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Hello Asifullah, The Galaxy tool "Get Data -> Upload File" has instructions for uploading data to the FTP server. We recommend using the 3rd party utility FileZilla as a desktop FTP client. http://file-zilla.com/ Hopefully this will get you started, Best! Jen Galaxy team ps: In the future, if you could send questions directly to galaxy-user@bx.psu.edu, it would be very helpful for us. -- Jennifer Jackson http://usegalaxy.org

Hello Asifullah, Click on the "save" icon for the dataset to initiate a download. This icon is shaped like a little purple disk on the very left side of the dataset's box in the right history pane. Hopefully this is helpful, Thank you, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org

Hello Asifullah, It would be helpful if you would be able to share your history. Please note which exact datasets (by number) you are having problems saving. Use Options -> Share or Publish -> click on the button to Share via link and then email that to me. Thank you, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org

Hello Vasu, Are you still having problems? Or did this other reply help? http://gmod.827538.n3.nabble.com/Bam-file-after-Tophat-run- td2089789.html#a2092204 If the problem is persistent, Galaxy needs to be updated to get better UI support for downloading BAM files. Hopefully the problem can be resolved, but please let us know if you need more help. Thanks! Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org

Hi Vasu, Very sorry to hear that you are still having problems. Have you been able to do the update? It was not clear from your email. The latest is: http://bitbucket.org/galaxy/galaxy- central/wiki/GetGalaxy new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: % hg pull -u -r ca0c4ad2bb39 When you reply, could you note which revision you are using (perhaps you are pulling from galaxy-central instead?) Thanks for helping us to diagnose the problem, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org