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


On 12/15/10 12:23 PM, vasu punj wrote:
I have submited your email to share job 31 and 25 are the Tophat runs
which I am trying to save as bam files from Floppy icon.
The job is run on our University cluster. I have alos enclosed screen
shot for your ready reference.
vasu

--- On *Wed, 12/15/10, Jennifer Jackson /<j...@bx.psu.edu>/* wrote:


    From: Jennifer Jackson <j...@bx.psu.edu>
    Subject: Re: [galaxy-user] Fwd: Need a generous help regarding uploading
    To: "vasu punj" <pu...@yahoo.com>
    Cc: "galaxy-u...@bx.psu.edu" <galaxy-u...@bx.psu.edu>
    Date: Wednesday, December 15, 2010, 10:02 AM

    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

    On 12/15/10 7:56 AM, vasu punj wrote:
     > I have done the same it gav eme bam index file when i removed the
     > extension index or as such it come out to be not right bam file
    format
     > as recognized by various tools
     > Thanks
     >
     > --- On *Wed, 12/15/10, Jennifer Jackson /<j...@bx.psu.edu
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=...@bx.psu.edu>>/* wrote:
     >
     >
     > From: Jennifer Jackson <j...@bx.psu.edu
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=...@bx.psu.edu>>
     > Subject: Re: [galaxy-user] Fwd: Need a generous help regarding
    uploading
     > To: "vasu punj" <pu...@yahoo.com
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=pu...@yahoo.com>>
     > Cc: "galaxy-u...@bx.psu.edu
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-u...@bx.psu.edu>"
    <galaxy-u...@bx.psu.edu
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-u...@bx.psu.edu>>
     > Date: Wednesday, December 15, 2010, 9:52 AM
     >
     > 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
     >
     > On 12/15/10 7:47 AM, vasu punj wrote:
     > > Hi,
     > > Can we save Bam file from Tophat out put if so how can we do that
     > please.
     > > Thanks.
     > >
     > > --- On *Wed, 12/15/10, Jennifer Jackson /<j...@bx.psu.edu
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=...@bx.psu.edu>
     > <http://us.mc1147.mail.yahoo.com/mc/compose?to=...@bx.psu.edu>>/*
    wrote:
     > >
     > >
     > > From: Jennifer Jackson <j...@bx.psu.edu
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=...@bx.psu.edu>
     > <http://us.mc1147.mail.yahoo.com/mc/compose?to=...@bx.psu.edu>>
     > > Subject: Re: [galaxy-user] Fwd: Need a generous help regarding
     > uploading
     > > To: "asifullah khan" <asifullah...@gmail.com
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=asifullah...@gmail.com>
     >
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=asifullah...@gmail.com>>
     > > Cc: galaxy-u...@bx.psu.edu
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-u...@bx.psu.edu>
     >
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-u...@bx.psu.edu>
     > > Date: Wednesday, December 15, 2010, 9:38 AM
     > >
     > > 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-u...@bx.psu.edu
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-u...@bx.psu.edu>
     >
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-u...@bx.psu.edu>
     > >
     >
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-u...@bx.psu.edu>,
     > > it would be very helpful for us.
     > >
     > > On 12/12/10 8:32 AM, Kelly Vincent wrote:
     > > >
     > > >
     > > > Begin forwarded message:
     > > >
     > > >> *From: *asifullah khan <asifullah...@gmail.com
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=asifullah...@gmail.com>
     >
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=asifullah...@gmail.com>
     > >
     >
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=asifullah...@gmail.com>
     > > >> <mailto:asifullah...@gmail.com
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=asifullah...@gmail.com>
     >
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=asifullah...@gmail.com>
     > >
     >
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=asifullah...@gmail.com>>>
     > > >> *Date: *December 12, 2010 11:01:27 AM EST
     > > >> *To: *galaxy-user-ow...@lists.bx.psu.edu
    
<http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-user-ow...@lists.bx.psu.edu>
     >
    
<http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-user-ow...@lists.bx.psu.edu>
     > >
     >
    
<http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-user-ow...@lists.bx.psu.edu>
     > > >> <mailto:galaxy-user-ow...@lists.bx.psu.edu
    
<http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-user-ow...@lists.bx.psu.edu>
     >
    
<http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-user-ow...@lists.bx.psu.edu>
     > >
     >
    
<http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-user-ow...@lists.bx.psu.edu>>
     > > >> *Subject: **Need a generous help regarding uploading*
     > > >>
     > > >> Dear All,
     > > >>
     > > >> I am in trouble to upload 1.2Gb illumine data on Galaxy page for
     > > >> subsequent assembling and analysis steps. I am basically a
     > biologist
     > > >> and new regarding utility of modern bioinformatics tools.
    some one
     > > >> have suggested to upload first your data on a http web page
     > then it
     > > >> would be easy to be uploaded on GALaxy. But it is also not
     > possible
     > > >> for me as having little computer knowledge. So could some one
     > > help me
     > > >> generously regarding these issue. I will highly appreciate
     > > his/her help.
     > > >>
     > > >> Regards
     > > >> Asifullah Khan
     > > >
     > > >
     > > >
     > > > _______________________________________________
     > > > galaxy-user mailing list
     > > > galaxy-user@lists.bx.psu.edu
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-u...@lists.bx.psu.edu>
     >
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-u...@lists.bx.psu.edu>
     > >
     >
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-u...@lists.bx.psu.edu>
     > > > http://lists.bx.psu.edu/listinfo/galaxy-user
     > >
     > > --
     > > Jennifer Jackson
     > > http://usegalaxy.org <http://usegalaxy.org/>
    <http://usegalaxy.org/> <http://usegalaxy.org/>
     > > _______________________________________________
     > > galaxy-user mailing list
     > > galaxy-user@lists.bx.psu.edu
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-u...@lists.bx.psu.edu>
     >
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-u...@lists.bx.psu.edu>
     > >
     >
    <http://us.mc1147.mail.yahoo.com/mc/compose?to=galaxy-u...@lists.bx.psu.edu>
     > > http://lists.bx.psu.edu/listinfo/galaxy-user
     > >
     > >
     >
     > --
     > Jennifer Jackson
     > http://usegalaxy.org <http://usegalaxy.org/> <http://usegalaxy.org/>
     >
     >

    --
    Jennifer Jackson
    http://usegalaxy.org <http://usegalaxy.org/>



--
Jennifer Jackson
http://usegalaxy.org
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