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New page for HPCDATAMGM-1862: CLU for dbGaP download tasks |
If your user account has the Read permission level on various collections, you can download one or more data files in those collections, from DME to dbGaP (Aspera).
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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.
Run the following command:
Panel borderColor silver borderStyle solid Clipboard AllowLineWrap true dm_download_dataobject_dbgap aspera [optional parameters] [DME data path] <Aspera destination> <destination bucket> <destination-path> [Aspera credentials file path]
The following table describes each parameter:
Parameter Description [-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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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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