Galaxy FTP Upload

File Upload via FTP

UPDATE: FTP upload is no longer supported on UseGalaxy.org. For more information and to learn about alternative options, please see https://help.galaxyproject.org/t/the-usegalaxy-org-ftp-service-will-be-decommissioned-on-august-12-2022/8318.

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.

Introduction

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 this example, FileZilla for MacOS is used. Point your client to the FTP server hostname provided in the upload modal window (usegalaxy.org for Galaxy Main).

If you are having trouble connecting to the Main server try enabling FTP with passive mode in your client. Please connect using FTP, FTPS, or FTP-TLS type of connections. All SFTP connections will be rejected.

In most clients, when a connection is made with FTP or 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.

Below you can see my files copied to the destination on Galaxy's FTP server.

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.

Command-line for lftp when connecting to the Public Main Galaxy server. Executing the command will prompt for your password. Your email (aka user@email.edu) and password are exactly the same as when logging into your account at https://usegalaxy.org.

For explicit FTPS:

$ lftp -u user@email.edu usegalaxy.org

For implicit FTPS:

$ lftp -u user@email.edu 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.

General 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 email (aka user@email.edu) and password is also server specific and the same as when logging in through a browser.

$ ftp -u user@email.edu 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.

Files not imported within 3 days will be cleaned up from the FTP site.

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.