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Comment: For HPCDATAMGM-1862: Revised based on recent Jira comment.

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  1. Consider whether you want to download a single data file or multiple data files: 

    • To download a single data file: Plan to specify the path for that data file in the command. 
    • To download multiple data files: In your local system, use a command line editor (such as vi editor) to create a file that lists the paths for all of the DME data files you want to download, delimited by newline. Plan to use the -f option to specify that file in the command. 
  2. Run the following command:

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    dm_download_dataobject_aspera [optional parameters] [DME data path] <Aspera destination> <destination bucket> <destination-path> [Aspera credentials file path]


    The following table describes each parameter:

    ParameterDescription
    [-D <REST-response>]

    An optional parameter, specifying a path and filename in your local system. The system always creates a response file:

    • If you specify this parameter, the system saves the response from the server to the specified file in the specified location.
    • If you omit this parameter, the system saves the file as download-dataobject-response-header.tmp in your home directory.
    [-o <output-json-file>]

    An optional parameter, specifying a path and filename in your local system. The system always creates an output file: 

    • If you specify this parameter, the system saves the output to the specified file in the specified location.
    • If you omit this parameter, the system saves the output as download-dataobject-response-message.json.tmp in your home directory.

    If the command is successful, the output file is empty.

    [-f <paths-file>]

    or

    [DME data path]

    One or more paths within DME. Select one of the following methods to specify the data file or data files that you want to download:

    • To specify multiple data files, use the -f parameter to specify a path and filename in your local system, of a file that lists the paths for all of the DME data files you want to download, delimited by newline.
    • To specify a single data file, specify the path for the DME data file you want to download.
    <Aspera<destination destination>bucket>
    The name of the destination Aspera destinationbucket.
    <destination path>
    The path to and the name of the folder in the destination Aspera bucket. Do not begin the path with a slash.  If If the destination folder structure you specify does not already exist, DME creates it.
    [Aspera credentials file path]

    The location of the credentials file. 

For some examples, consider the following code specified in a credentials file:

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Code Block
ASPERA_HOST=gap-submit.ncbi.nlm.nih.gov
ASPERA_USER=asp-dbgap
ASPERA_SCP_PASS=1234abcf-12c6-de34-9876abc7e543

If you omit ASPERA_HOST or ASPERA_USER, then the command uses dbGaP supplied values.

Single File Example

The following example uses the credentials file in a non-default location to download a data file from DME. 

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