scgpt.yml

name: scgpt
channels:
  - pytorch
  - nvidia
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=2_gnu
  - _r-mutex=1.0.1=anacondar_1
  - _sysroot_linux-64_curr_repodata_hack=3=h69a702a_13
  - binutils_impl_linux-64=2.40=hf600244_0
  - blas=1.0=mkl
  - brotli=1.0.9=h166bdaf_8
  - brotli-bin=1.0.9=h166bdaf_8
  - bwidget=1.9.14=ha770c72_1
  - bzip2=1.0.8=h7f98852_4
  - c-ares=1.19.1=hd590300_0
  - ca-certificates=2023.5.7=hbcca054_0
  - cairo=1.16.0=ha61ee94_1014
  - cffi=1.15.1=py38h4a40e3a_3
  - charset-normalizer=3.1.0=pyhd8ed1ab_0
  - cuda-cudart=11.7.99=0
  - cuda-cupti=11.7.101=0
  - cuda-libraries=11.7.1=0
  - cuda-nvrtc=11.7.99=0
  - cuda-nvtx=11.7.91=0
  - cuda-runtime=11.7.1=0
  - cudatoolkit=11.7.0=hd8887f6_11
  - curl=8.1.1=h409715c_0
  - expat=2.5.0=hcb278e6_1
  - ffmpeg=4.3=hf484d3e_0
  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
  - font-ttf-inconsolata=3.000=h77eed37_0
  - font-ttf-source-code-pro=2.038=h77eed37_0
  - font-ttf-ubuntu=0.83=hab24e00_0
  - fontconfig=2.14.2=h14ed4e7_0
  - fonts-conda-ecosystem=1=0
  - fonts-conda-forge=1=0
  - freetype=2.12.1=hca18f0e_1
  - fribidi=1.0.10=h36c2ea0_0
  - future=0.18.3=pyhd8ed1ab_0
  - gcc_impl_linux-64=12.2.0=hcc96c02_19
  - gettext=0.21.1=h27087fc_0
  - gfortran_impl_linux-64=12.2.0=h55be85b_19
  - gmp=6.2.1=h58526e2_0
  - gnutls=3.6.13=h85f3911_1
  - graphite2=1.3.13=h58526e2_1001
  - gsl=2.7=he838d99_0
  - gxx_impl_linux-64=12.2.0=hcc96c02_19
  - harfbuzz=6.0.0=h8e241bc_0
  - icu=70.1=h27087fc_0
  - idna=3.4=pyhd8ed1ab_0
  - intel-openmp=2023.1.0=hdb19cb5_46305
  - jpeg=9e=h166bdaf_2
  - kernel-headers_linux-64=4.18.0=he073ed8_0
  - keyutils=1.6.1=h166bdaf_0
  - krb5=1.20.1=h81ceb04_0
  - 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=1_h86c2bf4_netlib
  - libbrotlicommon=1.0.9=h166bdaf_8
  - libbrotlidec=1.0.9=h166bdaf_8
  - libbrotlienc=1.0.9=h166bdaf_8
  - libcblas=3.9.0=5_h92ddd45_netlib
  - libcublas=11.10.3.66=0
  - libcufft=10.7.2.124=h4fbf590_0
  - libcufile=1.6.1.9=0
  - libcurand=10.3.2.106=0
  - libcurl=8.1.1=h409715c_0
  - libcusolver=11.4.0.1=0
  - libcusparse=11.7.4.91=0
  - libdeflate=1.17=h0b41bf4_0
  - libedit=3.1.20191231=he28a2e2_2
  - libev=4.33=h516909a_1
  - libexpat=2.5.0=hcb278e6_1
  - libffi=3.4.2=h7f98852_5
  - libgcc-devel_linux-64=12.2.0=h3b97bd3_19
  - libgcc-ng=12.2.0=h65d4601_19
  - libgfortran-ng=12.2.0=h69a702a_19
  - libgfortran5=12.2.0=h337968e_19
  - libglib=2.76.3=hebfc3b9_0
  - libgomp=12.2.0=h65d4601_19
  - libhwloc=2.9.1=hd6dc26d_0
  - libiconv=1.17=h166bdaf_0
  - libjpeg-turbo=2.1.4=h166bdaf_0
  - liblapack=3.9.0=5_h92ddd45_netlib
  - libnghttp2=1.52.0=h61bc06f_0
  - libnpp=11.7.4.75=0
  - libnsl=2.0.0=h7f98852_0
  - libnvjpeg=11.8.0.2=0
  - libopenblas=0.3.23=pthreads_h80387f5_0
  - libpng=1.6.39=h753d276_0
  - libprotobuf=3.20.3=h3eb15da_0
  - libsanitizer=12.2.0=h46fd767_19
  - libsqlite=3.42.0=h2797004_0
  - libssh2=1.10.0=hf14f497_3
  - libstdcxx-devel_linux-64=12.2.0=h3b97bd3_19
  - libstdcxx-ng=12.2.0=h46fd767_19
  - libtiff=4.5.0=h6adf6a1_2
  - libuuid=2.38.1=h0b41bf4_0
  - libwebp-base=1.3.0=h0b41bf4_0
  - libxcb=1.13=h7f98852_1004
  - libxml2=2.10.3=hca2bb57_4
  - libzlib=1.2.13=h166bdaf_4
  - make=4.3=hd18ef5c_1
  - mkl=2023.1.0=h6d00ec8_46342
  - ncurses=6.3=h27087fc_1
  - nettle=3.6=he412f7d_0
  - openh264=2.1.1=h780b84a_0
  - openjpeg=2.5.0=hfec8fc6_2
  - openssl=3.1.0=hd590300_3
  - pango=1.50.14=hd33c08f_0
  - pcre2=10.40=hc3806b6_0
  - pip=23.1.2=pyhd8ed1ab_0
  - pixman=0.40.0=h36c2ea0_0
  - pthread-stubs=0.4=h36c2ea0_1001
  - pycparser=2.21=pyhd8ed1ab_0
  - pysocks=1.7.1=pyha2e5f31_6
  - python=3.8.16=he550d4f_1_cpython
  - python_abi=3.8=3_cp38
  - pytorch=1.13.0=py3.8_cuda11.7_cudnn8.5.0_0
  - pytorch-cuda=11.7=h778d358_5
  - pytorch-mutex=1.0=cuda
  - pyyaml=6.0=py38h0a891b7_5
  - r=4.2=r42hd8ed1ab_1006
  - r-base=4.2.3=ha7d60f8_0
  - r-boot=1.3_28.1=r42hc72bb7e_0
  - r-class=7.3_22=r42h57805ef_0
  - r-cluster=2.1.4=r42h8da6f51_0
  - r-codetools=0.2_19=r42hc72bb7e_0
  - r-foreign=0.8_84=r42h133d619_0
  - r-kernsmooth=2.23_21=r42h13b3f57_0
  - r-lattice=0.21_8=r42h133d619_0
  - r-mass=7.3_60=r42h57805ef_0
  - r-matrix=1.5_4.1=r42h316c678_0
  - r-mgcv=1.8_42=r42he1ae0d6_0
  - r-nlme=3.1_162=r42hac0b197_0
  - r-nnet=7.3_19=r42h57805ef_0
  - r-recommended=4.2=r42hd8ed1ab_1005
  - r-rpart=4.1.19=r42h06615bd_0
  - r-spatial=7.3_16=r42h133d619_0
  - r-survival=3.5_5=r42h133d619_0
  - readline=8.2=h8228510_1
  - requests=2.31.0=pyhd8ed1ab_0
  - sed=4.8=he412f7d_0
  - sysroot_linux-64=2.28=he073ed8_0
  - tbb=2021.9.0=hf52228f_0
  - tk=8.6.12=h27826a3_0
  - tktable=2.10=hb7b940f_3
  - torchaudio=0.13.0=py38_cu117
  - torchvision=0.14.0=py38_cu117
  - typing-extensions=4.6.0=hd8ed1ab_0
  - typing_extensions=4.6.0=pyha770c72_0
  - wheel=0.40.0=pyhd8ed1ab_0
  - xorg-kbproto=1.0.7=h7f98852_1002
  - xorg-libice=1.0.10=h7f98852_0
  - xorg-libsm=1.2.3=hd9c2040_1000
  - xorg-libx11=1.8.4=h0b41bf4_0
  - xorg-libxau=1.0.11=hd590300_0
  - xorg-libxdmcp=1.1.3=h7f98852_0
  - xorg-libxext=1.3.4=h0b41bf4_2
  - xorg-libxrender=0.9.10=h7f98852_1003
  - xorg-libxt=1.2.1=h7f98852_2
  - xorg-renderproto=0.11.1=h7f98852_1002
  - xorg-xextproto=7.3.0=h0b41bf4_1003
  - xorg-xproto=7.0.31=h7f98852_1007
  - xz=5.2.6=h166bdaf_0
  - yaml=0.2.5=h7f98852_2
  - zlib=1.2.13=h166bdaf_4
  - zstd=1.5.2=h3eb15da_6
  - pip:
      - absl-py==1.4.0
      - aiohttp==3.8.4
      - aiosignal==1.3.1
      - anndata==0.9.1
      - anndata2ri==1.1
      - anyio==3.6.2
      - appdirs==1.4.4
      - argon2-cffi==21.3.0
      - argon2-cffi-bindings==21.2.0
      - arrow==1.2.3
      - asttokens==2.2.1
      - async-timeout==4.0.2
      - attrs==23.1.0
      - backcall==0.2.0
      - backports-zoneinfo==0.2.1
      - beautifulsoup4==4.12.2
      - bleach==6.0.0
      - cached-property==1.5.2
      - cachetools==5.3.0
      - certifi==2023.5.7
      - chex==0.1.7
      - click==8.1.3
      - comm==0.1.3
      - contourpy==1.0.7
      - cycler==0.11.0
      - datasets==2.12.0
      - debugpy==1.6.7
      - decorator==5.1.1
      - defusedxml==0.7.1
      - deprecated==1.2.13
      - dill==0.3.6
      - dm-tree==0.1.8
      - docker-pycreds==0.4.0
      - docrep==0.3.2
      - dunamai==1.17.0
      - einops==0.6.1
      - et-xmlfile==1.1.0
      - etils==1.3.0
      - executing==1.2.0
      - fastjsonschema==2.17.1
      - filelock==3.12.0
      - flash-attn==1.0.4
      - flax==0.6.10
      - fonttools==4.39.4
      - fqdn==1.5.1
      - frozenlist==1.3.3
      - fsspec==2023.5.0
      - get-version==3.5.4
      - gitdb==4.0.10
      - gitpython==3.1.31
      - google-auth==2.18.1
      - google-auth-oauthlib==1.0.0
      - grpcio==1.55.0
      - h5py==3.8.0
      - huggingface-hub==0.14.1
      - igraph==0.9.11
      - importlib-metadata==6.6.0
      - importlib-resources==5.12.0
      - ipykernel==6.23.1
      - ipython==8.12.2
      - ipython-genutils==0.2.0
      - ipywidgets==8.0.6
      - isoduration==20.11.0
      - jax==0.4.10
      - jaxlib==0.4.10
      - jedi==0.18.2
      - jinja2==3.1.2
      - joblib==1.2.0
      - jsonpointer==2.3
      - jsonschema==4.17.3
      - jupyter==1.0.0
      - jupyter-client==8.2.0
      - jupyter-console==6.6.3
      - jupyter-core==5.3.0
      - jupyter-events==0.6.3
      - jupyter-server==2.5.0
      - jupyter-server-terminals==0.4.4
      - jupyterlab-pygments==0.2.2
      - jupyterlab-widgets==3.0.7
      - kiwisolver==1.4.4
      - leidenalg==0.8.10
      - llvmlite==0.40.0
      - loompy==3.0.7
      - louvain==0.7.2
      - markdown==3.4.3
      - markdown-it-py==2.2.0
      - markupsafe==2.1.2
      - matplotlib==3.7.1
      - matplotlib-inline==0.1.6
      - mdurl==0.1.2
      - mistune==2.0.5
      - ml-dtypes==0.1.0
      - msgpack==1.0.5
      - multidict==6.0.4
      - multipledispatch==0.6.0
      - multiprocess==0.70.14
      - natsort==8.3.1
      - nbclassic==1.0.0
      - nbclient==0.8.0
      - nbconvert==7.4.0
      - nbformat==5.8.0
      - nest-asyncio==1.5.6
      - networkx==3.1
      - ninja==1.11.1
      - notebook==6.5.4
      - notebook-shim==0.2.3
      - numba==0.57.0
      - numpy==1.21.1
      - numpy-groupies==0.9.22
      - numpyro==0.11.0
      - nvidia-cublas-cu11==11.10.3.66
      - nvidia-cuda-nvrtc-cu11==11.7.99
      - nvidia-cuda-runtime-cu11==11.7.99
      - nvidia-cudnn-cu11==8.5.0.96
      - oauthlib==3.2.2
      - openai==0.27.7
      - openpyxl==3.1.2
      - opt-einsum==3.3.0
      - optax==0.1.5
      - orbax-checkpoint==0.2.3
      - packaging==23.1
      - pandas==1.3.5
      - pandocfilters==1.5.0
      - parso==0.8.3
      - pathtools==0.1.2
      - patsy==0.5.3
      - pexpect==4.8.0
      - pickleshare==0.7.5
      - pillow==9.5.0
      - pkgutil-resolve-name==1.3.10
      - platformdirs==3.5.1
      - prometheus-client==0.16.0
      - prompt-toolkit==3.0.38
      - protobuf==3.20.1
      - psutil==5.9.5
      - ptyprocess==0.7.0
      - pure-eval==0.2.2
      - pyarrow==12.0.0
      - pyasn1==0.5.0
      - pyasn1-modules==0.3.0
      - pydeprecate==0.3.1
      - pydot==1.4.2
      - pygments==2.15.1
      - pynndescent==0.5.10
      - pyparsing==3.0.9
      - pyro-api==0.1.2
      - pyro-ppl==1.8.4
      - pyrsistent==0.19.3
      - python-dateutil==2.8.2
      - python-json-logger==2.0.7
      - pytorch-lightning==1.5.10
      - pytz==2023.3
      - pytz-deprecation-shim==0.1.0.post0
      - pyzmq==25.0.2
      - qtconsole==5.4.3
      - qtpy==2.3.1
      - regex==2023.5.5
      - requests-oauthlib==1.3.1
      - responses==0.18.0
      - rfc3339-validator==0.1.4
      - rfc3986-validator==0.1.1
      - rich==13.3.5
      - rpy2==3.5.12
      - rsa==4.9
      - scanpy==1.9.3
      - scgpt==0.1.2.post1
      - scib==1.0.4
      - scikit-learn==1.2.2
      - scikit-misc==0.1.4
      - scipy==1.10.1
      - scvi-tools==0.16.4
      - seaborn==0.12.2
      - send2trash==1.8.2
      - sentry-sdk==1.24.0
      - session-info==1.0.0
      - setproctitle==1.3.2
      - setuptools==59.5.0
      - six==1.16.0
      - smmap==5.0.0
      - sniffio==1.3.0
      - sophia-optimizer==0.2.1
      - soupsieve==2.4.1
      - stack-data==0.6.2
      - statsmodels==0.14.0
      - stdlib-list==0.8.0
      - tensorboard==2.13.0
      - tensorboard-data-server==0.7.0
      - tensorstore==0.1.36
      - terminado==0.17.1
      - texttable==1.6.7
      - threadpoolctl==3.1.0
      - tinycss2==1.2.1
      - tokenizers==0.13.3
      - toolz==0.12.0
      - torch==1.13.0
      - torchmetrics==0.11.4
      - torchtext==0.14.0
      - tornado==6.3.2
      - tqdm==4.65.0
      - traitlets==5.9.0
      - transformers==4.29.2
      - tzdata==2023.3
      - tzlocal==4.3
      - umap-learn==0.5.3
      - uri-template==1.2.0
      - urllib3==1.26.16
      - wandb==0.15.3
      - wcwidth==0.2.6
      - webcolors==1.13
      - webencodings==0.5.1
      - websocket-client==1.5.2
      - werkzeug==2.3.4
      - widgetsnbextension==4.0.7
      - wrapt==1.15.0
      - xxhash==3.2.0
      - yarl==1.9.2
      - zipp==3.15.0
prefix: /gpfs/gibbs/project/zhao/tl688/conda_envs/scgpt