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:
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:
| 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
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:
| 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