Uploading Files

Once your submission files have been prepared using the EgaCryptor, the resulting encrypted files and associated md5sum files can be uploaded to your submission account using Aspera or FTP.

Using Aspera to upload your prepared files

Downloading the Aspera ascp command line program

Aspera is a commercial file transfer protocol that may provide faster transfer speeds than ftp especially over longer distances.

The Aspera ascp command line client can be downloaded here . Please select *Aspera Connect*.

The ascp command line client is distributed as part of the aspera connect highperformance transfer browser plugin and is free to use, without registration.

Using the Aspera ascp command line program

The location of the 'ascp' program in the filesystem:

Mac: on the desktop go cd /Applications/Aspera\ Connect.app/Contents/Resources/ there you'll see the command line utilities where you're going to use 'ascp'.

Windows: the downloaded files are a bit hidden. For instance, in Windows 7 the ascp.exe is located in the users home directory in: AppData\Local\Programs\Aspera\Aspera Connect\bin\ascp.exe

Linux: should be in your user's home directory, cd /home/username/.aspera/connect/bin/ there you'll see the command line utilities where you're going to use 'ascp'.

Your command should look similar to this:
 ascp -P33001 -QT -l300M L file.gpg ega-box-N@fasp.ega.ebi.ac.uk:/.  
If you wish to uplaod several files without being requested the password , please use the below command :
 ASPERA_SCP_PASS=ega-box-password ascp -P33001 -QT -l300M L file.gpg ega-box-N@fasp.ega.ebi.ac.uk:/.  
Explanation of parameters

  • 'l300M' option sets the upload speed limit to 30MB/s. You may wish to lower this value to increase the reliability of the transfer.
  • 'L' option is for printing logs out while transferring
  • 'files to upload' can be a file mask (e.g. '/homes/submitter/*.srf) or a list of files.
  • 'egaboxN' is your submission account login.
  • Add 'k2' switch for transfer restarts

Check the command line transfer usage for more configuration details.

Using FTP to upload your prepared files

Using default FTP command line client in Windows

  1. Start the command line interpreter: press WinR, type cmd, hit enter
  2. Enter 'ftp ftp.ega.ebi.ac.uk'
  3. Enter your submission username
  4. Enter your submission password
  5. Type 'binary' to enter binary mode for transfer
  6. To see a list of available ftp commands type 'help'.
  7. Type 'ls' command to check the content of your submission account.
  8. Type 'prompt' to switch off confirmation for each file uploaded.
  9. Use 'mput' command to upload files: 'mput *.bam*'
  10. Use 'bye' command to exit the ftp client.
  11. Use 'exit' command to exit the command line interpreter.

Using default FTP command line client in Linux / Unix

  1. Open a terminal and type 'ftp ftp.ega.ebi.ac.uk'
  2. Enter your submission username
  3. Enter your submission password
  4. Type 'binary' to enter binary mode for transfer
  5. To see a list of available ftp commands type 'help'.
  6. Type 'ls' command to check the content of your submission account.
  7. Type 'prompt' to switch off confirmation for each file uploaded.
  8. Use 'mput' command to upload files: 'mput *.bam*'
  9. Use 'bye' command to exit the ftp client.

Using a FTP client

We recommend the use of Filezilla, a free FTP client . FileZilla is open source software distributed free of charge under the terms of the GNU General Public License

Use the following connection details (File=> Site Manager) and add your submission account username and password :

Using FTP client Filezilla

Select the files you wish to upload, then right click mouse, and select 'upload':

Using FTP client Filezilla

Troubleshooting

If you are having problems with Aspera connection timeouts, it can be down to either one of the following.

1 ) Transfers cannot start the connection fails instantly.
Ensure that TCP traffic on port 33001 is allowed (open) for outbound connections through your computer's firewall and network's firewall.

2 ) The connection is made, transfers are started, but 0 bytes (0%) are uploaded for each file.
Ensure that UDP traffic on port 33001 is allowed (open) for outbound connections through your computer's firewall and network's firewal