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

song-client-5.0.2/bin/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:

Option	Description
`-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:

Option	Description
`-hs`, `--hide-schema`	Hide the schema. Default is false
`-l`, `--limit`	Query limit
`-n`, `--names`	Filter analysisTypes by names
`-o`, `--offset`	Query offset
`-sd`, `--sort-direction`	Sorting direction. Default is DESC, possible values are DESC or ASC
`-so`, `--sort-order`	AnalysisType fields to sort on
`-u`, `--unrendered-only`	Only retrieve the unrenedered schema that was initially registered. Default is false
`-v`, `--versions`	Filter 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:

Option	Description
`-f`,`--file`	Supply the file path for the new analysis type

Search

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.

Option	Description
`-a`, `--analysis-id`	Search by a given analysisId
`-d`, `--donor-id`	Search by a given donorId
`-f`, `--file-id`	Search by a given fileId
`-sa`, `--sample-id`	Search by a given sampleId
`-sp`, `--specimen-id`	Search by a given specimenId

Manifest

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

Option	Description
`-a`, `--analysis-id`	Associated analysisId
`-f`, `--file`	Name and directory for outputted manifest file
`-d`, `---input-dir`	Directory containing the files used for upload

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

Publish

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:

Option	Description
`-a`, `--analysis-id`	Associated analysisId

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

Suppress

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

Option	Description
`-a`, `--analysis-id`	Associated 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:

Option	Description
`-a`, `--analysis-id`	Export payloads under a specified analysisId
`-f`, `--inputFile`	Path of input file containing a single column of analysisIds on each new line
`-o`, `--output-dir`	Directory to save the export to
`-s`, `--studyId`	Export payloads under a specified studyId
`-t`, `--threads`	Number of concurrent threads to use during the export process.

Update-File

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

Option	Description
`-a`, `--access`	Options: [open, controlled], Possible Values: [open, controlled]
`-d`, `--datatype`	The datatype of the file, e.g., BAM, VCF.
`-i`, `--info`	Additional metadata or information about the file.
`-m`, `--md5`	MD5 hash of the file.
`--object-id`	Unique object ID representing the file.
`-s`, `--size`	Size of the file in bytes.

Analysis Management

Song Github