Download help

Edinburgh Genomics makes use of Aspera technologies to securely and reliably deliver data at much higher speeds than traditional web and FTP transfers. Data is made available to users either via web browser or command line (CLI), and requires the installation of the Aspera Connect browser plugin.

 


 

 

Installing the plugin

 

Before you can begin downloading data, you will need to install the Aspera Connect browser plugin. This is a free-of-charge piece of software which handles Aspera downloads either within a web browser - it works with the latest releases of all major browsers on Windows, Mac OS X, and Linux - or from the command-line.

Please note that the browser plugin package also provides the command line client program, so you will need to install the Aspera Connect browser plugin even if you only wish to download via command-line.

 

Browser installation

 

In many cases, the easiest way to download the plugin is from within your web browser. If you don't already have the plugin installed when you connect to the Edinburgh Genomics server, you will be prompted to begin an automated installation of the appropriate version of the plugin.

 

Manual installation

 

If you have no means of installing the plugin via a web browser - for instance if installing on a headless machine - you'll need to install the plugin manually by downloading the appropriate version here.

 


 

Browser access

 

Once you have been notified that data for a particular project is ready, you'll be provided via e-mail with a URL to access it. Alternatively, you can login to the transfer server and see a list of all project directories containing your data:

https://transfer.genomics.ed.ac.uk/

 

You can select which directories or files you wish to download by selecting the relevant checkboxes. To begin the download, click the 'Download' button and the plugin will take care of the rest. The plugin software itself provides options to change the download location, transfer speed and various other options.

Please note that not all browser versions support the latest version of the plugin. Further information is available from the Aspera Connect page, and the user guide is available here.

 


 

Command Line access

 

Command-line access is provided via ascp, a binary executable for Linux and Mac which is installed locally on your computer when you install the Aspera Connect browser plugin. You can install the plugin from here.

When your project data is ready you'll be provided via e-mail with a URL which can also be used with ascp. In general, the syntax for downloading data (e.g. to the current directory) is as follows:

ascp -P 33001 -O 33001 <user>@transfer.genomics.ed.ac.uk:<project>/ <destination>

where <user> is your Edinburgh Genomics username, <project> is the project directory name, and <destination> is the destination directory on your computer. You will also need to enter your password if it's the first time you've connected.

 

You'll need to ensure that the location of the ascp binary is in your $PATH environment variable, or else specified directly on the command line. On Linux computers, this is usually:

~/.aspera/connect/bin/

and on Mac OS X:

~/Applications/Aspera Connect.app/Contents/Resources/

 

Further documentation is available here.

 

If your system does not allow the use or installation of Aspera on the command line, you can use FTP.

wget --ask-password --mirror ftp://<user>@transfer.genomics.ed.ac.uk:<project>/ <destination>

 

Access from unsupported platforms

 

To access your data from platforms unsupported by the Aspera Connect plugin, such as Solaris or FreeBSD, we may be able to provide an Aspera client package to facilitate the download. Please contact us for details.

 


 

Firewall considerations

 

Aspera utilizes non-standard TCP & UDP ports for transfer. You'll need to ensure that you're able to make outbound connections from your network on TCP & UDP port 33001 to fully make use of Aspera high-speed transfers. If for any reason these connections cannot be established, Aspera will fall back to standard (and slower) web transfer on ports 9080 & 9443.

Access via an FTP client

 

If you cannot use the Aspera client, a standard FTP client can be used to access your data. For example, on Windows, the WinSCP client can be used. The File protocol should be 'FTP'; Encryption should be 'TLS/SSL Explicit encryption; Host name is 'transfer.genomics.ed.ac.uk'; Port is '21'; and your user name and password as advised. You will be asked to accept the security certificate and should accept.