Upload longRNAseq Submission to the DCC using FTP Server

Below, we give two different ways of uploading your files:
  • LFTP command line client (Linux / Unix / Mac)
  • FileZilla

Please contact us at if your data archive is over 100GBs.

Uploading Submission via the LFTP 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 "lftp ftps://ftps.genboree.org -u [username]" to connect to our FTPs server, where [username] is your FTP login or Genboree username.
  • When prompted, enter your FTP password (Genboree password).
  • 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/".

Step 2. Uploading Your Files

  • Use the "put" command to upload your files by typing "put" followed by the respective names of your manifest file, metadata archive, and data archive.
  • Type "ls" 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 "exit" to exit the lftp client.

Example

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

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/longRNASeqData
lftp ftps://ftps.genboree.org -u username
# enter password
cd exrna-PICODE/
cd inbox/
put test_longRNAseq.manifest.json test_longRNAseq_metadata.zip test_longRNAseq_data.zip
ls
exit

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 password after the "lftp ftps://ftps.genboree.org -u <user name>" command.

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:
  • 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 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.
  • Drag and drop your submission (which should consist of two 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 will need to 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.

(If the file transfer completes after resuming from a previous transfer and the MD5 does not match to what you have provided, please remove the file and start from step 2 again.)

Send an email to notify us

  • Once all three files have been uploaded, please send an email at with your private lab folder name and file names.

Sending the data via a hard drive

Please coordinate with us at and provide the following information prior to sending the hard drive
  • PI name
  • Name of the study
  • total number of samples
  • size of the data archive (GBs/TBs?)
Copy the data archive, metadata, and manifest into the external hard drive
  • make sure the data archive is transferred correctly by checking the MD5 checksum of the file on the external hard drive.
  • Send the hard drive to:
    David Chen
    C/O BRL@ Baylor College of Medicine
    1 Baylor Plaza
    Jewish Building 400DM
    Houston, TX 77030

Notify us that you are sending the hard drive by emailing us at with the tracking number and the return information.

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