Command Reference

To invoke a command, run the song-client executable and append any options required after the command with the necessary input values.

For information on the available commands, use the following:

shell
docker exec song-client sh -c "sing --help"

The following is provided as a reference to all the commands and command options currently supported by the Song client.

Config

The config command shows the current configuraion settings.

Submit

The submit command is used to submit a payload to create an analysis. For more information, see our documentation on submitting data with Song.

Ping

The ping command can ping (test) the Song server.

Get-Analysis-Type

The get-analysis-types command is used to retrieve specific analysis type schema information based on the given parameters:

OptionDescription
-n, --name
-u, --unrendered-only
-v, --version

List-Analysis-Types

The list-analysis-types command is used to list all analysis types with filtering and viewing options based on the provided parameters:

OptionDescription
-hs, --hide-schemaHide the schema. Default is false
-l, --limitQuery limit
-n, --namesFilter analysisTypes by names
-o, --offsetQuery offset
-sd, --sort-directionSorting direction. Default is DESC, possible values are DESC or ASC
-so, --sort-orderAnalysisType fields to sort on
-u, --unrendered-onlyOnly retrieve the unrenedered schema that was initially registered. Default is false
-v, --versionsFilter analysisTypes by versions

Register-Analysis-Type

The register-analysis-type command is used to register a new analysis-type schema based on the provided file:

OptionDescription
-f,--fileSupply the file path for the new analysis type

The search command searches for analysis objects based on various input parameters. Unless specified by one of the following options, the search command will search for analysis within the current studyId.

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

Manifest

The manifest command generates a manifest file for an analysis with an associated analysisId.

OptionDescription
-a, --analysis-idAssociated analysisId
-f, --fileName and directory for outputted manifest file
-d, ---input-dirDirectory containing the files used for upload

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

Publish

The publish command is used to publish an analysis based on it's analysis Id: | Option | Description | |--|--| |-a, --analysis-id| Associated analysisId | |-i, --ignore-undefined-md5| If set, the publishing process will proceed even if the md5 hash of any file is not defined. |

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

Unpublish

The unpublish command is used to mark data as unavailable to downstream services:

OptionDescription
-a, --analysis-idAssociated analysisId

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

Suppress

The suppress command is used to block data from being accessed:

OptionDescription
-a, --analysis-idAssociated analysisId

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

Export

The export command is used to export a payload based on a variety of input parameters:

OptionDescription
-a, --analysis-idExport payloads under a specified analysisId
-f, --inputFilePath of input file containing a single column of analysisIds on each new line
-o, --output-dirDirectory to save the export to
-s, --studyIdExport payloads under a specified studyId
-t, --threadsNumber of concurrent threads to use during the export process.

Update-File

The update-file command is used to update file metadata:

OptionDescription
-a, --accessOptions: [open, controlled], Possible Values: [open, controlled]
-d, --datatypeThe datatype of the file, e.g., BAM, VCF.
-i, --infoAdditional metadata or information about the file.
-m, --md5MD5 hash of the file.
--object-idUnique object ID representing the file.
-s, --sizeSize of the file in bytes.