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).
To download one or more data files to dbGaP:
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:
dm_download_dataobject_aspera [optional parameters] [DME data path] <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.
<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 File Example
The following example uses the credentials file in a non-default location to download a data file from DME.
In this example, the command performs the following:
- Locates or creates a folder1 folder in the bucket1 bucket.
- Locates or creates a subfolder1 folder within the folder1 folder.
- Downloads the data.txt file from the Project_1 collection in DME.
- Saves that file in the subfolder1 folder as file1.txt.
Multiple Files Example
For another example, consider the following command.
With the following code in the specified file-list.txt file, the above command uses the credentials file in a default location to download multiple data files from various locations in DME.
/Example_Archive/PI_Lab2/Project_1/data.txt /Example_Archive/PI_Lab2/Project_2/image.jpg /Example_Archive/PI_Lab3/Project_1/image.png
In this example, the command performs the following:
- Locates or creates a folder1 folder in the bucket1 bucket.
- Locates or creates a subfolder1 folder within the folder1 folder.
- Downloads from DME all files listed in the specified file-list.txt file.
- Saves those files in the subfolder1 folder with the same file names they have in DME.
