name: biomni_e1 channels: - bioconda - conda-forge - defaults dependencies: - altair=5.5.0 - asttokens=3.0.0 - attrs=25.3.0 - aws-c-auth=0.9.0 - aws-c-cal=0.9.2 - aws-c-common=0.12.4 - aws-c-compression=0.3.1 - aws-c-event-stream=0.5.5 - aws-c-http=0.10.4 - aws-c-io=0.21.2 - aws-c-mqtt=0.13.3 - aws-c-s3=0.8.6 - aws-c-sdkutils=0.2.4 - aws-checksums=0.2.7 - aws-crt-cpp=0.33.1 - aws-sdk-cpp=1.11.606 - azure-core-cpp=1.16.0 - azure-identity-cpp=1.12.0 - azure-storage-blobs-cpp=12.14.0 - azure-storage-common-cpp=12.10.0 - azure-storage-files-datalake-cpp=12.12.0 - bedtools=2.31.1 - biopython=1.85 - blast=2.16.0 - blinker=1.9.0 - bokeh=3.7.3 - bowtie2=2.5.4 - brotli-bin=1.1.0 - brotli-python=1.1.0 - bwa=0.7.19 - bzip2=1.0.8 - c-ares=1.34.5 - ca-certificates=2025.8.3 - cairo=1.18.4 - certifi=2025.8.3 - cffi=1.17.1 - charset-normalizer=3.4.2 - contourpy=1.3.3 - curl=8.14.1 - cycler=0.12.1 - decorator=5.2.1 - diamond=2.1.13 - entrez-direct=22.4 - exceptiongroup=1.3.0 - executing=2.2.0 - fastqc=0.12.1 - font-ttf-dejavu-sans-mono=2.37 - font-ttf-inconsolata=3.000 - font-ttf-source-code-pro=2.038 - font-ttf-ubuntu=0.83 - fontconfig=2.15.0 - fonts-conda-ecosystem=1 - fonts-conda-forge=1 - fonttools=4.59.0 - freetype=2.13.3 - gflags=2.2.2 - giflib=5.2.2 - gitdb=4.0.12 - gitpython=3.1.45 - glog=0.7.1 - gmp=6.3.0 - graphite2=1.3.14 - gseapy=1.1.9 - h2=4.2.0 - harfbuzz=11.3.3 - hpack=4.1.0 - htslib=1.22.1 - hyperframe=6.1.0 - icu=75.1 - idna=3.10 - importlib-metadata=8.7.0 - infernal=1.1.5 - ipython=9.4.0 - ipython_pygments_lexers=1.1.1 - jedi=0.19.2 - jinja2=3.1.6 - jsonschema=4.25.0 - jsonschema-specifications=2025.4.1 - kiwisolver=1.4.8 - krb5=1.21.3 - lcms2=2.17 - lerc=4.0.0 - libabseil=20250512.1 - libarrow=21.0.0 - libarrow-acero=21.0.0 - libarrow-compute=21.0.0 - libarrow-dataset=21.0.0 - libarrow-substrait=21.0.0 - libasprintf=0.25.1 - libblas=3.9.0 - libbrotlicommon=1.1.0 - libbrotlidec=1.1.0 - libbrotlienc=1.1.0 - libcblas=3.9.0 - libcrc32c=1.1.2 - libcurl=8.14.1 - libdeflate=1.22 - libedit=3.1.20250104 - libev=4.33 - libevent=2.1.12 - libexpat=2.7.1 - libffi=3.4.6 - libfreetype=2.13.3 - libfreetype6=2.13.3 - libgettextpo=0.25.1 - libgfortran=15.1.0 - libgfortran5=15.1.0 - libglib=2.84.2 - libgoogle-cloud=2.39.0 - libgoogle-cloud-storage=2.39.0 - libgrpc=1.73.1 - libiconv=1.18 - libidn2=2.3.8 - libjpeg-turbo=3.1.0 - liblapack=3.9.0 - liblzma=5.8.1 - libnghttp2=1.64.0 - libopenblas=0.3.30 - libopentelemetry-cpp=1.21.0 - libopentelemetry-cpp-headers=1.21.0 - libparquet=21.0.0 - libpng=1.6.50 - libprotobuf=6.31.1 - libre2-11=2025.07.22 - libsqlite=3.50.4 - libssh2=1.11.1 - libthrift=0.22.0 - libtiff=4.7.0 - libunistring=0.9.10 - libutf8proc=2.10.0 - libwebp-base=1.6.0 - libxml2=2.13.8 - libzlib=1.3.1 - lz4-c=1.10.0 - mafft=7.526 # - mageck=0.5.9.5 - markupsafe=3.0.2 - matplotlib-base=3.10.5 - matplotlib-inline=0.1.7 - mpfr=4.2.1 - munkres=1.1.4 - narwhals=2.0.1 - ncbi-vdb=3.2.1 - ncurses=6.5 - nlohmann_json=3.12.0 - openjdk=23.0.2 - openjpeg=2.5.3 - openssl=3.5.1 - orc=2.1.3 - packaging=25.0 - pandas=2.3.1 - parso=0.8.4 - pcre2=10.45 - perl=5.32.1 - perl-archive-tar=3.04 - perl-carp=1.50 - perl-common-sense=3.75 - perl-compress-raw-bzip2=2.201 - perl-compress-raw-zlib=2.202 - perl-encode=3.21 - perl-exporter=5.74 - perl-exporter-tiny=1.002002 - perl-extutils-makemaker=7.70 - perl-io-compress=2.201 - perl-io-zlib=1.15 - perl-json=4.10 - perl-json-xs=4.03 - perl-list-moreutils=0.430 - perl-list-moreutils-xs=0.430 - perl-parent=0.243 - perl-pathtools=3.75 - perl-scalar-list-utils=1.70 - perl-storable=3.15 - perl-types-serialiser=1.01 - pexpect=4.9.0 - pickleshare=0.7.5 - pillow=11.3.0 - pip=25.2 - pixman=0.46.4 # - plannotate=1.2.0 - prometheus-cpp=1.3.0 - prompt-toolkit=3.0.51 - protobuf=6.31.1 - ptyprocess=0.7.0 - pure_eval=0.2.3 - pyarrow=21.0.0 - pyarrow-core=21.0.0 - pycparser=2.22 - pydeck=0.9.1 - pygments=2.19.2 - pyopengl=3.1.9 - pyparsing=3.2.3 - pysocks=1.7.1 - python=3.11.13 - python-dateutil=2.9.0.post0 - python-tzdata=2025.2 - python_abi=3.11 - pytz=2025.2 - pyyaml=6.0.2 - qhull=2020.2 - re2=2025.07.22 - readline=8.2 - referencing=0.36.2 - requests=2.32.4 - ripgrep=14.1.1 - rpds-py=0.26.0 - rpsbproc=0.5.0 - s2n=1.5.23 - samtools=1.22.1 - setuptools=80.9.0 - six=1.17.0 - smmap=5.0.2 - snappy=1.2.2 - stack_data=0.6.3 - streamlit=1.47.1 - tabulate=0.9.0 - tenacity=9.1.2 - tk=8.6.13 - toml=0.10.2 - tornado=6.5.1 - traitlets=5.14.3 - trimmomatic=0.39 - trnascan-se=2.0.12 - typing-extensions=4.14.1 - typing_extensions=4.14.1 - tzdata=2025b - unicodedata2=16.0.0 - urllib3=2.5.0 - watchdog=6.0.0 - wcwidth=0.2.13 - wget=1.21.4 - wheel=0.45.1 - xyzservices=2025.4.0 - yaml=0.2.5 - zipp=3.23.0 - zlib=1.3.1 - zstd=1.5.7 - pip: - absl-py==2.3.1 - adjusttext==1.3.0 - aiobotocore - aiofiles==24.1.0 - aiohappyeyeballs==2.6.1 - aiohttp==3.12.15 - aioitertools==0.12.0 - aiosignal==1.4.0 - airr==1.5.1 - alabaster==1.0.0 - anndata==0.12.1 - annotated-types==0.7.0 - annoy==1.17.3 - anthropic==0.60.0 - anyio==4.9.0 - appdirs==1.4.4 - arboreto==0.1.6 - argon2-cffi==25.1.0 - argon2-cffi-bindings==25.1.0 - array-api-compat==1.12.0 - arrow==1.3.0 - arviz==0.22.0 - arxiv==2.2.0 - asciitree==0.3.3 - async-lru==2.0.5 - authlib==1.6.1 - autograd==1.8.0 - autograd-gamma==0.5.0 - awkward==2.8.6 - awkward-cpp==48 - babel==2.17.0 - beautifulsoup4==4.13.4 - bibtexparser==1.4.3 - biom-format==2.1.16 # - biomni==0.0.8 - biopandas==0.5.1 - biotite==1.4.0 - biotraj==1.2.2 - bleach==6.2.0 - blitzgsea==1.3.54 - blosc2==3.6.1 - boltons==25.0.0 - boto3 - botocore - brotli==1.1.0 - cachetools==5.5.2 - cellpose==4.0.6 - cellxgene-census==1.17.0 - cftime==1.6.4.post1 - chex==0.1.90 - click==8.2.1 - clikit==0.6.2 - cloudpickle==3.1.1 - cobra==0.29.1 - colorcet==3.1.0 - coloredlogs==15.0.1 - comm==0.2.3 - community==1.0.0b1 - cooler==0.10.4 - crashtest==0.3.1 - cryosparc-tools==4.7.1 - cryptography==45.0.5 - ctxcore==0.2.0 - cyclopts==3.22.5 - cython==0.29.37 - cytoolz==1.0.1 - cyvcf2==0.31.1 - dask==2024.11.2 - dask-expr==1.1.19 - dask-image==2024.5.3 - dataclasses==0.6 - dataclasses-json==0.6.7 - datashader==0.18.1 - debugpy==1.8.15 - decoupler==2.1.1 - defusedxml==0.7.1 - demes==0.2.3 - depinfo==2.2.0 - deprecated==1.2.18 - deprecation==2.1.0 - dill==0.4.0 - diskcache==5.6.3 - distributed==2024.11.2 - distro==1.9.0 - dnspython==2.7.0 - docrep==0.3.2 - docstring-parser==0.17.0 - docutils==0.21.2 - domdf-python-tools==3.10.0 - drmaa==0.7.9 - email-validator==2.2.0 - enum-tools==0.13.0 - equinox==0.13.0 - et-xmlfile==2.0.0 - etils==1.13.0 - faiss-cpu==1.11.0.post1 - fake-useragent==2.2.0 - fanc==0.9.28 - fast-array-utils==1.2.1 - fastapi==0.116.1 - fasteners==0.19 - fastjsonschema==2.21.1 - fastmcp==2.11.0 - fastprogress==1.0.3 - fastremap==1.17.2 - fcsparser==0.2.4 - feedparser==6.0.11 - ffmpy==0.6.1 - filelock==3.18.0 - filetype==1.2.0 - fill-voids==2.1.0 - flask==3.1.1 - flax==0.11.0 - flowcytometrytools==0.5.1 - formulaic==1.2.0 - formulaic-contrasts==1.0.0 - fqdn==1.5.1 - free-proxy==1.1.3 - frozendict==2.4.6 - frozenlist==1.7.0 - fsspec==2025.7.0 - future==1.0.0 - fuzzywuzzy==0.18.0 - genomic-regions==0.0.10 - geopandas==1.1.1 - gget==0.29.2 - google-ai-generativelanguage==0.6.18 - google-api-core==2.25.1 - google-auth==2.40.3 - googleapis-common-protos==1.70.0 - googlesearch-python==1.3.0 - gradio==5.39.0 - gradio-client==1.11.0 - graphql-core==3.2.6 - greenlet==3.2.3 - gridmap==0.15.0 - groovy==0.1.2 - grpcio==1.74.0 - grpcio-status==1.74.0 - h11==0.16.0 - h5netcdf==1.6.3 - h5py==3.14.0 - harmony-pytorch==0.1.8 - hf-xet==1.1.5 - hmmlearn==0.3.3 - httpcore==1.0.9 # - httpstan==4.13.0 - httpx==0.28.1 - httpx-sse==0.4.1 - huggingface-hub==0.34.3 - humanfriendly==10.0 - humanize==4.12.3 - igraph==0.11.9 - imagecodecs==2025.8.2 - imageio==2.37.0 - imagesize==1.4.1 - importlib-resources==6.5.2 - inflect==7.5.0 - iniconfig==2.1.0 - interface-meta==1.3.0 - interlap==0.2.7 - intervaltree==3.1.0 - ipykernel==6.30.0 - ipywidgets==8.1.7 - isodate==0.7.2 - isoduration==20.11.0 - itsdangerous==2.2.0 - jax==0.6.2 - jaxlib==0.6.2 - jaxopt==0.8.5 - jaxtyping==0.3.2 - jiter==0.10.0 - jmespath==1.0.1 - joblib==1.5.1 - json5==0.12.0 - jsonpatch==1.33 - jsonpointer==3.0.0 - jsonschema-path==0.3.4 - jupyter==1.1.1 - jupyter-client==8.6.3 - jupyter-console==6.6.3 - jupyter-core==5.8.1 - jupyter-events==0.12.0 - jupyter-lsp==2.2.6 - jupyter-server==2.16.0 - jupyter-server-terminals==0.5.3 - jupyterlab==4.4.5 - jupyterlab-pygments==0.3.0 - jupyterlab-server==2.27.3 - jupyterlab-widgets==3.0.15 - lamin-utils==0.15.0 - langchain==0.3.27 - langchain-anthropic==0.3.18 - langchain-community==0.3.27 - langchain-core==0.3.72 # - langchain-google-genai==2.1.8 - langchain-ollama==0.3.6 - langchain-openai==0.3.28 - langchain-text-splitters==0.3.9 - langgraph==0.3.18 - langgraph-checkpoint==2.1.1 - langgraph-prebuilt==0.1.8 - langgraph-sdk==0.1.74 - langsmith==0.4.10 - lark==1.2.2 - lazy-loader==0.4 - lazy-object-proxy==1.11.0 - legacy-api-wrap==1.4.1 - legendkit==0.3.6 - levenshtein==0.27.1 - lifelines==0.30.0 - lightning==2.5.2 - lightning-utilities==0.15.0 - lineax==0.0.8 - llvmlite==0.44.0 - locket==1.0.0 - logomaker==0.8.7 - loompy==3.0.8 - looseversion==1.1.2 - lxml==6.0.0 - lz4==4.4.4 - macs2==2.2.9.1 - markdown==3.8.2 - markdown-it-py==3.0.0 - marshmallow==3.26.1 - marsilea==0.5.4 - matplotlib-scalebar==0.9.0 - mcp==1.12.3 - mdurl==0.1.2 - mistune==3.1.3 - ml-collections==1.1.0 - ml-dtypes==0.5.3 - mmtf-python==1.1.3 - more-itertools==10.7.0 - mpmath==1.3.0 - msgpack==1.1.1 - msgpack-numpy==0.4.8 - msprime==1.3.4 - mudata==0.3.2 - multidict==6.6.3 - multipledispatch==1.0.0 - multiprocess==0.70.18 - multiprocessing-on-dill==3.5.0a4 - multiscale-spatial-image==2.0.2 - muon==0.1.7 - mypy-extensions==1.1.0 - mysql-connector-python==9.4.0 - natsort==8.4.0 - nbclient==0.10.2 - nbconvert==7.16.6 - nbformat==5.10.4 - ncls==0.0.70 - ndindex==1.10.0 - nest-asyncio==1.6.0 - netcdf4==1.7.2 - networkx==3.5 - newick==1.10.0 - notebook==7.4.4 - notebook-shim==0.2.4 - numba==0.61.2 - numcodecs==0.15.1 - numexpr==2.11.0 - numpy==2.1.0 - numpy-groupies==0.11.3 - numpyro==0.18.0 # - nvidia-cublas-cu12==12.6.4.1 # - nvidia-cuda-cupti-cu12==12.6.80 # - nvidia-cuda-nvrtc-cu12==12.6.77 # - nvidia-cuda-runtime-cu12==12.6.77 # - nvidia-cudnn-cu12==9.5.1.17 # - nvidia-cufft-cu12==11.3.0.4 # - nvidia-cufile-cu12==1.11.1.6 # - nvidia-curand-cu12==10.3.7.77 # - nvidia-cusolver-cu12==11.7.1.2 # - nvidia-cusparse-cu12==12.5.4.2 # - nvidia-cusparselt-cu12==0.6.3 # - nvidia-nccl-cu12==2.26.2 # - nvidia-nvjitlink-cu12==12.6.85 # - nvidia-nvtx-cu12==12.6.77 - ollama==0.5.1 - ome-zarr==0.11.1 - omnipath==1.0.12 - openai==1.98.0 - openapi-core==0.19.5 - openapi-pydantic==0.5.1 - openapi-schema-validator==0.6.3 - openapi-spec-validator==0.7.2 - opencv-python==4.12.0.88 - opencv-python-headless==4.12.0.88 - openmm==8.3.1 - openpyxl==3.1.5 - opt-einsum==3.4.0 - optax==0.2.5 - optlang==1.8.3 - orbax-checkpoint==0.11.20 - orjson==3.11.1 - ormsgpack==1.10.0 - ott-jax==0.5.1 - outcome==1.3.0.post0 - overrides==7.7.0 - pandocfilters==1.5.1 - param==2.2.1 - parse==1.20.2 - partd==1.4.2 - pastel==0.2.1 - pathable==0.4.4 - patsy==1.0.1 - pertpy==1.0.1 - pims==0.7 - platformdirs==4.3.8 - pluggy==1.6.0 - ply==3.11 - pooch==1.8.2 - progressbar2==4.5.0 - prometheus-client==0.22.1 - propcache==0.3.2 - proto-plus==1.26.1 - psutil==7.0.0 - pubchempy==1.0.4 - py-cpuinfo==9.0.0 - pyarrow-hotfix==0.7 - pyasn1==0.6.1 - pyasn1-modules==0.4.2 - pybedtools==0.12.0 - pybigwig==0.3.24 - pyct==0.5.0 - pydantic==2.11.7 - pydantic-core==2.33.2 - pydantic-settings==2.10.1 - pydeseq2==0.5.2 - pydub==0.25.1 - pyfaidx==0.8.1.4 - pykalman==0.10.1 - pylev==1.4.0 - pyliftover==0.4.1 - pymassspec==2.6.0.post1 - pymc3==3.11.4 - pymed==0.8.9 - pymzml==2.5.11 - pynndescent==0.5.13 - pyogrio==0.11.1 - pyomo==6.9.2 - pypdf2==3.0.1 - pyperclip==1.9.0 - pyproj==3.7.1 - pyranges==0.1.4 - pyro-api==0.1.2 - pyro-ppl==1.9.1 - pysam==0.23.3 - pyscenic==0.12.1 - pysimdjson==6.0.2 # - pystan==3.10.0 - pytdc==0.4.0 - pytest==8.4.1 - python-dotenv==1.1.1 - python-json-logger==3.3.0 - python-levenshtein==0.27.1 - python-libsbml==5.20.5 - python-multipart==0.0.20 - python-utils==3.9.1 - pytorch-lightning==2.5.2 - pyzmq==27.0.1 - rapidfuzz==3.13.0 - rdkit==2025.3.5 - rdkit-pypi==2022.9.5 - regex==2025.7.34 - reportlab==4.4.3 - requests-toolbelt==1.0.0 - rfc3339-validator==0.1.4 - rfc3986-validator==0.1.1 - rfc3987-syntax==1.1.0 - rich==14.1.0 - rich-rst==1.3.1 - roifile==2025.5.10 - roman-numerals-py==3.1.0 - rsa==4.9.1 - ruamel-yaml==0.18.14 - ruamel-yaml-clib==0.2.12 - ruff==0.12.7 - s3fs==2025.7.0 - s3transfer==0.13.1 - safehttpx==0.1.6 - safetensors==0.5.3 - scanpy==1.11.4 - scholarly==1.7.11 - scikit-base==0.12.4 - scikit-bio==0.7.0 - scikit-image==0.25.2 - scikit-learn==1.7.1 - scikit-misc==0.5.1 - scipy==1.15.0 - scirpy==0.22.1 - scrublet==0.2.3 - scvelo==0.3.3 - scvi-tools==1.3.3 - sdjson==0.5.0 - seaborn==0.13.2 - segment-anything==1.0 - selenium==4.34.2 - semantic-version==2.10.0 - semver==3.0.4 - send2trash==1.8.3 - sentencepiece==0.2.0 - session-info==1.0.1 - session-info2==0.2 - sgmllib3k==1.0.0 - shapely==2.1.1 - shellingham==1.5.4 - simplejson==3.20.1 - slicerator==1.1.0 - sniffio==1.3.1 - snowballstemmer==3.0.1 - somacore==1.0.28 - sorted-nearest==0.0.39 - sortedcontainers==2.4.0 - soupsieve==2.7 - sparse==0.17.0 - sparsecca==0.3.1 - spatial-image==1.2.2 - spatialdata==0.4.0 - sphinx==8.2.3 - sphinx-rtd-theme==3.0.2 - sphinxcontrib-applehelp==2.0.0 - sphinxcontrib-devhelp==2.0.0 - sphinxcontrib-htmlhelp==2.1.0 - sphinxcontrib-jquery==4.1 - sphinxcontrib-jsmath==1.0.1 - sphinxcontrib-qthelp==2.0.0 - sphinxcontrib-serializinghtml==2.0.0 - sqlalchemy==2.0.42 - squarify==0.4.4 - squidpy==1.6.5 - sse-starlette==3.0.2 - starlette==0.47.2 - statsmodels==0.14.5 - stdlib-list==0.11.1 - swiglpk==5.0.12 - sympy==1.14.0 - tables==3.10.2 - tblib==3.1.0 - tensorboard==2.20.0 - tensorboard-data-server==0.7.2 - tensorstore==0.1.76 - terminado==0.18.1 - texttable==1.7.0 - theano-pymc==1.1.2 - threadpoolctl==3.6.0 - tifffile==2025.6.11 - tiktoken==0.9.0 - tiledbsoma==1.17.1 - tinycss2==1.4.0 - tokenizers==0.21.4 - tomlkit==0.13.3 - tooluniverse==0.2.0 - toolz==1.0.0 - torch==2.7.1 - torchmetrics==1.8.0 - torchvision==0.22.1 - tqdm==4.67.1 - trackpy==0.7 - transformers==4.54.1 - treescope==0.1.9 - trio==0.30.0 - trio-websocket==0.12.2 # - triton==3.3.1 - tskit==0.6.4 - typeguard==4.4.4 - typer==0.16.0 - types-python-dateutil==2.9.0.20250708 - typing-inspect==0.9.0 - typing-inspection==0.4.1 - umap-learn==0.5.9.post2 - uri-template==1.3.0 - uvicorn==0.35.0 - validators==0.35.0 - viennarna==2.7.0 - wadler-lindig==0.1.7 - webargs==8.7.0 - webcolors==24.11.1 - webencodings==0.5.1 - websocket-client==1.8.0 - websockets==15.0.1 - werkzeug==3.1.1 - widgetsnbextension==4.0.14 - wrapt==1.17.2 - wsproto==1.2.0 - xarray==2024.11.0 - xarray-dataclass==3.0.0 - xarray-dataclasses==1.9.1 - xarray-einstats==0.9.1 - xarray-schema==0.0.3 - xarray-spatial==0.4.0 - yamlordereddictloader==0.4.2 - yarl==1.20.1 - zarr==2.18.7 - zict==3.0.0 - zstandard==0.23.0 - mi-googlesearch-python==1.3.0.post1