The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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NCBI SRA Import

NCBI SRA Import is a utility for importing accessions from the NCBI read archives using the fast Aspera network protocol. Files imported this way, rather than via the FTP interface, will appear in the iPlant Data Store anywhere from 5-25x more quickly.

Quick Start

  • To use NCBI SRA Import, navigate to the SRA accession you wish to import. Right click on the sra or sra-lite link and copy the FTP URL to your clipboard. Paste this value into the FTP URL field in the NCBI SRA import tool. The import process will be launched as a job. This is different than the process for importing from URLs or from the desktop, which is done right in the Data window in the Discovery Environment.
  • Resources: http://www.asperasoft.com/downloads/

Test Data

All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > ncbi_sra_import

Note that this directory contains outputs only

Input File(s)

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

  • Default parameters only, no further configuration needed.

Output File(s)

  • Expect an SRA or SRA-Lite file as output. For the test case, you will find the result in fileSRR001355.lite.sra. Please note that this file is hidden below 2-3 directories that recapitulate the structure of the NCBI remote resource.

Tool Source for App

  • Developed by Matthew Vaughn using code from AsperaSoft

1 Comment

  1. It Would be great if this can take a list of urls from the user and download a list of the urls.