6.3
      - websockets==11.0.3
      - werkzeug==2.3.7
      - widgetsnbextension==4.0.9
      - wrapt==1.15.0
      - xarray==2023.8.0
      - yarl==1.9.2
      - zipp==3.17.0

```

---

<div class="post-metadata">

**Author:** ![jagraz](https://avatars.discourse-cdn.com/v4/letter/j/e99b99/32.png) [@jagraz](https://discourse.scverse.org/u/jagraz)\
**Post date:** [October 11, 2023, 3:20pm UTC](https://discourse.scverse.org/t/enviroment-yml-file-scvi-installation-problems/1803/8 "2023-10-11T15:20:55Z")

</div>

Hi Mark,  
Your enviroment.yml file did not work for either python 3.10 or 3.11. However, I successfully installed scvi using the command below in your Docker file and changing the AnnaData package version

git clone [GitHub - scverse/scvi-tools: Deep probabilistic analysis of single-cell omics data](https://github.com/scverse/scvi-tools.git)  
cd scvi-tools  
conda create -n scvi-env-p311 python=3.11  
conda activate scvi-env-p311  
pip install --no-cache-dir “scvi-tools[all]==1.0.3”  
conda install -c conda-forge pyarrow  
conda install -c conda-forge scanpy python-igraph leidenalg  
conda install -c conda-forge anndata=0.9.2

Reference Docker file

> <https://github.com/YosefLab/scvi-tools-docker/blob/main/images/linux/cuda/devel/Dockerfile>

---

<div class="post-metadata">

**Author:** ![martinkim0](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/martinkim0/32/881_2.png) [@martinkim0](https://discourse.scverse.org/u/martinkim0)\
**Post date:** [October 11, 2023, 5:01pm UTC](https://discourse.scverse.org/t/enviroment-yml-file-scvi-installation-problems/1803/9 "2023-10-11T17:01:50Z")

</div>

Hi @jagraz, glad you were able to figure out the installation. As a side note, I would recommend not installing all optional dependencies of scvi-tools (`pip install scvi-tools[all]`) unless you really are trying to use all the optional functions in the package, since this can lead to more dependency conflicts. Additionally, if you’re trying to install from source, please use the `-e` flag in `pip install`.