Below, we give two different ways of uploading your files:
  • FileZilla (recommended and very easy to use!)
  • FTP command line client (Linux / Unix / Mac)
    • Note that the Windows command line client is not supported.

Uploading Submission via the FileZilla FTP Client

Step 1. Setup

  • Download and install the FileZilla Client.
  • After opening the client, make sure that you change your transfer type to binary mode (from the default type of Auto).
    This is done to ensure that your files are uploaded properly to our server.
    To change your transfer type, go to the menu bar at the top of the window and select the following:
    Transfer -> Transfer type -> Binary.
  • Fill in the following information just below the menu bar:
    • Host:
    • User name: Your Genboree username
    • Password: Your Genboree password
    • The port can remain blank, as our FTP server uses the default of 21.
  • Click "Quickconnect" to connect to the FTP server.
  • You will see your own files displayed on the left side of the window ("Local site") and the FTP server's files displayed on the right side of the window ("Remote site").

Step 2. Uploading Your Files

  • Navigate to the directory that contains your manifest file, metadata archive, and data archive using the left side of the window.
  • Navigate to your upload directory (unique and private to your lab/group) using the right side of the window.
    • This directory will look something like "/exrna-amilo1/inbox"
  • Drag and drop your submission (which should consist of three files) from the lower left panel to the lower right panel.
  • Once your transfer is successful (you can see the progress of your transfer in the panel at the bottom of the window), close FileZilla - you're done!

Resuming File Upload (If Upload Fails)

If your transfer fails before it completes, you can easily resume it from the point where it failed.
  • When you open FileZilla, there should be information about incompletely transferred files in the bottom panel of the window (under "Queued files").
  • Right click anywhere in that panel and click "Process Queue". Make sure that you type your password in when requested.
  • Select the action "Resume" from the options listed and click OK.
  • Repeat this last step for each file that you want to resume.

Uploading Submission via the FTP Command Line Client (Linux / Unix / Mac)

Step 1. Setup

  • Open up a terminal and navigate to the directory on your local computer that contains the 3 files that you're going to submit.
  • Type "ftp" to connect to our FTP server.
  • When prompted, enter your FTP login (Genboree username) and FTP password (Genboree password).
  • Switch to binary transfer mode by typing "bin" - this will ensure that your files are transferred correctly.
  • Navigate to your lab's private directory. You can do this by typing "cd [PRIVATE_DIR]", where [PRIVATE_DIR] is your lab's private directory (given to you via e-mail).
  • Next, navigate to your lab's inbox directory by typing "cd inbox/".
  • Type "prompt" to switch off confirmation for each file uploaded.

Step 2. Uploading Your Files

  • Use the "mput" command to upload your files by typing "mput" followed by the respective names of your manifest file, metadata archive, and data archive.
  • Type "dir" to ensure all your files have been copied and the file size of the copied file is same as the original file size.
  • After the file transfers are complete, type "bye" to exit the FTP client.


Imagine that I had the following set of three files:
  • Manifest named test.manifest.json
  • Metadata archive named
  • Data archive named

Furthermore, all 3 files are stored at the following location on my local computer: /home/myHome/myDataDir/smallRNASeqData.
I would perform the following commands to upload all three files to the FTP server (replacing PICODE with whatever my PI code is):

cd /home/myHome/myDataDir/smallRNASeqData
# enter login name and password
cd exrna-PICODE/
cd inbox/
mput test.manifest.json

Please note that any lines that begin with # are comments and are not actual commands that you should type!
For example, you shouldn't actually type "# enter login name and password" - that's just me informing you that
you'll need to enter your login name and password after the "ftp" command.

Resuming File Uploads (If Upload Fails)

If your upload fails and you want to resume it, you will need to reconnect to the FTP server and navigate back to your
upload directory (remember to type "bin" and "prompt" just like before!).
  • Check the file size of your partially-transferred files by typing "dir". You can compare their respective
    byte sizes with your local versions of the files - if the versions on the FTP server are smaller, that means that the files were
    only partially transferred. For each partially transferred file, you will want to complete the following process:
  • Type "restart" followed by the total number of bytes in the partially-transferred file.
    • Example: If my partially-transferred file was 1000 bytes, I would type "restart 1000".
  • Type "put", hit enter, and then fill in the name of the file, when prompted, for both local and remote. You will put the
    same name ("", for example) for both local and remote.
  • Type "dir" to check that the file transfer completed successfully, and then type "bye" to log off.
# enter login name and password
cd exrna-PICODE/
cd inbox/
# to restart uploading a partially transferred file with file size 1000 bytes
restart 1000

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