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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SRA Submission Report Retrieval App

Description and Quick Start

Please see NCBI SRA Submission Tutorial for more on how this App fits into the larger NCBI Sequence Read Archive (SRA) Submission Pipeline process.

After you have sent your submission package to the NCBI Sequence Read Archive (SRA), and received email notification of the status of the submission from the SRA, you can use this App to retrieve the SRA system report on your submission. If the SRA detected errors that must be corrected for resubmission, i.e., the submission failed at the SRA, this report will help you with error correction. Note that this is not a required step for submission to the SRA.

Example Data

Input and output example data for this App appears directly in the Discovery Environment in the Data window under /iplant/home/shared/iplantcollaborative/example_data/SRA_submission/1_SubmissionOutput/BioProjectCreateExample/TESTVERSIONNCBISRASubmissionDinkinsNOBP22-2015-06-02-00-08-21.8/jdebarry.81784634-08ba-11e5-a9ae-3c4a92e4a804 and 2_SRA_Report_Retrieval_Output

Input File(s)

Select the CyVerse Analysis output folder named for your CyVerse username that was generated when you submitted to the SRA. The report will be fetched from the SRA and placed in a new Analysis output folder.

In the above example this is jdebarry.81784634-08ba-11e5-a9ae-3c4a92e4a804

  • Note: if report.xml is not retrieved that does not mean submission failed.

Parameters Used in App

None

Output File(s)

report.xml file retrieved from the SRA that contains the SRA-generated report on this submission you entered as input.

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