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How to ensure reproducibility in Galaxy?

Ensure reproducibility in Galaxy by maintaining consistent tools, documenting steps, using workflows, managing data, verifying results, and collaborating effectively.

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How to ensure reproducibility in Galaxy?

 

Setting Up a Consistent Galaxy Environment

 

  • Ensure that all tools and versions used on Galaxy are the same every time. Keep track of tool versions and update history for reproducibility.
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  • Use the same Galaxy instance and avoid using different servers to run analyses, as configuration differences can affect results.

 

Documenting Every Step

 

  • Keep a detailed record of every step, including parameters used and the sequence of operations. This helps in tracing and replicating the analysis workflow.
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  • Encourage the use of Galaxy’s history feature to save workflows, enabling easy re-run and sharing of analysis with collaborators.

 

Using Workflow Tools

 

  • Leverage Galaxy's workflow editor to create and document a structured workflow. This ensures all steps are captured and can be reused.
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  • Export and save workflows as files, providing an easy way to archive and share reproducible processes.

 

Managing Data Inputs

 

  • Use consistent and well-documented datasets. Ensure input data is version-controlled if possible to prevent discrepancies in analysis results.
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  • Utilize Galaxy’s data libraries to organize and manage datasets efficiently.

 

Verifying Results

 

  • Regularly verify results against known benchmarks or previously published data to ensure reproducibility and reliability.
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  • Compare outputs across different runs and document any discrepancies for further investigation.

 

Collaborative Practices

 

  • Share workflows and datasets with collaborators through Galaxy's sharing features to allow them to replicate and validate your findings.
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  • Encourage feedback and verification by peers, enhancing the reproducibility and trust in the results generated.

 

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