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Client Reference

Commands and options supported by the Song client.

General Commands​

Config​

  • The config command shows the current configuration settings.

  • Usage: song-client config

Ping​

  • The ping command can test the connection to the Song server.

  • Usage: song-client ping

Analysis Management Commands​

Get-Analysis-Type​

  • Retrieves specific analysis type schema information.

  • Usage: song-client get-analysis-type [OPTIONS]

    OptionDescription
    -n, --nameName of the analysis type
    -u, --unrendered-onlyRetrieve only the unrendered schema
    -v, --versionVersion of the analysis type

List-Analysis-Types​

  • Lists all analysis types with filtering and viewing options.

  • Usage: song-client list-analysis-types [OPTIONS]

    OptionDescription
    -hs, --hide-schemaHide the schema (Default: false)
    -l, --limitQuery limit
    -n, --namesFilter analysis types by names
    -o, --offsetQuery offset
    -sd, --sort-directionSorting direction (Default: DESC, Options: DESC or ASC)
    -so, --sort-orderAnalysis type fields to sort on
    -u, --unrendered-onlyOnly retrieve the unrendered schema (Default: false)
    -v, --versionsFilter analysis types by versions

Register-Analysis-Type​

  • Registers a new analysis-type schema.

  • Usage: song-client register-analysis-type [OPTIONS]

    OptionDescription
    -f, --fileFile path for the new analysis type

Submit​

  • Searches for analysis objects based on various parameters.

  • Usage: song-client search [OPTIONS]

    OptionDescription
    -a, --analysis-idSearch by analysisId
    -d, --donor-idSearch by donorId
    -f, --file-idSearch by fileId
    -sa, --sample-idSearch by sampleId
    -sp, --specimen-idSearch by specimenId

Manifest​

  • Generates a manifest file for an analysis.

  • Usage: song-client manifest [OPTIONS]

    OptionDescription
    -a, --analysis-idAssociated analysisId
    -f, --fileOutput manifest file name and directory
    -d, --input-dirDirectory containing upload files
    info

    For more information, see our documentation on submitting data with Song.

Publish​

  • Publishes an analysis.

  • Usage: song-client publish [OPTIONS]

    OptionDescription
    -a, --analysis-idAssociated analysisId
    -i, --ignore-undefined-md5Proceed if any file's md5 hash is undefined

Unpublish​

  • Marks data as unavailable to downstream services.

  • Usage: song-client unpublish [OPTIONS]

    OptionDescription
    -a, --analysis-idAssociated analysisId

Suppress​

  • Blocks data from being accessed.

  • Usage: song-client suppress [OPTIONS]

    OptionDescription
    -a, --analysis-idAssociated analysisId
    info

    For more information on analysis management, see our documentation on Song publication controls.

Export​

  • Exports payloads based on various parameters.

  • Usage: song-client export [OPTIONS]

    OptionDescription
    -a, --analysis-idExport payloads for a specific analysisId
    -f, --inputFilePath to file with analysisIds (one per line)
    -o, --output-dirDirectory to save the export
    -s, --studyIdExport payloads for a specific studyId
    -t, --threadsNumber of concurrent export threads

Update-File​

  • Updates file metadata.

  • Usage: song-client update-file [OPTIONS]

    OptionDescription
    -a, --accessFile access (Options: open, controlled)
    -d, --datatypeFile datatype (e.g., BAM, VCF)
    -i, --infoAdditional file metadata
    -m, --md5File MD5 hash
    --object-idUnique object ID of the file
    -s, --sizeFile size in bytes

Need Help?​

If you encounter any issues or have questions, please don't hesitate to reach out through our relevant community support channels