Files Submission

How to Submit Files

Hint

See also

Accessing the Files’ Web Page

The Files’ web page can be accessed from the Components button or Actions button associated with a profile [1].

Use Components’ Button to Navigate to Files’ Web Page

Click the profile-components-button button associated with a profile. Then, click the files-component-button from the popup menu displayed as shown below:

Stand-alone Files' profile component

Stand-alone Profile Components: Files component button

Use Actions’ Button to Navigate to Files’ Web Page

Click the profile-actions-button button associated with a profile. Then, click the action, Upload Files action from the popup menu displayed as shown below:

Stand-alone Files' profile action

Stand-alone Profile Actions: ‘Upload Files’ action

Submit Files from your Local (Computer) System

Note

The total maximum file size that can be uploaded from your local (computer) system is around 2 GB. If you have a file larger than 2 GB or have multiple files whose combined total size exceeds 2 GB, please submit the file(s) via the terminal.

  1. Click the add-files-via-computer-button button on the Files web page to add a new file by browsing your local file system

    'Add new file by browsing local file system' button

    Files web page: ‘Add new file by browsing local file system’ button


  2. An Upload File dialogue is displayed. Click the Upload button to choose a file from your local system.

    Upload File dialogue

    Files submission: Upload File dialogue


  3. The new file(s) will be displayed on the Files web page after a successful submission.

    File(s) submitted

    Files submission: Files’ web page displaying the uploaded file(s)



    Hint

    To add more files from your local system, click the add-files-via-computer-button1 button (once files have been submitted to the profile) as an alternative to clicking the add-files-via-computer-button button.

Submit Files via the Terminal

  1. Click the add-files-via-terminal-button button on the Files web page to add a new file from a cluster via the terminal.

    'Add new file via terminal' button

    Files web page: ‘Add new file via terminal’ button


  2. A Move Data dialogue is displayed. Follow the instructions displayed then, click the Process button to submit the file(s) to the profile.

    Move Data dialogue

    Files submission: Move Data dialogue

    Terminal with command inputted

    Input $ ls - F1 command in the terminal


    Move Data dialogue with details inputted

    Move Data dialogue: Input the filename(s) returned after having ran the $ ls - F1 command in the terminal. Then, click the Process button.


    Move Data dialogue with result (a command) after having clicked the "Process" button

    Move Data dialogue: Command outputted after having clicked command in the Process button. Download the command displayed.

    The downloaded file will have unknown or download as the file name depending on the browser you are using.


    Terminal with command pasted

    Paste the copied command in the terminal

    Alternatively, you can make the downloaded file executable then, run the file in the directory where the files are located:



  3. The new file(s) will be displayed on the Files web page after a successful file submission via the terminal i.e. after the command has been executed successfully in the terminal.

    Files submitted

    Files submission: Files’ web page displaying the uploaded file(s)



    Hint

    To add more files via the terminal, click the add-files-via-terminal-button1 button (once files have been submitted to the profile) as an alternative to clicking the add-files-via-terminal-button button.

How to Delete Files

Click the desired file from the list of files displayed on the Files’ web page. Then, click the Delete button (located in the top-right corner of the table) as shown below:

Delete files button

File deletion: Click the “Delete” button to remove the highlighted file from the profile

Files deleted successfully

File deletion: File has been deleted

Checking ENA File Upload Status

Note

A reads, annotations or assembly submission must be completed before the file(s) can be uploaded to ENA (European Nucleotide Archive).

After having completed a reads, annotations or assembly submission and associated a file(s) to it during the submission process in COPO, the file(s) are submitted to ENA (European Nucleotide Archive).

The status of the file(s) uploaded to the ENA can be checked in the column, ENA File Processing Status, on the reads, annotations or assembly web page.

The ENA File Processing Status column is highlighted with a red rectangle border in the image below:

ENA (European Nucleotide Archive) File Processing Status column on the reads, annotations or assembly web page

ENA File Processing Status: The status of the file(s) uploaded to ENA (European Nucleotide Archive)


Hint

  • Rows with a status of “File archived: PUBLIC” or in a green colour indicate that the file(s) have been successfully submitted to ENA.

  • Rows with a status of “Invalid file integrity: PRIVATE” or in a red colour indicate that the file(s) failed to be submitted to ENA.


Footnotes