Hi Mathew,
Does the progress bar in the Upload window show any progress?
Thanks,
Sam
On Wed, Jul 9, 2014 at 10:27 AM, Dannon Baker
wrote:
> How large are the files you're attempting to upload?
>
> Another method for uploading with more reliability than web browsers would
> be to use FTP. See
How large are the files you're attempting to upload?
Another method for uploading with more reliability than web browsers would
be to use FTP. See the documentation here for more details:
https://wiki.galaxyproject.org/FTPUpload
-Dannon
On Tue, Jul 8, 2014 at 9:45 AM, Matthew Birnie wrote:
>
Hi,
I am having trouble uploading files. I have been attempting to upload four
files since noon (GMT) yesterday however the problem shows that the files
are still uploading.
I have cancelled the operation a couple of times hours after starting the
upload to try again but still nothing is happeni
ssage-
From: Kandalaft, Iyad [mailto:iyad.kandal...@agr.gc.ca]
Sent: Monday, June 02, 2014 2:01 PM
To: Curtis Hendrickson (Campus); John Chilton
Cc: galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Uploading files to galaxy from a folder
Hi Curtis,
I recall coming across the external chown s
June 02, 2014 2:27 PM
To: Kandalaft, Iyad; John Chilton
Cc: galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Uploading files to galaxy from a folder
John,
For us, it's not just a question of deleting the file, but of having permission
to do python's copystat (see stack trac
axy-dev-boun...@lists.bx.psu.edu] On Behalf Of Kandalaft, Iyad
Sent: Sunday, June 01, 2014 7:31 PM
To: John Chilton
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Uploading files to galaxy from a folder
Hi John
I will review the galaxy code more closely and implement it as you sugge
om]
Sent: June 1, 2014 7:53 PM
To: Kandalaft, Iyad
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Uploading files to galaxy from a folder
Hello Iyad,
Thanks for taking the time to describe your problem and share your
solution - I am sure other institutions have desires to harness the
ftp up
Hello Iyad,
Thanks for taking the time to describe your problem and share your
solution - I am sure other institutions have desires to harness the
ftp upload option the way you are doing it.
Is the only problem that occurs if the ownership is incorrect that
Galaxy cannot delete the files? If
Hi Everyone
I'm throwing this out there for some feedback and recommendations.
Objective: Facilitate transferring large files (> 2GB) from an HPC cluster (and
its associated fast tier storage) to galaxy for my clients. I enabled the FTP
upload option in galaxy but it involves users learning t
Thanks a lot for the answer !
kind regards,
Nicolas Cybulski
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Officially, I want to say that the data import tool cannot support
this request. You should download the data and upload it through FTP
or directly through the web interface. See this site for more
information: http://wiki.galaxyproject.org/FTPUpload.
Unofficially, you could try modifying the URL
Hi all,
I am trying to upload data from a password protected website
(http://ddlab.sci.univr.it/~centrogenomica/huang_no_project/).
My stdout is (obviously0 "Enter username for Reserved Area at
ddlab.sci.univr.it:") which is kind of normal but not what I wont of course.
Is there a way around
Hey Neil,
Just last week pull request 94 was accepted into galaxy-central that
direct upload of files to history (without needing a URL). The python
bioblend (https://github.com/afgane/bioblend) API client does not yet
have it but it would be relatively easy to add, you will want to look
at uplo
This is the most recent thread on uploading files via the API; this approach
uses a URL for uploading a dataset to the history:
http://dev.list.galaxyproject.org/Uploading-to-history-via-JavaScript-td4657068.html
In general, using the Galaxy Web search and/or mailing list search to see if
your
Hi,
It seems the API documentation is a bit scarce. I'd like to upload a file
from the command line using the API rather than the GUI, but would like to see
the file in the history. Does anyone have any information how to do this/ any
tools that are available.
Thanks
Neil
__
I just tried setting up galaxy to use xSendFile[1] but that didn't
make any difference.
What's odd is that I'm still getting the same error in the galaxy log.
By using xsendfile shouldn't I now be avoiding using Galaxy to
process the upload over a socket?
Perhaps xsendfile isn't working?
-Greg
LimitRequestBody has a max value of 2147483647 (2GB). You probably want
to set it to zero to disable the limit:
http://httpd.apache.org/docs/current/mod/core.html#limitrequestbody
Also, you may be running into memory limits on the server, especially if
it's running a 32-bit OS (where each process
Hmm, no luck on the large uploads.
I tried using a recent version of Google Chrome.
I added these settings to /etc/httpd/conf/httpd.conf
Timeout 6000
LimitRequestBody 32147483647
And restarted apache.
But when I try to upload a 3.7GB file I get this error in Galaxy:
"Bad Gateway
The proxy se
This says Google Chrome can support uploads larger than 4 GB.
http://www.motobit.com/help/scptutl/pa98.htm
Maybe I just need to configure Apache?
I'll let you guys know what I find.
-Greg
On Thu, Nov 29, 2012 at 11:22 AM, greg wrote:
> Follow up question. What's the deal with the 2GB limit it
Follow up question. What's the deal with the 2GB limit it mentions?
I think it would be pretty convienent to allow larger uploads. We're
on a fast local network so even 10 or 20 GB uploads pretty fast.
Can I increase the limit in Apache? Which browsers are limited? This
is an internal install
On Nov 29, 2012, at 10:54 AM, greg wrote:
> Thanks. That seemed to have worked. Can you explain what happened?
> (I'm curious)
It's due to a bug that we've done quite a bit of work to investigate, but
haven't yet found the cause. It seems to have cropped up more frequently in
the past few w
Thanks. That seemed to have worked. Can you explain what happened?
(I'm curious)
-Greg
On Thu, Nov 29, 2012 at 8:43 AM, Nate Coraor wrote:
> On Nov 28, 2012, at 1:23 PM, greg wrote:
>
>> I just finished setting up a local install on our cluster but I'm
>> having trouble uploading files.
>>
>>
On Nov 28, 2012, at 1:23 PM, greg wrote:
> I just finished setting up a local install on our cluster but I'm
> having trouble uploading files.
>
> I was able to (successfully?) upload one 160MB fasta file. But any
> further uploads I try, they just hang.
Hi Greg,
Could you try the following:
I apologize for potentially sending this 2 (or 3?) times. I just
realized I might have sent it to the wrong address?
galaxy-dev@lists.bx.psu.edu != galaxy-...@bx.psu.edu?
Thanks again,
Greg
On Wed, Nov 28, 2012 at 1:23 PM, greg wrote:
> I just finished setting up a local install on our cluste
Hi guys,
I wanted to make sure this made it through to the dev list. I'm still
stuck on this :-(
Thanks,
Greg
On Wed, Nov 28, 2012 at 1:23 PM, greg wrote:
> I just finished setting up a local install on our cluster but I'm
> having trouble uploading files.
>
> I was able to (successfully?) up
I just finished setting up a local install on our cluster but I'm
having trouble uploading files.
I was able to (successfully?) upload one 160MB fasta file. But any
further uploads I try, they just hang.
Here's the information from the log file:
paste.httpserver.ThreadPool INFO 2012-11-28 12:15
You can determine what revision you have by running "hg tip" in the
galaxy checkout. Are you checking out from galaxy-dist or
galaxy-central?
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, Nov 8, 2012 at 10:41 AM, John Clayton
wrote:
> How can I determine if I have r
Dear Sir or Madam,
I am having difficult loading files onto my local galaxy instance. I
have given myself admin status, but when I attempt to add files to a new
library, I get the following message:
Error attempting to display contents of library (New data library):
(OperationalError) no suc
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