ugbio-omics 1.3.0

Ultima Genomics bioinfo utils for working iwth AWS Health-Omics

ugbio_omics

This module includes Python scripts for working with AWS HealthOmics.

Log in with SSH to the desired AWS account before running tools in this package.

List of tools:

1. Compare Cromwell vs. Omics - Process cost and performance on both platforms and save results into comparable CSV files. Also saves metadata and intermediate cost and performance files. Additionally, you can find a plots folder with a variety of HTML plots. Omics cost information is collected using Omics Run Analyzer.

   Run uv run compare_cromwell_omics --help for more details.

2. Compare Omics Runs - Process cost and performance and compare between multiple Omics runs. Omics cost information is collected using Omics Run Analyzer.

   Run uv run compare_omics_runs --help for more details.

3. Get Run Logs - Download logs of an Omics run. You can download the logs for all tasks or for a specific task in the run.

   Run uv run get_omics_logs --help for more details.

4. Manifest Log - Download and parse the manifest log of an Omics run. The manifest log contains a lot of information about storage usage, CPU and memory usage per task, Docker images, inputs, and general information about the run.

   Run uv run manifest_log --help for more details.