Client Reference

Commands and options supported by the Score client.

Download

• The download command retrieves file object(s) from the remote storage repository.

• Usage: score-client download [OPTIONS]

  Option	Description
  --analysis-id	Download files for a specific Song analysis ID
  --force	Force re-download of existing file (overrides local file)
  --index	Also download file index if available
  --length	Limit number of bytes to download (default: entire file)
  --manifest	Download files based on manifest file ID, URL, or path
  --object-id	Download a specific file object ID
  --offset	Starting byte position for download (default: 0)
  --output-dir	Path to download directory
  --output-layout	Layout of output directory (bundle, filename, or id)
  --program-id	Download files for a specific Song program ID
  --study-id	Download files for a specific Song study ID
  --validate	Perform MD5 checksum validation if available
  --verify-connection	Verify connection to object storage repository first

Help

• The help command displays detailed information about Score client commands and options.

Info

• The info command shows active configuration details of the Score client.

• Usage: score-client info [OPTIONS]

  Option	Description
  --verbose	Display all Score client configuration properties

Manifest

• The manifest command shows entries of a specific Score manifest file.

• Usage: score-client manifest [OPTIONS]

  Option	Description
  --manifest	Manifest file ID, URL, or path to display

Mount

• The mount command provides a read-only FUSE filesystem view of the object storage repository.

• Usage: score-client mount [OPTIONS]

  Option	Description
  --cache-metadata	Cache metadata on local disk for faster load times
  --daemonize	Run mount point in background
  --layout	Mount point directory layout (bundle or object-id)
  --manifest	Manifest file to mount contents for
  --mount-point	FUSE file system mount point
  --options	Additional file system mount options
  --verify-connection	Verify connection to object storage repository first

Upload

• The upload command sends file object(s) to the remote storage repository.

• Usage: score-client upload [OPTIONS]

  Option	Description
  --file	Path to specific file for upload
  --force	Force re-upload of existing file (overrides repository file)
  --manifest	Upload files using manifest file ID, URL, or path
  --md5	MD5 checksum of file to upload
  --object-id	Upload specific file by object ID
  --validate	Perform MD5 checksum validation if available
  --verify-connection	Verify connection to object storage repository first

Url

• The url command reveals the URL of a specific file object in the storage repository.

• Usage: score-client url [OPTIONS]

  Option	Description
  --object-id	Object ID of file to display URL for

Version

• The version command provides current version details of the Score client.

View

• The view command stores locally and showcases a SAM or BAM file.

• Usage: score-client view [OPTIONS]

  Option	Description
  --bed-query	BED format file with ranges to query (overrides --query)
  --contained	Output alignments completely contained in specified region
  --header-only	Output only the SAM/BAM file header
  --input-file	Local path to BAM file for querying
  --input-file-index	Local path to index file (requires --input-file)
  --manifest	Manifest file for querying object IDs and ranges
  --object-id	Specific object ID to download slice from
  --output-file	Name of output file
  --output-format	Output file format (SAM or BAM)
  --output-dir	Path to output directory (with --manifest)
  --output-index	Write index files to output (with --manifest)
  --output-original-header	Output entire original header
  --output-type	Structure of output file (CROSS, MERGED, or TRIMMED)
  --query	Query for BAM file content extraction (coordinate format)
  --reference-file	Local path to FASTA file for CRAM decoding
  --stdout	Send output to stdout (forces SAM format)
  --verify-connection	Verify connection to object storage repository first

Additional Options

Additional option flags available for the score-client executable:

Option	Description
--profile	Define specific environment profile for configuration
--quiet	Run client in quiet mode with minimal info messages
--silent	Run client in silent mode without any info messages

Need Help?

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