new image for Google cloud Vertex

images/hail-gcp-vertex-workbench/Dockerfile

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+# description of slim base container https://cloud.google.com/vertex-ai/docs/workbench/instances/create-custom-container#slim-base-container
+# NB: uses micromamba, NOT conda
+FROM gcr.io/deeplearning-platform-release/workbench-container-slim:latest AS base
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    git \
+    htop \
+    unzip \
+    bzip2 \
+    zip \
+    tar \
+    rsync \
+    xsltproc pandoc \
+    openjdk-11-jdk-headless \
+    liblapack3 \
+    libopenblas-dev \
+    libpq-dev \
+    liblz4-dev \
+    g++ \
+    gcc \
+    cmake \
+    apt-transport-https \
+    ca-certificates \
+    gnupg \
+    curl && \
+    rm -rf /var/lib/apt/lists/*
+
+FROM base AS gcp_build
+# gcloud install
+RUN curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | gpg --dearmor -o /usr/share/keyrings/cloud.google.gpg && \
+    echo "deb [signed-by=/usr/share/keyrings/cloud.google.gpg] https://packages.cloud.google.com/apt cloud-sdk main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list && \
+    apt-get update && \
+    apt-get install -y \
+    google-cloud-cli
+
+FROM gcp_build AS hail_build
+ARG VERSION=${VERSION:-0.2.135}
+ENV KERNEL_DISPLAY_NAME="hail-${VERSION}"
+ENV ENVIRONMENT_NAME="hail-${VERSION}"
+ENV MICROMAMBA_ENV_HOME="/opt/micromamba/envs"
+COPY requirements.txt requirements.txt
+
+# create env and install hail + dependencies
+RUN micromamba create --prefix "${MICROMAMBA_ENV_HOME}"/"${ENVIRONMENT_NAME}" python=3.10 ipykernel && \
+    micromamba run -p "${MICROMAMBA_ENV_HOME}"/"${ENVIRONMENT_NAME}" pip install --no-cache-dir --no-deps -r requirements.txt && \
+    micromamba run -p "${MICROMAMBA_ENV_HOME}"/"${ENVIRONMENT_NAME}" python -m ipykernel install --name "${ENVIRONMENT_NAME}" --display-name "${KERNEL_DISPLAY_NAME}" && \
+    curl -o "$(micromamba run -p "${MICROMAMBA_ENV_HOME}"/"${ENVIRONMENT_NAME}" find_spark_home.py)/jars/gcs-connector-hadoop2-2.2.28.jar" https://storage.googleapis.com/hadoop-lib/gcs/gcs-connector-hadoop2-2.2.28.jar

images/hail-gcp-vertex-workbench/requirements.txt

@@ -0,0 +1,226 @@
+aiodns==2.0.0
+aiohappyeyeballs==2.6.1
+aiohttp==3.12.15
+aiosignal==1.4.0
+annoy==1.17.3
+anyio==4.10.0
+argon2-cffi==25.1.0
+argon2-cffi-bindings==25.1.0
+asttokens==3.0.0
+async-timeout==5.0.1
+attrs==25.3.0
+avro==1.11.3
+azure-common==1.1.28
+azure-core==1.35.0
+azure-identity==1.23.1
+azure-mgmt-core==1.6.0
+azure-mgmt-storage==20.1.0
+azure-storage-blob==12.26.0
+azure-storage-file-datalake==12.21.0
+backoff==2.2.1
+beautifulsoup4==4.13.4
+bigquery_jupyter_plugin==0.0.1
+biocommons.seqrepo==0.6.11
+bioutils==0.6.1
+bleach==6.2.0
+bokeh==3.4.3
+boto3==1.40.3
+botocore==1.40.3
+cachetools==5.5.2
+canonicaljson==2.0.0
+certifi==2025.8.3
+cffi==1.17.1
+cfgv==3.4.0
+charset-normalizer==3.4.2
+click==8.2.1
+cloudpathlib==0.21.1
+coloredlogs==15.0.1
+comm==0.2.3
+commonmark==0.9.1
+configparser==7.2.0
+contourpy==1.3.2
+cpg-utils==5.4.1
+cryptography==45.0.6
+cycler==0.12.1
+dataproc_jupyter_plugin==0.1.74
+debugpy==1.8.15
+decorator==4.4.2
+defusedxml==0.7.1
+Deprecated==1.2.18
+dill==0.3.9
+distlib==0.4.0
+exceptiongroup==1.3.0
+executing==2.2.0
+fastjsonschema==2.21.1
+filelock==3.18.0
+flatbuffers==25.2.10
+fonttools==4.59.0
+frozendict==2.4.6
+frozenlist==1.7.0
+fsspec==2025.7.0
+ga4gh.vrs==0.8.4
+gcsfs==2025.7.0
+gnomad==0.8.2
+google-api-core==2.25.1
+google-auth==2.40.3
+google-auth-oauthlib==0.8.0
+google-cloud-artifact-registry==1.16.1
+google-cloud-core==2.4.3
+google-cloud-jupyter-config==0.0.10
+google-cloud-secret-manager==2.24.0
+google-cloud-storage==3.2.0
+google-crc32c==1.7.1
+google-resumable-media==2.7.2
+googleapis-common-protos==1.70.0
+gql==3.5.3
+graphql-core==3.2.6
+grpc-google-iam-v1==0.14.2
+grpcio==1.74.0
+grpcio-status==1.74.0
+hail==0.2.135
+hdbscan==0.8.40
+hgvs==1.5.5
+humanfriendly==10.0
+humanize==4.12.3
+identify==2.6.12
+idna==3.10
+importlib_metadata==8.7.0
+importlib_resources==6.5.2
+inflection==0.5.1
+ipykernel==6.30.1
+ipython==8.37.0
+ipywidgets==8.1.7
+isodate==0.7.2
+janus==1.0.0
+jedi==0.19.2
+Jinja2==3.1.6
+jmespath==1.0.1
+joblib==1.5.1
+jproperties==2.1.2
+jsonpointer==3.0.0
+jsonschema==3.2.0
+jupyter_client==8.6.3
+jupyter_core==5.8.1
+jupyter-events==0.6.3
+jupyter_server==2.10.0
+jupyter_server_terminals==0.5.3
+jupyterlab_pygments==0.3.0
+jupyterlab_widgets==3.0.15
+kernels-mixer==0.0.15
+kiwisolver==1.4.8
+Markdown==3.8.2
+MarkupSafe==3.0.2
+matplotlib==3.10.5
+matplotlib-inline==0.1.7
+metamist==7.10.2
+mistune==3.1.3
+mpmath==1.3.0
+msal==1.33.0
+msal-extensions==1.3.1
+msrest==0.7.1
+multidict==6.6.3
+nbclient==0.10.2
+nbconvert==7.16.6
+nbformat==5.10.4
+nest_asyncio==1.6.0
+networkx==3.4.2
+nodeenv==1.9.1
+numpy==2.2.6
+oauthlib==3.3.1
+onnx==1.18.0
+onnxruntime==1.22.1
+orjson==3.11.1
+overrides==7.7.0
+packaging==25.0
+pandas==2.3.1
+pandocfilters==1.5.1
+parsimonious==0.10.0
+Parsley==1.3
+parso==0.8.4
+patsy==1.0.1
+pendulum==3.1.0
+pexpect==4.9.0
+pickleshare==0.7.5
+pillow==11.3.0
+pip==25.2
+platformdirs==4.3.8
+plotly==5.24.1
+polars==1.32.0
+pre-commit==3.8.0
+prometheus_client==0.22.1
+prompt_toolkit==3.0.51
+propcache==0.3.2
+proto-plus==1.26.1
+protobuf==6.31.1
+psutil==7.0.0
+psycopg2-binary==2.9.10
+ptyprocess==0.7.0
+pure_eval==0.2.3
+py4j==0.10.9.7
+pyasn1==0.6.1
+pyasn1_modules==0.4.2
+pycares==4.10.0
+pycparser==2.22
+pydantic==1.10.22
+Pygments==2.19.2
+PyJWT==2.10.1
+pyparsing==3.2.3
+pyrsistent==0.20.0
+pysam==0.23.3
+pyspark==3.5.6
+python-dateutil==2.9.0.post0
+python-json-logger==2.0.7
+python-jsonschema-objects==0.4.6
+pytz==2025.2
+PyYAML==6.0.2
+pyzmq==27.0.1
+regex==2025.7.34
+requests==2.32.4
+requests-oauthlib==2.0.0
+requests-toolbelt==1.0.0
+rfc3339-validator==0.1.4
+rfc3986-validator==0.1.1
+rich==12.6.0
+rsa==4.9.1
+s3transfer==0.13.1
+scikit-learn==1.7.1
+scipy==1.15.3
+Send2Trash==1.8.3
+setuptools==80.9.0
+shellingham==1.5.4
+six==1.17.0
+skl2onnx==1.19.1
+slack_sdk==3.39.0
+sniffio==1.3.1
+sortedcontainers==2.4.0
+soupsieve==2.7
+sqlparse==0.5.3
+stack_data==0.6.3
+statsmodels==0.14.5
+sympy==1.14.0
+tabulate==0.9.0
+tenacity==9.1.2
+terminado==0.18.1
+threadpoolctl==3.6.0
+tinycss2==1.4.0
+toml==0.10.2
+tornado==6.5.1
+tqdm==4.67.1
+traitlets==5.14.3
+typer==0.16.0
+typing_extensions==4.14.1
+tzdata==2025.2
+urllib3==2.5.0
+uvloop==0.21.0
+virtualenv==20.33.1
+wcwidth==0.2.13
+webcolors==24.11.1
+webencodings==0.5.1
+websocket-client==1.8.0
+wheel==0.45.1
+widgetsnbextension==4.0.14
+wrapt==1.17.2
+xyzservices==2025.4.0
+yarl==1.20.1
+yoyo-migrations==9.0.0
+zipp==3.23.0