If your user account has the Read permission level on various collections, you can download one or more of those collections, from DME to dbGaP (Aspera).
To download one or more collections to dbGaP:
Consider whether you want to download a single collection or multiple collections:
Run the following command:
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The following table describes each parameter:
Parameter | Description |
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[-D <REST-response>] | An optional parameter, specifying a path and filename in your local system. The system always creates a response file:
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[-o <output-json-file>] | An optional parameter, specifying a path and filename in your local system. The system always creates an output file:
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:
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<destination bucket> | The name of the destination Aspera bucket. |
<destination path> | The path to and the name of the folder in the Aspera 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. |
For some examples, consider the following code specified in a credentials file:
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 Collection Example
The following example uses the credentials file in a non-default location to download a collection from DME.
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In this example, the command performs the following:
Multiple Collections Example
For another example, consider the following command.
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With the following code in the specified collection-list.txt file, the above command uses the credentials file in a default location to download multiple collections from various locations in DME.
/Example_Archive/PI_Lab2/Project_1 /Example_Archive/PI_Lab2/Project_2 /Example_Archive/PI_Lab3/Project_1 |
In this example, the command performs the following: