Conda env yml to make installation clearer

[giuliaelgarcia]

Is it possible to get a conda env yaml to make installation easier because I keep getting many dependency errors due to version specifications. I use a CentOS7 HPC.

[wenghan1]

I'm happy to share my environment. If there are any differences, please use the author's settings as the standard.

I built the environment by executing the following code:

conda create -n scgpt_2
conda activate scgpt_2
conda install python=3.10.11 cudatoolkit=11.7 cudatoolkit-dev 'gxx>=6.0.0,<12.0' cudnn -c conda-forge
pip install torch==1.13.0+cu117 torchvision==0.14.0+cu117 torchaudio==0.13.0 --extra-index-url https://download.pytorch.org/whl/cu117
pip install packaging
pip install flash-attn==1.0.4 --no-build-isolation
conda install r-base r-devtools
pip install --no-deps scgpt
pip install ipykernel
python -m ipykernel install --user --name=scgpt_2
pip install pandas
pip install scanpy
pip install scvi-tools
pip install numba --upgrade
pip install numpy==1.24.4
pip install torchtext==0.14.0
pip install scib
pip install datasets==2.14.5 transformers==4.33.2

I exported the following via conda env export:

name: scgpt_2
channels:
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
  - https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
  - conda-forge
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - _r-mutex=1.0.0=anacondar_1
  - binutils_impl_linux-64=2.40=hf600244_0
  - bzip2=1.0.8=hd590300_5
  - ca-certificates=2024.2.2=hbcca054_0
  - cairo=1.14.8=0
  - cuda-version=11.7=h67201e3_2
  - cudatoolkit=11.7.1=h4bc3d14_13
  - cudatoolkit-dev=11.7.0=h1de0b5d_6
  - cudnn=6.0=0
  - curl=7.26.0=1
  - fontconfig=2.12.1=3
  - freetype=2.5.5=2
  - gcc=11.4.0=h7baecda_2
  - gcc_impl_linux-64=11.4.0=h7aa1c59_5
  - glib=2.50.2=1
  - gsl=2.2.1=0
  - gxx=11.4.0=h7baecda_2
  - gxx_impl_linux-64=11.4.0=h7aa1c59_5
  - harfbuzz=0.9.39=2
  - icu=54.1=0
  - jbig=2.1=0
  - jpeg=8d=2
  - kernel-headers_linux-64=2.6.32=he073ed8_17
  - ld_impl_linux-64=2.40=h41732ed_0
  - libffi=3.4.2=h7f98852_5
  - libgcc=7.2.0=h69d50b8_2
  - libgcc-devel_linux-64=11.4.0=h922705a_105
  - libgcc-ng=13.2.0=h807b86a_5
  - libgomp=13.2.0=h807b86a_5
  - libiconv=1.14=0
  - libnsl=2.0.1=hd590300_0
  - libpng=1.6.30=1
  - libsanitizer=11.4.0=h4dcbe23_5
  - libstdcxx-devel_linux-64=11.4.0=h922705a_105
  - libstdcxx-ng=13.2.0=h7e041cc_5
  - libtiff=4.0.6=2
  - libuuid=1.41.5=h5eee18b_0
  - libxml2=2.9.4=0
  - ncurses=6.4=h59595ed_2
  - openssl=1.1.1w=h7f8727e_0
  - pango=1.40.3=1
  - pcre=8.39=1
  - pip=24.0=pyhd8ed1ab_0
  - pixman=0.34.0=0
  - python=3.10.11=h7a1cb2a_2
  - r-base=3.3.2=0
  - r-curl=2.3=r3.3.2_0
  - r-devtools=1.12.0=r3.3.2_0
  - r-digest=0.6.10=r3.3.2_0
  - r-git2r=0.16.0=r3.3.2_0
  - r-httr=1.2.1=r3.3.2_0
  - r-jsonlite=1.1=r3.3.2_0
  - r-memoise=1.0.0=r3.3.2_0
  - r-mime=0.5=r3.3.2_0
  - r-openssl=0.9.5=r3.3.2_0
  - r-r6=2.2.0=r3.3.2_0
  - r-rstudioapi=0.6=r3.3.2_0
  - r-whisker=0.3_2=r3.3.2_2
  - r-withr=1.0.2=r3.3.2_0
  - readline=8.2=h8228510_1
  - setuptools=69.0.3=pyhd8ed1ab_0
  - sqlite=3.41.2=h5eee18b_0
  - sysroot_linux-64=2.12=he073ed8_17
  - tk=8.6.12=h1ccaba5_0
  - wheel=0.42.0=pyhd8ed1ab_0
  - xz=5.2.10=h5eee18b_1
  - zlib=1.2.13=h5eee18b_0
  - pip:
      - absl-py==2.1.0
      - aiohttp==3.9.3
      - aiosignal==1.3.1
      - anndata==0.10.5.post1
      - array-api-compat==1.4.1
      - asttokens==2.4.1
      - async-timeout==4.0.3
      - attrs==23.2.0
      - certifi==2024.2.2
      - cffi==1.16.0
      - charset-normalizer==3.3.2
      - chex==0.1.85
      - click==8.1.7
      - cmake==3.28.3
      - comm==0.2.1
      - contextlib2==21.6.0
      - contourpy==1.2.0
      - cryptography==38.0.4
      - cycler==0.12.1
      - datasets==2.14.5
      - debugpy==1.8.1
      - decorator==5.1.1
      - deprecated==1.2.14
      - dill==0.3.7
      - docker-pycreds==0.4.0
      - docrep==0.3.2
      - einops==0.7.0
      - etils==1.7.0
      - exceptiongroup==1.2.0
      - executing==2.0.1
      - filelock==3.13.1
      - flash-attn==1.0.4
      - flax==0.8.1
      - fonttools==4.49.0
      - frozenlist==1.4.1
      - fsspec==2023.6.0
      - gitdb==4.0.11
      - gitpython==3.1.42
      - grpcio==1.60.1
      - h5py==3.10.0
      - huggingface-hub==0.20.3
      - idna==3.6
      - igraph==0.11.4
      - importlib-resources==6.1.1
      - ipaddress==1.0.23
      - ipykernel==6.29.2
      - ipython==8.21.0
      - jax==0.4.24
      - jaxlib==0.4.24
      - jedi==0.19.1
      - jinja2==3.1.3
      - joblib==1.3.2
      - jupyter-client==8.6.0
      - jupyter-core==5.7.1
      - kiwisolver==1.4.5
      - leidenalg==0.10.2
      - lightning==2.1.4
      - lightning-utilities==0.10.1
      - lit==17.0.6
      - llvmlite==0.42.0
      - markdown-it-py==3.0.0
      - markupsafe==2.1.5
      - matplotlib==3.8.3
      - matplotlib-inline==0.1.6
      - mdurl==0.1.2
      - ml-collections==0.1.1
      - ml-dtypes==0.3.2
      - mpmath==1.3.0
      - msgpack==1.0.7
      - mudata==0.2.3
      - multidict==6.0.5
      - multipledispatch==1.0.0
      - multiprocess==0.70.15
      - natsort==8.4.0
      - nest-asyncio==1.6.0
      - networkx==3.2.1
      - numba==0.59.0
      - numpy==1.24.4
      - numpyro==0.13.2
      - 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-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==2.19.3
      - nvidia-nvjitlink-cu12==12.3.101
      - nvidia-nvtx-cu11==11.7.91
      - nvidia-nvtx-cu12==12.1.105
      - opt-einsum==3.3.0
      - optax==0.1.9
      - orbax-checkpoint==0.5.3
      - packaging==23.2
      - pandas==1.5.3
      - parso==0.8.3
      - pathtools==0.1.2
      - patsy==0.5.6
      - pexpect==4.9.0
      - pillow==10.2.0
      - platformdirs==4.2.0
      - promise==2.3
      - prompt-toolkit==3.0.43
      - protobuf==3.20.3
      - psutil==5.9.8
      - ptyprocess==0.7.0
      - pure-eval==0.2.2
      - pyarrow==15.0.0
      - pycparser==2.21
      - pydot==2.0.0
      - pygments==2.17.2
      - pyjwt==2.8.0
      - pynndescent==0.5.11
      - pyopenssl==22.1.0
      - pyparsing==3.1.1
      - pyro-api==0.1.2
      - pyro-ppl==1.8.6
      - python-dateutil==2.8.2
      - pytorch-lightning==2.2.0.post0
      - pytz==2024.1
      - pyyaml==6.0.1
      - pyzmq==25.1.2
      - regex==2023.12.25
      - requests==2.31.0
      - rich==13.7.0
      - safetensors==0.4.2
      - scanpy==1.9.8
      - schedule==1.2.1
      - scib==1.1.4
      - scikit-learn==1.4.1.post1
      - scikit-misc==0.3.1
      - scipy==1.12.0
      - scvi-tools==1.1.0.post2
      - seaborn==0.13.2
      - sentry-sdk==1.40.4
      - session-info==1.0.0
      - setproctitle==1.3.3
      - shortuuid==1.0.11
      - six==1.16.0
      - smmap==5.0.1
      - stack-data==0.6.3
      - statsmodels==0.14.1
      - stdlib-list==0.10.0
      - sympy==1.12
      - tensorstore==0.1.53
      - texttable==1.7.0
      - threadpoolctl==3.3.0
      - tokenizers==0.13.3
      - toolz==0.12.1
      - torch==1.13.0+cu117
      - torchaudio==0.13.0+cu117
      - torchmetrics==1.3.1
      - torchtext==0.14.0
      - torchvision==0.14.0+cu117
      - tornado==6.4
      - tqdm==4.66.2
      - traitlets==5.14.1
      - transformers==4.33.2
      - triton==2.2.0
      - typing-extensions==4.9.0
      - tzdata==2024.1
      - umap-learn==0.5.5
      - urllib3==1.26.18
      - wcwidth==0.2.13
      - wrapt==1.16.0
      - xxhash==3.4.1
      - yarl==1.9.4
      - zipp==3.17.0
prefix: /home/tiger/miniconda3/envs/scgpt_2

I referenced rpeys's comment. https://github.com/bowang-lab/scGPT/issues/69#issuecomment-1737520314

[ChloeXWang]

name: scGPT_base
channels:
  - defaults
dependencies:
  - _libgcc_mutex=0.1=main
  - _openmp_mutex=5.1=1_gnu
  - _r-mutex=1.0.0=anacondar_1
  - _sysroot_linux-64_curr_repodata_hack=3=haa98f57_10
  - binutils_impl_linux-64=2.38=h2a08ee3_1
  - binutils_linux-64=2.38.0=hc2dff05_0
  - blas=1.0=openblas
  - bwidget=1.9.16=h9eba36c_0
  - bzip2=1.0.8=h5eee18b_5
  - c-ares=1.19.1=h5eee18b_0
  - ca-certificates=2024.3.11=h06a4308_0
  - cairo=1.16.0=hb05425b_5
  - curl=8.5.0=hdbd6064_0
  - expat=2.5.0=h6a678d5_0
  - fontconfig=2.14.1=h4c34cd2_2
  - freetype=2.12.1=h4a9f257_0
  - fribidi=1.0.10=h7b6447c_0
  - gcc_impl_linux-64=11.2.0=h1234567_1
  - gcc_linux-64=11.2.0=h5c386dc_0
  - gfortran_impl_linux-64=11.2.0=h1234567_1
  - gfortran_linux-64=11.2.0=hc2dff05_0
  - glib=2.78.4=h6a678d5_0
  - glib-tools=2.78.4=h6a678d5_0
  - graphite2=1.3.14=h295c915_1
  - gxx_impl_linux-64=11.2.0=h1234567_1
  - gxx_linux-64=11.2.0=hc2dff05_0
  - harfbuzz=4.3.0=hf52aaf7_2
  - icu=73.1=h6a678d5_0
  - jpeg=9e=h5eee18b_1
  - kernel-headers_linux-64=3.10.0=h57e8cba_10
  - krb5=1.20.1=h143b758_1
  - ld_impl_linux-64=2.38=h1181459_1
  - lerc=3.0=h295c915_0
  - libcurl=8.5.0=h251f7ec_0
  - libdeflate=1.17=h5eee18b_1
  - libedit=3.1.20230828=h5eee18b_0
  - libev=4.33=h7f8727e_1
  - libffi=3.4.4=h6a678d5_0
  - libgcc-devel_linux-64=11.2.0=h1234567_1
  - libgcc-ng=11.2.0=h1234567_1
  - libgfortran-ng=11.2.0=h00389a5_1
  - libgfortran5=11.2.0=h1234567_1
  - libglib=2.78.4=hdc74915_0
  - libgomp=11.2.0=h1234567_1
  - libiconv=1.16=h7f8727e_2
  - libnghttp2=1.57.0=h2d74bed_0
  - libopenblas=0.3.21=h043d6bf_0
  - libpng=1.6.39=h5eee18b_0
  - libssh2=1.10.0=hdbd6064_2
  - libstdcxx-devel_linux-64=11.2.0=h1234567_1
  - libstdcxx-ng=11.2.0=h1234567_1
  - libtiff=4.5.1=h6a678d5_0
  - libuuid=1.41.5=h5eee18b_0
  - libwebp-base=1.3.2=h5eee18b_0
  - libxcb=1.15=h7f8727e_0
  - libxml2=2.10.4=hf1b16e4_1
  - lz4-c=1.9.4=h6a678d5_0
  - make=4.2.1=h1bed415_1
  - ncurses=6.4=h6a678d5_0
  - openssl=3.0.13=h7f8727e_0
  - pango=1.50.7=h05da053_0
  - pcre2=10.42=hebb0a14_0
  - pip=23.3.1=py39h06a4308_0
  - pixman=0.40.0=h7f8727e_1
  - python=3.9.19=h955ad1f_0
  - r=3.6.0=r43_0
  - r-base=4.3.1=h1ae530e_0
  - r-boot=1.3_28.1=r43h6115d3f_0
  - r-class=7.3_22=r43h76d94ec_0
  - r-cluster=2.1.4=r43h640688f_0
  - r-codetools=0.2_19=r43h6115d3f_0
  - r-foreign=0.8_85=r43h76d94ec_0
  - r-kernsmooth=2.23_22=r43h640688f_0
  - r-lattice=0.22_5=r43h76d94ec_0
  - r-mass=7.3_60=r43h76d94ec_0
  - r-matrix=1.6_1.1=r43h76d94ec_0
  - r-mgcv=1.9_0=r43h76d94ec_0
  - r-nlme=3.1_163=r43h640688f_0
  - r-nnet=7.3_19=r43h76d94ec_0
  - r-recommended=3.6.0=r43_0
  - r-rpart=4.1.21=r43h76d94ec_0
  - r-spatial=7.3_17=r43h76d94ec_0
  - r-survival=3.5_7=r43h76d94ec_0
  - readline=8.2=h5eee18b_0
  - sqlite=3.41.2=h5eee18b_0
  - sysroot_linux-64=2.17=h57e8cba_10
  - tk=8.6.12=h1ccaba5_0
  - tktable=2.10=h3d55465_1
  - xz=5.4.6=h5eee18b_0
  - zlib=1.2.13=h5eee18b_0
  - zstd=1.5.5=hc292b87_0
  - pip:
      - absl-py==0.15.0
      - aiohttp==3.8.1
      - aiosignal==1.2.0
      - anndata==0.8.0
      - anndata2ri==1.0.6
      - appdirs==1.4.4
      - argon2-cffi==21.3.0
      - argon2-cffi-bindings==21.2.0
      - async-timeout==4.0.2
      - attrs==21.4.0
      - backcall==0.2.0
      - beautifulsoup4==4.11.1
      - bleach==5.0.0
      - cached-property==1.5.2
      - cachetools==4.2.4
      - cell-gears==0.0.1
      - certifi==2022.6.15
      - cffi==1.15.0
      - charset-normalizer==2.0.12
      - chex==0.1.3
      - click==8.1.7
      - colorama==0.4.5
      - commonmark==0.9.1
      - cycler==0.11.0
      - datasets==2.3.2
      - debugpy==1.6.0
      - decorator==5.1.1
      - defusedxml==0.7.1
      - deprecated==1.2.13
      - dill==0.3.5.1
      - dm-tree==0.1.7
      - docker-pycreds==0.4.0
      - docrep==0.3.2
      - dunamai==1.12.0
      - einops==0.7.0
      - entrypoints==0.4
      - et-xmlfile==1.1.0
      - etils==0.9.0
      - faiss-cpu==1.8.0
      - faiss-gpu==1.7.2
      - fastjsonschema==2.15.3
      - filelock==3.7.1
      - flash-attn==1.0.4
      - flatbuffers==1.12
      - flax==0.4.1
      - fonttools==4.33.3
      - frozenlist==1.3.0
      - fsspec==2024.3.1
      - future==0.18.2
      - get-version==3.5.4
      - gitdb==4.0.11
      - gitpython==3.1.42
      - google-auth==1.35.0
      - google-auth-oauthlib==0.4.6
      - grpcio==1.47.0
      - h5py==3.1.0
      - huggingface-hub==0.17.3
      - idna==3.3
      - igraph==0.9.11
      - importlib-metadata==4.12.0
      - importlib-resources==5.8.0
      - ipykernel==6.15.0
      - ipython==7.34.0
      - ipython-genutils==0.2.0
      - ipywidgets==7.7.1
      - jax==0.4.13
      - jaxlib==0.4.13
      - jedi==0.18.1
      - jinja2==3.1.2
      - joblib==1.1.0
      - jsonschema==4.6.0
      - jupyter-client==7.3.4
      - jupyter-core==4.10.0
      - jupyterlab-pygments==0.2.2
      - jupyterlab-widgets==1.1.1
      - kiwisolver==1.4.3
      - leidenalg==0.8.10
      - llvmlite==0.38.1
      - louvain==0.7.1
      - markdown==3.3.7
      - markupsafe==2.1.1
      - matplotlib==3.5.2
      - matplotlib-inline==0.1.3
      - mistune==0.8.4
      - ml-dtypes==0.3.2
      - more-itertools==8.13.0
      - mpmath==1.3.0
      - msgpack==1.0.4
      - multidict==6.0.2
      - multipledispatch==0.6.0
      - multiprocess==0.70.13
      - natsort==8.1.0
      - nbclient==0.6.4
      - nbconvert==6.5.0
      - nbformat==5.4.0
      - nest-asyncio==1.5.5
      - networkx==2.6.3
      - notebook==6.4.12
      - numba==0.55.2
      - numpy==1.21.6
      - numpyro==0.9.2
      - nvidia-cublas-cu11==11.10.3.66
      - nvidia-cublas-cu12==12.1.3.1
      - nvidia-cuda-cupti-cu12==12.1.105
      - 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-cu12==11.0.2.54
      - nvidia-curand-cu12==10.3.2.106
      - nvidia-cusolver-cu12==11.4.5.107
      - nvidia-cusparse-cu12==12.1.0.106
      - nvidia-nccl-cu12==2.18.1
      - nvidia-nvjitlink-cu12==12.4.99
      - nvidia-nvtx-cu12==12.1.105
      - oauthlib==3.2.0
      - openpyxl==3.0.10
      - opt-einsum==3.3.0
      - optax==0.1.2
      - orbax==0.1.0
      - packaging==21.3
      - pandas==1.3.5
      - pandocfilters==1.5.0
      - parso==0.8.3
      - patsy==0.5.2
      - pexpect==4.8.0
      - pickleshare==0.7.5
      - pillow==9.1.1
      - pluggy==0.13.1
      - prometheus-client==0.14.1
      - prompt-toolkit==3.0.29
      - protobuf==3.19.4
      - psutil==5.9.1
      - ptyprocess==0.7.0
      - py==1.11.0
      - pyarrow==8.0.0
      - pyasn1==0.4.8
      - pyasn1-modules==0.2.8
      - pycparser==2.21
      - pydeprecate==0.3.1
      - pydot==1.4.2
      - pygments==2.12.0
      - pynndescent==0.5.7
      - pyparsing==3.0.9
      - pyro-api==0.1.2
      - pyro-ppl==1.8.0
      - pyrsistent==0.18.1
      - pytest==5.4.3
      - python-dateutil==2.8.2
      - python-igraph==0.9.11
      - pytorch-lightning==1.5.10
      - pytz==2022.1
      - pytz-deprecation-shim==0.1.0.post0
      - pyyaml==6.0
      - pyzmq==23.2.0
      - regex==2023.12.25
      - requests==2.28.0
      - requests-oauthlib==1.3.1
      - responses==0.18.0
      - rich==11.2.0
      - rpy2==3.4.2
      - rsa==4.8
      - safetensors==0.4.2
      - scanpy==1.9.1
      - scgpt==0.2.1
      - scib==1.0.3
      - scikit-learn==1.0.2
      - scikit-misc==0.1.4
      - scipy==1.7.3
      - scvi-tools==0.16.4
      - seaborn==0.11.2
      - send2trash==1.8.0
      - sentry-sdk==1.43.0
      - session-info==1.0.0
      - setproctitle==1.3.3
      - setuptools==59.5.0
      - setuptools-scm==7.0.2
      - six==1.15.0
      - smmap==5.0.1
      - soupsieve==2.3.2.post1
      - statsmodels==0.13.2
      - stdlib-list==0.8.0
      - sympy==1.12
      - tensorboard==2.8.0
      - tensorboard-data-server==0.6.1
      - tensorboard-plugin-wit==1.8.1
      - tensorstore==0.1.28
      - terminado==0.15.0
      - texttable==1.6.4
      - threadpoolctl==3.1.0
      - tinycss2==1.1.1
      - tokenizers==0.14.1
      - tomli==2.0.1
      - toolz==0.11.2
      - torch==2.1.2
      - torch-geometric==2.3.0
      - torchaudio==2.1.2+cu121
      - torchdata==0.7.1
      - torchmetrics==0.9.1
      - torchtext==0.16.2
      - torchvision==0.16.2+cu121
      - tornado==6.1
      - tqdm==4.64.0
      - traitlets==5.3.0
      - transformers==4.34.0
      - triton==2.1.0
      - typing-extensions==4.2.0
      - tzdata==2022.1
      - tzlocal==4.2
      - umap-learn==0.5.3
      - urllib3==1.26.12
      - wandb==0.16.4
      - wcwidth==0.2.5
      - webencodings==0.5.1
      - werkzeug==2.1.2
      - wheel==0.37.1
      - widgetsnbextension==3.6.1
      - wrapt==1.12.1
      - xxhash==3.0.0
      - yarl==1.7.2
      - zipp==3.8.0
prefix: /home/chloewxq/.conda/envs/scGPT_base

Thank you for sharing the env! Here is to share another option if you work with newer version of cuda.

[epalo]

Hello!

I encountered an issue when installing scgpt led to an automatic upgrade of PyTorch to version 2.1.2, which is incompatible with my system's CUDA version 11.6 and NVIDIA driver version 510.54. The scgpt installation uninstalled my existing torch 1.13.0, which is the version compatible with my CUDA.

To resolve this, I manually reverted to the correct version of PyTorch after the installation of scgpt and related packages. I also made sure to install a compatible version of pyro-ppl.

Here is the Singularity definition file that I used to successfully build my image:

Bootstrap: docker
From: pytorch/pytorch:1.13.0-cuda11.6-cudnn8-devel

%post
    # Set environment variable to prevent interactive prompts
    export DEBIAN_FRONTEND=noninteractive

    # Update the package list and install packages
    apt-get update -y
    apt-get install -y git r-base tzdata

    # Install Python packages using pip
    pip install packaging
    pip install scgpt "flash-attn<1.0.5"
    pip install markupsafe==2.0.1
    pip install wandb
    pip uninstall torch -y
    pip install torch==1.13.0+cu116 -f https://download.pytorch.org/whl/torch_stable.html
    pip install pyro-ppl==1.8.6

%environment
    export DEBIAN_FRONTEND=noninteractive
    export PATH=/opt/conda/bin:$PATH

%runscript
    exec "$@"

I hope this helps anyone facing similar issues!