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Comment: For HPCDATAMGM-1884: Corrected the command name.

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  1. Consider whether you want to download a single collection or multiple collections: 

    • To download a single collection: Plan to specify the path for that collection in the command. 
    • To download multiple collections: 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 collections 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_collection_dbgap aspera [optional parameters] [DME data path] <Aspera destination> <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-collection-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-collection-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 collection or collections that you want to download:

    • To specify multiple collections, 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 collections you want to download, delimited by newline.
    • To specify a single collection, specify the path for the DME collection you want to download.
    <Aspera destination>
    The name of the Aspera destination.
    <destination path>
    The path to and the name of the folder in the destination bucket. Do not begin the path with a slash. If the destination folder structure you specify does not already exist, DME creates it. 
    [Aspera credentials file path]

    The location of the credentials file. 

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dm_download_collection_dbgap aspera /Example_Archive/PI_Lab1/Project_1 bucket1 folder1/subfolder1/ /NCI/JaneDoe/Aspera/credentials

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dm_download_collection_dbgap aspera -f collection-list.txt bucket1 folder1/subfolder1/

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