We found while creating our VMs for the GCC Training Day that browsers within
the VM (Ubuntu 12.04) were not able to consistently upload using the
AJAX/Hidden iframe method that Galaxy uses by default. I'm investigating the
problem. Are you able to upload using Firefox/Chrome/Safari on other OS's, or
is the problem specific to Fedora?
On Aug 1, 2012, at 9:33 AM, David Roquis wrote:
> Hello again,
> I've read on the mailing list that some galaxy users are facing the same
> problem as I do, and that it seems to be related to the internet browser.
> Indeed, I noticed that I have no problem uploading data while using IE 8 or
> 9, but that it almost never works with Firefox, Chrome or Safari. I also
> noticed that when it doesn't work, the script upload.py is not launched at
> Thanks again for possible help
> From: david_roq...@hotmail.com
> To: firstname.lastname@example.org
> Date: Mon, 16 Jul 2012 09:50:34 -0400
> Subject: [galaxy-dev] Problem with get data/uploading file
> Dear Galaxy community,
> I have a problem with uploading data on Galaxy, using the get data/upload
> file tool, and I can't figure out where the trouble comes from.
> Basically, when I try to upload files (size ranging from less than 1 Mo up to
> 600 Mo), sometimes it works, sometimes it doesn't (keep uploading forever),
> and I don't get any error message when it doesn't work. I can't find a
> pattern on when it works or not, it seems pretty random. It don't think it is
> related to the files I use, because I tried with different files, of
> different types and format, and the exact same file can sometimes be
> uploaded, sometimes not. One thing I have noticed is that when the upload is
> successful, a file is created in /tmp/, and when the upload runs forever, no
> new file appears in /tmp/.
> I have tried a couple of basic things to solve the problem: emptying the
> /tmp/, restarting galaxy, deleting permanently my history, etc. Sometimes I
> can upload 4-5 files in a row, then it stops working, and some other time I
> can't even upload one. When one upload keep running forever, even if I cancel
> it, no further uploads will work. I have to stop the uploads and restart
> galaxy, but it doesn't work 100% of the time (sometimes I have to try 2-3
> times before I can upload again).
> I am facing this problem on two different instances of galaxy. A development
> one that I simply installed on my /home/ using mercurial and didn't modified
> at all, and a production one that I just set up following the Galaxy Team
> recommendations (using PostgreSQL and nginx with the upload module, and
> working on a dedicated Galaxy user account). I am a beginner in informatics,
> and since I get no error message, I don't know where to look for a way to
> solve this annoying problem.
> Uploading files using data libraries under the admin menu seems to be working
> perfectly all the time.
> Thank you very much for your help and advice.
> David Roquis
> Ph.D. student
> University of Perpignan
> additional info:
> - I am using the latest version of galaxy, and my OS is Fedora 16
> - I tried working with and without virtualenv (made no difference).
> - I don't know if this is related or not, but it seems quite strange to me.
> Whenever I try to access "manage jobs" in the admin section (on both
> instances), I get the following error message: "This Galaxy instance is not
> the job manager. If using multiple servers, please directly access the job
> manager instance to manage jobs." How is that possible since I am not using
> multiple servers (especially for the development instance, which I haven't
> modified at all)?
> - debug = False is causing me a server error in the history frame (so I use
> True instead).
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Please keep all replies on the list by using "reply all"
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