Command Reference
Invoking a Command
Invoke a command by running the score-client executable and appending the necessary options and input values.
For instance, to use the upload command with the --manifest option:
docker exec score-client sh -c "score-client upload --manifest ./<directory>/manifest.txt"
Commands
The sections below provide a reference for all commands and their respective options supported by the Score client.
Download
The download command is used to retrieve file object(s) from the remote storage repository and can be used with the following option flags:
| Option | Description |
|---|---|
--analysis-id | Download files for a specific Song analysis ID. |
--force | Force a re-download of the file if it already exists locally (overrides local file). |
--index | If available, also download the file index. |
--length | Limit the number of bytes to download to this value. By default, if this option is not specified, all of the file will be downloaded. |
--manifest | Download specific files based on a manifest file ID, manifest file URL, or path to the manifest file. |
--object-id | Download a specific file object ID. |
--offset | Byte position in the source file to begin download from. By default, if this option is not specified, all of the file will be downloaded. |
--output-dir | Path to the output directory where files will be downloaded to. |
--output-layout | Layout of the output directory, one of: |
* bundle : Saved according to the filename under the Song bundle ID directory. | |
* filename : Saved according to the filename in the output directory. | |
* id : Saved according to the object ID in the output directory. | |
--program-id | Download files for a specific Song program ID. |
--study-id | Download files for a specific Song study ID. |
--validate | If available, perform validation on file MD5 checksum. |
--verify-connection | First verify the connection to the object storage repository. |
Help
The help command can be used to display detailed information about Score client commands and their options.
Info
The info command shows the active configuration details of the Score client. It can be used with the following option flag:
| Option | Description |
|---|---|
--verbose | Displays an exhaustive list of all Score client configuration properties. Without this option, only a reduced, minimal set of properties is displayed. |
Manifest
The manifest command shows entries of a specific Score manifest file. It can be used with the following option flag:
| Option | Description |
|---|---|
--manifest | Manifest file ID, manifest file URL, or path to the manifest file that you want to display the contents for. |
Mount
The mount command is a read-only FUSE filesystem view of the object storage repository in use by Score, and it can be used with the following optional flags:
| Option | Description |
|---|---|
--cache-metadata | To make load times faster, you can optionally cache metadata on the local disk and use the cache if available. |
--daemonize | Optionally detach the mount point and run it in the background instead. |
--layout | Layout of the mount point directory, one of: |
* bundle : Nests files in the bundle directory. | |
* object-id : Uses a flat list of files named by their associated object ID. | |
--manifest | Manifest file ID, manifest file URL, or path to the manifest file that you want to specifically mount contents for. |
--mount-point | The mount point of the FUSE file system. For this command to work, the mount point must exist, be empty and be executable by the current user. |
--options | Additional mount options of the file system that you want to use. This may vary depending on the file system. E.g. user_allow_other, allow_other, fsname=debug, etc. |
--verify-connection | First verify the connection to the object storage repository. |
Upload
The upload command sends file object(s) to the remote storage repository. It can be used with the following option flags:
| Option | Description |
|---|---|
--file | Upload a specific file by providing the path to that file. |
--force | Force a re-upload of the file if it already exists in the object storage (overrides file in the repository). |
--manifest | Upload specific files using a manifest by providing the manifest file ID, manifest file URL, or path to the manifest file. |
--md5 | MD5 checksum value of the file to upload. |
--object-id | Upload a specific file by providing its object ID. |
--validate | If available, perform validation on file MD5 checksum. |
--verify-connection | First verify the connection to the object storage repository. |
Url
The url command reveals the URL of a specific file object in the object storage repository. It is used with the following option flag:
| Option | Description |
|---|---|
--object-id | Object ID of the specific file you want to display the URL for. |
Version
The version command provides the current version details of the Score client.
View
The view command stores locally and showcases a SAM or BAM file. It can be used with the following option flags:
| Option | Description |
|---|---|
--bed-query | You can optionally specify a file in BED format containing specific ranges to query. This option overrides the --query option. |
--contained | Only output sequence alignments completely contained in a specific region. If this option is not used, then by default any alignment that intersects with a specified region will be returned. |
--header-only | Only output the header of the SAM or BAM file. |
--input-file | Local path to the BAM file being queried. This option supercedes the --object-id option. |
--input-file-index | Local path to index file. This requires the --input-file option to also be provided. |
--manifest | Manifest file ID, manifest file URL, or path to the manifest file containing object IDs and ranges that you want to query for. |
--object-id | Specific object ID inside a BAM file from which to download a slice from. This option supercedes the --manifest option. |
--output-file | Name of the file to write output to. If not specified, then the metadata filename or the original input filename will be used by default. |
--output-format | File format being queried and written to output, either SAM or BAM. |
--output-dir | Path to the output directory where the output file will be stored. Only used with the --manifest option. |
--output-index | Indicates whether to write index files to output. Only used with the --manifest option. |
--output-original-header | Output the original header in its entirety. |
--output-type | Structure of the output file containing query results. One of: CROSS, MERGED, or TRIMMED. Only used with the --manifest option. |
--query | Query used to define what contents to extract from a BAM file. You must use coordinate format (sequence:start-end). Note that multiple ranges must be separate by a space. |
--reference-file | Local path to the FASTA file that a CRAM file was encoded with. |
--stdout | Indicates whether to send output to stdout instead of a file. Only used with the --object-id option and output will always be forced to SAM format. |
--verify-connection | First verify the connection to the object storage repository. |
Additional Options
Below is a table of supplementary option flags available for the score-client executable:
| Option | Description |
|---|---|
--profile | Define a specific environment profile used to resolve configuration properties. If not specified, the default profile is used. |
--quiet | Run client in quiet mode, with a reduced, minimal set of info messages displayed during execution. |
--silent | Run client in silent mode, without any additional info messages displayed during execution. |
Downloading Data