Hello Alicia, Your local administrator can set up the local instance to accept SFTP connections (instead of FTP connections). As an end-user, you would basically follow the same protocol as when using FTP, either direct by command line (using SFTP instead of FTP) or by setting the client (Filezilla, etc) to use SFTP. Your admin would follow these instructions for set-up: http://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP If they need more assistance to do this, the galaxy-dev@bx.psu.edu mailing list is the correct place to ask for more help. Details about the configuration will help the developers to offer the most useful feedback. There are other ways to load local data, including adding data as loaded/linked libraries or via file URLs into the "Get Data -> Upload File" tool. Your admin should be able to help you decide which was the intended usage path to avoid data duplication or to manage internal network bandwidth. Best, Jen Galaxy team On 10/24/13 12:20 PM, Alicia Linford wrote:

Hi, I have been using the Main galaxy instance for analysis of ChIP-Seq data. My university has recently installed a local instance of Galaxy and we have an SFTP server available. Is there an easy way to upload fastq files to Galaxy by SFTP rather than FTP?

Thanks

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