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LEARNING MATERIALS
 

 

 

 

 

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  • The App chosen must match the BioProject metadata template for BioProject Creation or BioProject Update.
  • The same App will be run twice, once for validation, and once for submission.
  • If you made any changes to the submission package contents or file/folder names or metadata since last saving the BioProject metadata file remember to resave the BioProject metadata file before running an App.
  • The information buttons in the App info_button.png (to the left of the app name in the Apps list) provide important details.
  • The Validation stage is optional but may highly reduce errors detected by the SRA.  This is suggested for first time users.
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    For either validation or submission, if the App fails and no submission.xml file is created, there are one or more errors in the submission package.  See the Analysis log files (especially condor-stderr-0) for information to assist with error correction. After you correct each error, be sure to recreate the metadata file and revalidate it. The analysis will fail with the first error it encounters, so this step may need to be run multiple times.
  • Successful validation within the DE does not guarantee that the SRA will not detect additional errors.  
  • No analyses are performed by the App.  Metadata will be aggregated into the submission.xml file (Validation and Submission stages) and the package will be transferred to the SRA (Submission Stage).

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Step 4a - Validation  - Select  either the ‘ NCBI SRA Submission - BioProject Creation ’ or ‘  NCBI SRA Submission - BioProject Update ’ app. Run the app with the 'Validate metadata file only' option (Tutorial for running Apps in the DE).  If the submission.xml file is created in the DE Analysis output folder, the package has successfully passed validation . Move – move on to submission. If validation fails check the log files to find out why.

  •  Input:  The BioProject folder (top level of the submission package) and the BioProject metadata file (saved from the top-level of the submission package).
  • Output: 

    • Logs folder with information on job execution.

    • 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).

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