Version Compatibility

FlowAgent automatically handles version compatibility for Kallisto indices:

Version Checking

• Checks Kallisto version before index creation
• Validates index compatibility using kallisto inspect
• Stores version information in workflow metadata

Error Prevention

• Detects version mismatches before execution
• Provides detailed error messages for incompatible indices
• Suggests resolution steps for version conflicts

Metadata Management

• Tracks index versions across workflows
• Maintains compatibility information
• Enables reproducible analyses

Updating the Environment

To update your conda environment with new dependencies:

conda env update -f conda/environment/environment.yml

Managing Multiple Environments

For development or testing, you can create a separate environment:

conda env create -f conda/environment/environment.yml -n flowagent-dev