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This guidance creates a scalable environment in AWS to prepare genomic, clinical, mutation, expression and imaging data for large-scale analysis and perform interactive queries against a data lake. The solution also demonstrates the use of Amazon Omics for multi-modal analysis.

Home Page: https://aws.amazon.com/solutions/guidance/multi-omics-and-multi-modal-data-integration-and-analysis/

License: Apache License 2.0

Shell 5.17% Jupyter Notebook 75.38% Python 19.44%
aws life-sciences multimodal multimodality

guidance-for-multi-omics-and-multi-modal-data-integration-and-analysis-on-aws's Issues

Package import error in notebook

File:
genomics-tertiary-analysis-and-data-lakes-using-aws-glue-and-amazon-athena/source/GenomicsAnalysisCode/resources/notebooks/runbook.ipynb

Environment:
Current version of Sagemaker Jupyter and JupyterLab (as of June 2021)

Bug:
Notebook fails to run due to package import error

Error:
ImportError: cannot import name 'as_pandas'

Fix:
from pyathena.util import as_pandas -> change to -> from pyathena.pandas.util import as_pandas

Update to Hail 0.2?

Can this solution be used with Hail 0.2, which is considered a formal release? We tried several ways to use Hail 0.2 in this solution but it failed for various reasons.

Is it possible for this solution to work with the latest Hail?

Thank you.

error

An error occurred (EntityNotFoundException) when calling the StartCrawler operation: Crawler with name genomicsanalysis-annotation does not exist

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