Galaxy FTP Upload
File Upload via FTP
Uploading data directly from the browser can be unreliable and cumbersome. Because of this some Galaxies including the Main allow you to upload data via FTP. FTP will allow you to monitor the upload status as well as resume interrupted transfers. Compression types .gz/.gzip, .bz/.bzip, .bz2/.bzip2, and single-file .zip are also supported.
If you are completely new to FTP transfers you might benefit from reading a wikihow page about it.
To get started using FTP with Galaxy, you'll need to have registered a regular Galaxy account. Once registered, you can initiate an FTP connection in your preferred FTP client. Please see the comparison of available FTP clients.
Upload with a client
In most clients, when a connection is made with
FTPS, a pop-up server certificate authentication will need to be accepted.
In this video, the changes for
FTPS are explained along with how to configure
FTP client settings and verfify the target server's certificate.
Need more help? See: Galaxy Help
Upload with lftp (command line)
In this example,
lftp for MacOS is used.
First, check to see if
lftp is installed. Type in the command and the prompt will result, as show below, if installed. Type
exit at the prompt to back out of the session.
$ lftp lftp :~>
If the command is not found,
brew can be used to install
lftp. Instructions when using MacOS.
lftp when connecting to the Public Main Galaxy server. Executing the command will prompt for your password. Your
password are exactly the same as when logging into your account at https://usegalaxy.org.
For explicit FTPS:
$ lftp -u firstname.lastname@example.org usegalaxy.org
For implicit FTPS:
$ lftp -u email@example.com ftps://usegalaxy.org
If you are using a different Galaxy server,
FTPS may or may not be enabled, or the server may only accept implicit or explicit
FTP/FTPS connections. Check with the administrators of that server if you are not sure.
FTP instructions for a Galaxy server that has
FTP enabled but not
FTPS. The base URL for the server is used for
othergalaxy.org in the command below. The
password is also server specific and the same as when logging in through a browser.
$ ftp -u firstname.lastname@example.org othergalaxy.org
Import to Galaxy
Files uploaded to the FTP server won't automatically be imported to your history - rather, you will be presented with a list of the contents of your FTP directory in the standard upload interface. Select the ones you want to import and hit Start.
Configure for your Galaxy
FTP upload can be configured in local installations of Galaxy, instructions to do so can be found at admin/config/upload-via-ftp.