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 Submission - BioProject Update

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. This documentation is meant to instruct you on launching this App, not preparing an SRA submission package.

This App is used to update an existing NCBI BioProject by submitting a prepared SRA submission package to the SRA. Please see the link above for instructions on how to prepare the submission package.

Test 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/0SubmissionInput/BioProjectCreateExample and 1SubmissionOutput/BioProject_Create_Example

  • Note: These test files are for an example that Creates a BioProject as opposed to Updating a BioProject. The primary difference is the metadata entered during the assembly of the submission package. See the tutorial linked above for more.

Input File(s)

A complete SRA submission package is required for submission to the NCBI Sequence Read Archive (SRA). A The package will be contained in a 'BioProject' folder. The contents of the folder and associated metadata are described in the SRA Submission Tutorial.

A BioProject folder metadata file is required as the second input. The creation of this file is described in the SRA Submission Tutorial.

  • Note: Even though the button to submit is labeled “Launch Analysis”, no actual analyses are being run for these apps. The metadata will be aggregated into the submission.xml file and the package will be transferred to the SRA.
  • Note: All sequence files be compressed before submission.
  • Note: All sequence file names must be unique.submission. to the SRA. with this App, and each filename under a BioProject must be unique.

Parameters Used in App

If the “validate metadata file only” box is checked, nothing will be submitted to the SRA. The metadata you entered will be validated, and if it passes CyVerse quality checks, the submission.xml file will be created in the Analysis output folder. If the metadata fails validation, no submission.xml file will be created and the error will be logged in the Analysis output folder in the logs/condor-stderr-0 folder.

Output File(s)

Just like other CyVerse jobs, output will be generated in an analysis folder Output contains 2 folders:

  • logs folder with information on job execution that includes a ‘.manifest.txt’. file with a log of the files transferred to the SRA servers.
  • folder named with your CyVerse username and the top-level BioProject folder ID that contains the submission.xml (metadata file formatted for ingestion by the SRA) and a submit.ready file used to signal SRA systems that submission is complete and to process the submission package.

What happens after submission?

 What happens at SRA?  CyVerse systems connect to SRA systems and create the submission folder on the SRA side.  Files are transferred and a submit.ready file is sent to the SRA to signal that the submission package is complete and they can begin processing.  The SRA system validates the submission package and generates a report.xml file containing any errors detected.  The SRA system sends  notification email(s) to the contact email  provided in the BioProject metadata template, and to the CyVerse team to notify of either a successful or failed submission.  If there are errors, you can retrieve the submission report.xml file from SRA servers with the  'NCBI SRA Submission Report Retrieval' App in the DE, make corrections, and resubmit (see below).


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