x86_64 default spatial notebook f046cc86b8ad - huchlab/sequencing-docker-stacks GitHub Wiki

Build manifest for image: spatial-notebook:f046cc86b8ad

Build Info

  • Build timestamp: 2025-04-07T15:50:16Z
  • Docker image: quay.io/fbnrst/spatial-notebook:f046cc86b8ad
  • Docker image size: 9.07GB
  • Git commit SHA: f046cc86b8ade43871cd77dbccbc211a71e240fe
  • Git commit message:
Move 'scikit-misc' installation to pip section in Dockerfile

Python Packages

Python 3.12.9

conda info:

     active environment : None
       user config file : /home/jovyan/.condarc
 populated config files : /opt/conda/.condarc
                          /home/jovyan/.condarc
          conda version : 25.3.1
    conda-build version : not installed
         python version : 3.12.9.final.0
                 solver : libmamba (default)
       virtual packages : __archspec=1=zen2
                          __conda=25.3.1=0
                          __glibc=2.39=0
                          __linux=6.8.0=0
                          __unix=0=0
       base environment : /opt/conda  (writable)
      conda av data dir : /opt/conda/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
          package cache : /opt/conda/pkgs
                          /home/jovyan/.conda/pkgs
       envs directories : /opt/conda/envs
                          /home/jovyan/.conda/envs
               platform : linux-64
             user-agent : conda/25.3.1 requests/2.32.3 CPython/3.12.9 Linux/6.8.0-1021-azure ubuntu/24.04.2 glibc/2.39 solver/libmamba conda-libmamba-solver/25.3.0 libmambapy/2.0.8
                UID:GID : 1000:100
             netrc file : None
           offline mode : False

mamba info:

       libmamba version : 2.0.8
          mamba version : 2.0.8
           curl version : libcurl/8.13.0 OpenSSL/3.4.1 zlib/1.3.1 zstd/1.5.7 libssh2/1.11.1 nghttp2/1.64.0
     libarchive version : libarchive 3.7.7 zlib/1.3.1 liblzma/5.6.3 bz2lib/1.0.8 liblz4/1.10.0 libzstd/1.5.6
       envs directories : /opt/conda/envs
          package cache : /opt/conda/pkgs
                          /home/jovyan/.mamba/pkgs
            environment : base
           env location : /opt/conda
      user config files : /home/jovyan/.mambarc
 populated config files : /home/jovyan/.condarc
                          /opt/conda/.condarc
       virtual packages : __unix=0=0
                          __linux=6.8.0=0
                          __glibc=2.39=0
                          __archspec=1=x86_64_v3
               channels : https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
       base environment : /opt/conda
               platform : linux-64

mamba list:

List of packages in environment: "/opt/conda"

  Name                               Version         Build                         Channel
────────────────────────────────────────────────────────────────────────────────────────────────
  _libgcc_mutex                      0.1             conda_forge                   conda-forge
  _openmp_mutex                      4.5             2_gnu                         conda-forge
  _r-mutex                           1.0.1           anacondar_1                   conda-forge
  absl-py                            2.2.0           pyhd8ed1ab_0                  conda-forge
  adjusttext                         1.3.0           pyhd8ed1ab_0                  conda-forge
  aiohappyeyeballs                   2.6.1           pyhd8ed1ab_0                  conda-forge
  aiohttp                            3.11.16         py312h178313f_0               conda-forge
  aiosignal                          1.3.2           pyhd8ed1ab_0                  conda-forge
  alembic                            1.15.2          pyhd8ed1ab_0                  conda-forge
  altair                             5.5.0           pyhd8ed1ab_1                  conda-forge
  anndata                            0.11.4          pyhd8ed1ab_0                  conda-forge
  anndata2ri                         1.3.2           pyhdfd78af_0                  bioconda
  annotated-types                    0.7.0           pyhd8ed1ab_1                  conda-forge
  anyio                              4.9.0           pyh29332c3_0                  conda-forge
  aom                                3.9.1           hac33072_0                    conda-forge
  arboreto                           0.1.6           pyh3252c3a_0                  bioconda
  archspec                           0.2.5           pyhd8ed1ab_0                  conda-forge
  argcomplete                        3.6.2           pyhd8ed1ab_0                  conda-forge
  argon2-cffi                        23.1.0          pyhd8ed1ab_1                  conda-forge
  argon2-cffi-bindings               21.2.0          py312h66e93f0_5               conda-forge
  arpack                             3.9.1           nompi_hf03ea27_102            conda-forge
  array-api-compat                   1.11.2          pyh29332c3_0                  conda-forge
  arrow                              1.3.0           pyhd8ed1ab_1                  conda-forge
  asciitree                          0.3.3           py_2                          conda-forge
  astor                              0.8.1           pyhd8ed1ab_1                  conda-forge
  asttokens                          3.0.0           pyhd8ed1ab_1                  conda-forge
  async-lru                          2.0.5           pyh29332c3_0                  conda-forge
  async_generator                    1.10            pyhd8ed1ab_2                  conda-forge
  attr                               2.5.1           h166bdaf_1                    conda-forge
  attrs                              25.3.0          pyh71513ae_0                  conda-forge
  aws-c-auth                         0.8.0           hb921021_15                   conda-forge
  aws-c-cal                          0.8.1           h1a47875_3                    conda-forge
  aws-c-common                       0.10.6          hb9d3cd8_0                    conda-forge
  aws-c-compression                  0.3.0           h4e1184b_5                    conda-forge
  aws-c-event-stream                 0.5.0           h7959bf6_11                   conda-forge
  aws-c-http                         0.9.2           hefd7a92_4                    conda-forge
  aws-c-io                           0.15.3          h173a860_6                    conda-forge
  aws-c-mqtt                         0.11.0          h11f4f37_12                   conda-forge
  aws-c-s3                           0.7.7           hf454442_0                    conda-forge
  aws-c-sdkutils                     0.2.1           h4e1184b_4                    conda-forge
  aws-checksums                      0.2.2           h4e1184b_4                    conda-forge
  aws-crt-cpp                        0.29.7          hd92328a_7                    conda-forge
  aws-sdk-cpp                        1.11.458        hc430e4a_4                    conda-forge
  azure-core-cpp                     1.14.0          h5cfcd09_0                    conda-forge
  azure-identity-cpp                 1.10.0          h113e628_0                    conda-forge
  azure-storage-blobs-cpp            12.13.0         h3cf044e_1                    conda-forge
  azure-storage-common-cpp           12.8.0          h736e048_1                    conda-forge
  azure-storage-files-datalake-cpp   12.12.0         ha633028_1                    conda-forge
  babel                              2.17.0          pyhd8ed1ab_0                  conda-forge
  bbknn                              1.6.0           py312h0fa9677_4               bioconda
  beautifulsoup4                     4.13.3          pyha770c72_0                  conda-forge
  binutils_impl_linux-64             2.43            h4bf12b8_4                    conda-forge
  bioconductor-beachmat              2.18.0          r43hf17093f_1                 bioconda
  bioconductor-biobase               2.62.0          r43ha9d7317_3                 bioconda
  bioconductor-biocgenerics          0.48.1          r43hdfd78af_2                 bioconda
  bioconductor-biocio                1.12.0          r43hdfd78af_0                 bioconda
  bioconductor-biocneighbors         1.20.0          r43hf17093f_1                 bioconda
  bioconductor-biocparallel          1.36.0          r43hf17093f_2                 bioconda
  bioconductor-biocsingular          1.18.0          r43hf17093f_1                 bioconda
  bioconductor-biocviews             1.70.0          r43hdfd78af_0                 bioconda
  bioconductor-bluster               1.12.0          r43hf17093f_1                 bioconda
  bioconductor-complexheatmap        2.18.0          r43hdfd78af_0                 bioconda
  bioconductor-data-packages         20250401        hdfd78af_0                    bioconda
  bioconductor-delayedarray          0.28.0          r43ha9d7317_2                 bioconda
  bioconductor-delayedmatrixstats    1.24.0          r43hdfd78af_0                 bioconda
  bioconductor-edger                 4.0.16          r43hf17093f_1                 bioconda
  bioconductor-genomeinfodb          1.38.1          r43hdfd78af_1                 bioconda
  bioconductor-genomeinfodbdata      1.2.11          r43hdfd78af_1                 bioconda
  bioconductor-genomicranges         1.54.1          r43ha9d7317_2                 bioconda
  bioconductor-graph                 1.80.0          r43ha9d7317_1                 bioconda
  bioconductor-hdf5array             1.30.0          r43ha9d7317_1                 bioconda
  bioconductor-hsmmsinglecell        1.22.0          r43hdfd78af_0                 bioconda
  bioconductor-iranges               2.36.0          r43ha9d7317_2                 bioconda
  bioconductor-limma                 3.58.1          r43ha9d7317_1                 bioconda
  bioconductor-loomexperiment        1.20.0          r43hdfd78af_0                 bioconda
  bioconductor-mast                  1.28.0          r43hdfd78af_0                 bioconda
  bioconductor-matrixgenerics        1.14.0          r43hdfd78af_3                 bioconda
  bioconductor-metapod               1.10.0          r43hf17093f_3                 bioconda
  bioconductor-milor                 1.10.0          r43hdfd78af_0                 bioconda
  bioconductor-monocle               2.30.0          r43hf17093f_1                 bioconda
  bioconductor-rbgl                  1.78.0          r43hf17093f_1                 bioconda
  bioconductor-rhdf5                 2.46.1          r43hf17093f_1                 bioconda
  bioconductor-rhdf5filters          1.14.1          r43hf17093f_1                 bioconda
  bioconductor-rhdf5lib              1.24.0          r43ha9d7317_2                 bioconda
  bioconductor-s4arrays              1.2.0           r43ha9d7317_2                 bioconda
  bioconductor-s4vectors             0.40.2          r43ha9d7317_2                 bioconda
  bioconductor-scaledmatrix          1.10.0          r43hdfd78af_0                 bioconda
  bioconductor-scater                1.30.1          r43hdfd78af_0                 bioconda
  bioconductor-scran                 1.30.0          r43hf17093f_1                 bioconda
  bioconductor-scuttle               1.12.0          r43hf17093f_1                 bioconda
  bioconductor-singlecellexperiment  1.24.0          r43hdfd78af_0                 bioconda
  bioconductor-sparsearray           1.2.2           r43ha9d7317_2                 bioconda
  bioconductor-sparsematrixstats     1.14.0          r43hf17093f_1                 bioconda
  bioconductor-summarizedexperiment  1.32.0          r43hdfd78af_0                 bioconda
  bioconductor-xvector               0.42.0          r43ha9d7317_2                 bioconda
  bioconductor-zlibbioc              1.48.0          r43ha9d7317_2                 bioconda
  biopython                          1.85            py312h66e93f0_1               conda-forge
  blas                               2.131           openblas                      conda-forge
  blas-devel                         3.9.0           31_h1ea3ea9_openblas          conda-forge
  bleach                             6.2.0           pyh29332c3_4                  conda-forge
  bleach-with-css                    6.2.0           h82add2a_4                    conda-forge
  blinker                            1.9.0           pyhff2d567_0                  conda-forge
  blosc                              1.21.6          he440d0b_1                    conda-forge
  bokeh                              3.7.2           pyhd8ed1ab_1                  conda-forge
  boltons                            24.0.0          pyhd8ed1ab_1                  conda-forge
  bottleneck                         1.4.2           py312hc0a28a1_0               conda-forge
  branca                             0.8.1           pyhd8ed1ab_0                  conda-forge
  brotli                             1.1.0           hb9d3cd8_2                    conda-forge
  brotli-bin                         1.1.0           hb9d3cd8_2                    conda-forge
  brotli-python                      1.1.0           py312h2ec8cdc_2               conda-forge
  brunsli                            0.1             h9c3ff4c_0                    conda-forge
  bwidget                            1.10.1          ha770c72_0                    conda-forge
  bzip2                              1.0.8           h4bc722e_7                    conda-forge
  c-ares                             1.34.4          hb9d3cd8_0                    conda-forge
  c-blosc2                           2.15.2          h3122c55_1                    conda-forge
  ca-certificates                    2025.1.31       hbcca054_0                    conda-forge
  cached-property                    1.5.2           hd8ed1ab_1                    conda-forge
  cached_property                    1.5.2           pyha770c72_1                  conda-forge
  cairo                              1.18.4          h3394656_0                    conda-forge
  cellbender                         0.3.0           pypi_0                        pypi
  cellrank                           2.0.6           pyhd8ed1ab_1                  conda-forge
  celltypist                         1.6.3           pyhdfd78af_0                  bioconda
  certifi                            2025.1.31       pyhd8ed1ab_0                  conda-forge
  certipy                            0.2.2           pyhd8ed1ab_0                  conda-forge
  cffi                               1.17.1          py312h06ac9bb_0               conda-forge
  charls                             2.4.2           h59595ed_0                    conda-forge
  charset-normalizer                 3.4.1           pyhd8ed1ab_0                  conda-forge
  chex                               0.1.88          pyhd8ed1ab_1                  conda-forge
  click                              8.1.8           pyh707e725_0                  conda-forge
  click-default-group                1.2.4           pyhd8ed1ab_1                  conda-forge
  cloudpickle                        3.1.1           pyhd8ed1ab_0                  conda-forge
  colorama                           0.4.6           pyhd8ed1ab_1                  conda-forge
  colorcet                           3.1.0           pyhd8ed1ab_1                  conda-forge
  comm                               0.2.2           pyhd8ed1ab_1                  conda-forge
  conda                              25.3.1          py312h7900ff3_0               conda-forge
  conda-libmamba-solver              25.3.0          pyhd8ed1ab_0                  conda-forge
  conda-package-handling             2.4.0           pyh7900ff3_2                  conda-forge
  conda-package-streaming            0.11.0          pyhd8ed1ab_1                  conda-forge
  contourpy                          1.3.1           py312h68727a3_0               conda-forge
  cpp-expected                       1.1.0           hf52228f_0                    conda-forge
  cpython                            3.12.9          py312hd8ed1ab_1               conda-forge
  cryptography                       44.0.2          py312hda17c39_0               conda-forge
  curl                               8.13.0          h332b0f4_0                    conda-forge
  cycler                             0.12.1          pyhd8ed1ab_1                  conda-forge
  cython                             3.0.12          py312h2614dfc_0               conda-forge
  cytoolz                            1.0.1           py312h66e93f0_0               conda-forge
  dask                               2024.11.2       pyhff2d567_1                  conda-forge
  dask-core                          2024.11.2       pyhff2d567_1                  conda-forge
  dask-expr                          1.1.19          pyhd8ed1ab_0                  conda-forge
  dask-image                         2024.5.3        pyhd8ed1ab_0                  conda-forge
  datashader                         0.17.0          pyhd8ed1ab_0                  conda-forge
  dav1d                              1.2.1           hd590300_0                    conda-forge
  debugpy                            1.8.13          py312h2ec8cdc_0               conda-forge
  decorator                          5.2.1           pyhd8ed1ab_0                  conda-forge
  decoupler-py                       1.8.0           pyhd8ed1ab_1                  conda-forge
  defusedxml                         0.7.1           pyhd8ed1ab_0                  conda-forge
  deprecated                         1.2.18          pyhd8ed1ab_0                  conda-forge
  dill                               0.3.9           pyhd8ed1ab_1                  conda-forge
  distributed                        2024.11.2       pyhff2d567_1                  conda-forge
  distro                             1.9.0           pyhd8ed1ab_1                  conda-forge
  docformatter                       1.7.5           pyhd8ed1ab_1                  conda-forge
  docrep                             0.3.2           pyh44b312d_0                  conda-forge
  dunamai                            1.23.1          pyhd8ed1ab_0                  conda-forge
  et_xmlfile                         2.0.0           pyhd8ed1ab_1                  conda-forge
  etils                              1.12.2          pyhd8ed1ab_0                  conda-forge
  exceptiongroup                     1.2.2           pyhd8ed1ab_1                  conda-forge
  executing                          2.1.0           pyhd8ed1ab_1                  conda-forge
  fastcluster                        1.2.6           pypi_0                        pypi
  fasteners                          0.19            pyhd8ed1ab_1                  conda-forge
  fbpca                              1.0             pyhd8ed1ab_1                  conda-forge
  fcsparser                          0.2.8           pyhd8ed1ab_0                  conda-forge
  fftw                               3.3.10          mpi_openmpi_h99e62ba_10       conda-forge
  filelock                           3.18.0          pyhd8ed1ab_0                  conda-forge
  flax                               0.10.2          pyhd8ed1ab_0                  conda-forge
  flexcache                          0.3             pyhd8ed1ab_1                  conda-forge
  flexparser                         0.4             pyhd8ed1ab_1                  conda-forge
  fmt                                11.1.4          h07f6e7f_1                    conda-forge
  folium                             0.19.5          pyhd8ed1ab_0                  conda-forge
  font-ttf-dejavu-sans-mono          2.37            hab24e00_0                    conda-forge
  font-ttf-inconsolata               3.000           h77eed37_0                    conda-forge
  font-ttf-source-code-pro           2.038           h77eed37_0                    conda-forge
  font-ttf-ubuntu                    0.83            h77eed37_3                    conda-forge
  fontconfig                         2.15.0          h7e30c49_1                    conda-forge
  fonts-conda-ecosystem              1               0                             conda-forge
  fonts-conda-forge                  1               0                             conda-forge
  fonttools                          4.56.0          py312h178313f_0               conda-forge
  formulaic                          1.1.1           pyhd8ed1ab_0                  conda-forge
  formulaic-contrasts                1.0.0           pyhdfd78af_0                  bioconda
  fqdn                               1.5.1           pyhd8ed1ab_1                  conda-forge
  freetype                           2.13.3          h48d6fc4_0                    conda-forge
  freexl                             2.0.0           h9dce30a_2                    conda-forge
  fribidi                            1.0.10          h36c2ea0_0                    conda-forge
  frozendict                         2.4.6           py312h66e93f0_0               conda-forge
  frozenlist                         1.5.0           py312h178313f_1               conda-forge
  fsspec                             2025.3.2        pyhd8ed1ab_0                  conda-forge
  future                             1.0.0           pyhd8ed1ab_2                  conda-forge
  gcc_impl_linux-64                  14.2.0          hdb7739f_2                    conda-forge
  geopandas                          1.0.1           pyhd8ed1ab_3                  conda-forge
  geopandas-base                     1.0.1           pyha770c72_3                  conda-forge
  geos                               3.13.1          h97f6797_0                    conda-forge
  geosketch                          1.3             pyhdfd78af_0                  bioconda
  geotiff                            1.7.4           h239500f_2                    conda-forge
  get_version                        3.5.5           pyhd8ed1ab_1                  conda-forge
  gflags                             2.2.2           h5888daf_1005                 conda-forge
  gfortran_impl_linux-64             14.2.0          h0ee6e4a_2                    conda-forge
  giflib                             5.2.2           hd590300_0                    conda-forge
  git                                2.49.0          pl5321h59d505e_0              conda-forge
  gitdb                              4.0.12          pyhd8ed1ab_0                  conda-forge
  gitpython                          3.1.44          pyhff2d567_0                  conda-forge
  glog                               0.7.1           hbabe93e_0                    conda-forge
  glpk                               5.0             h445213a_0                    conda-forge
  gmp                                6.3.0           hac33072_2                    conda-forge
  gmpy2                              2.1.5           py312h7201bc8_3               conda-forge
  graphite2                          1.3.13          h59595ed_1003                 conda-forge
  graphlib-backport                  1.0.3           pyhd8ed1ab_0                  conda-forge
  greenlet                           3.1.1           py312h2ec8cdc_1               conda-forge
  grpcio                             1.67.1          py312h374181b_0               conda-forge
  gseapy                             1.1.8           py312h004ce86_0               bioconda
  gsl                                2.7             he838d99_0                    conda-forge
  gxx_impl_linux-64                  14.2.0          h2ead766_2                    conda-forge
  h11                                0.14.0          pyhd8ed1ab_1                  conda-forge
  h2                                 4.2.0           pyhd8ed1ab_0                  conda-forge
  h5py                               3.13.0          nompi_py312hedeef09_100       conda-forge
  harfbuzz                           9.0.0           hda332d3_1                    conda-forge
  harmonypy                          0.0.10          pyhdfd78af_0                  bioconda
  hdf5                               1.14.3          mpi_openmpi_h39ae36c_9        conda-forge
  hnswlib                            0.8.0           py312hc39e661_0               conda-forge
  hpack                              4.1.0           pyhd8ed1ab_0                  conda-forge
  httpcore                           1.0.7           pyh29332c3_1                  conda-forge
  httpx                              0.28.1          pyhd8ed1ab_0                  conda-forge
  humanize                           4.12.2          pyhd8ed1ab_0                  conda-forge
  hyperframe                         6.1.0           pyhd8ed1ab_0                  conda-forge
  hypre                              2.31.0          mpi_openmpi_h834c3d3_1        conda-forge
  icu                                75.1            he02047a_0                    conda-forge
  idna                               3.10            pyhd8ed1ab_1                  conda-forge
  igraph                             0.10.15         he44f51b_1                    conda-forge
  imagecodecs                        2024.12.30      py312h097a544_0               conda-forge
  imageio                            2.37.0          pyhfb79c49_0                  conda-forge
  importlib-metadata                 8.6.1           pyha770c72_0                  conda-forge
  importlib_resources                6.5.2           pyhd8ed1ab_0                  conda-forge
  inflect                            7.5.0           pyhd8ed1ab_0                  conda-forge
  interface_meta                     1.3.0           pyhd8ed1ab_1                  conda-forge
  intervaltree                       3.1.0           pyhd8ed1ab_1                  conda-forge
  ipykernel                          6.29.5          pyh3099207_0                  conda-forge
  ipympl                             0.9.7           pyhd8ed1ab_1                  conda-forge
  ipython                            9.0.2           pyhfb0248b_0                  conda-forge
  ipython_genutils                   0.2.0           pyhd8ed1ab_2                  conda-forge
  ipython_pygments_lexers            1.1.1           pyhd8ed1ab_0                  conda-forge
  ipywidgets                         8.1.5           pyhd8ed1ab_1                  conda-forge
  isoduration                        20.11.0         pyhd8ed1ab_1                  conda-forge
  jax                                0.4.35          pyhd8ed1ab_1                  conda-forge
  jaxlib                             0.4.35          cpu_py312h7d5f655_0           conda-forge
  jedi                               0.19.2          pyhd8ed1ab_1                  conda-forge
  jinja2                             3.1.6           pyhd8ed1ab_0                  conda-forge
  joblib                             1.4.2           pyhd8ed1ab_1                  conda-forge
  jq                                 1.7.1           hd590300_0                    conda-forge
  json-c                             0.18            h6688a6e_0                    conda-forge
  json5                              0.12.0          pyhd8ed1ab_0                  conda-forge
  jsonpatch                          1.33            pyhd8ed1ab_1                  conda-forge
  jsonpointer                        3.0.0           py312h7900ff3_1               conda-forge
  jsonschema                         4.23.0          pyhd8ed1ab_1                  conda-forge
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