Moving Data to Galaxy

Galaxy Data Management

The first big hurdle to overcome for any bioinformatics analysis is to collect the data and get it to the right place. You've gotten this far, which means you have some data collected and you are eager to see what it means. There are a number of ways to get your raw data into Galaxy and get it into working order. We will start with the basics.

Galaxy Upload Data Tool for local files

This is the easiest option, but also the most limited. If you have a very small file (2MB or less), than you can put the file into Galaxy from your local computer using this tool. There is a strict limit of 2GB due to the nature of transferring data using HTTP - anything big will take forever and end up failing.

Using a URL

Galaxy allows users to paste a URL containing their data and will handle the transfer of the file in a similar way to local files.

Using SFTP

Trinity Galaxy has a running SFTP server where you can deposit large files that you need to use in your analysis. This allows you to use secure protocols to move your data to Galaxy.

Use an SFTP client to move your files onto the server. Graphical clients include FileZilla for many platforms, WinSCP for Windows and Cyberduck for the Mac.

Use the following settings to make the connection:

  • Protocol: SFTP (Secure File Transfer Protocol)
  • Server: galaxy.ncgas-trinity.indiana.edu
  • Port: 2222
  • Credentials: You must use your Galaxy username (email) and password to authenticate for the file transfer
  • Path: Upload your files to the uploads directory, and download files from the downloads directory

If you cannot access the server or if you experience problems moving the files, please contact NCGAS for assistance.