Dear all,
I'm installing a local version of Galaxy but I'm having issues
configuring the FTP upload functionality that I need. I assume the
documentation in the wiki about configuring proftpd is outdated since
Galaxy has recently changed authentication method.
I apologize in advance for the le
Hi Rob,
Indeed, I had/have some difficulties with setting temporary
directories. The problem was that FTP uploaded data was first copied to
TMPDIR prior to being put in the database directory.
My solution: I extended the /tmp partition to several GB's, by mounting
a bigger device over it.
Joachim, Nate,
Leon Mei pointed me to a mailing list post of August 2012 where you two
discussed a problem with uploads to Galaxy filling up /tmp. I think I have
traced this down now after we suffered from this too several times.
There are a number of places where temporary files are configurable
On Oct 24, 2012, at 9:09 PM, Oliver Berkowitz wrote:
> Hi,
>
> I am having an issue withuploading data via FTP. I get the following error:
>
> Response:530 Sorry, the maximum number of clients (3) for this user
> are already connected.
> Error: Critical error
> Error: Could not co
Hi,
I am having an issue withuploading data via FTP. I get the following
error:
Response:530 Sorry, the maximum number of clients (3) for this
user are already connected.
Error: Critical error
Error: Could not connect to server
Is this because I try to upload too many file
Hi Nate,
I have set the new_file_path to the FTP upload directory as you
suggested. new_file_path=/mnt/galaxydb/ftp
This did not succeed however: still there is copying to the /tmp directory.
I also see that importing data sets into data libraries from a directory
of files behaves similarly
On Aug 17, 2012, at 3:17 AM, Joachim Jacob wrote:
> Hi Nate,
>
> thanks. Do you know what's the reason for using copying first the contents to
> the /tmp directory, before copying it into a the database/files/... Seems
> inefficient to do so, or is this not how it works perhaps?
Hi Joachim,
I
Hi Nate,
thanks. Do you know what's the reason for using copying first the
contents to the /tmp directory, before copying it into a the
database/files/... Seems inefficient to do so, or is this not how it
works perhaps?
Regards,
Joachim
Joachim Jacob, PhD
Rijvisschestraat 120, 9052 Zwijnaa
On Aug 16, 2012, at 11:09 AM, Joachim Jacob wrote:
> Excuses for the repost, but I really need to solve this.
>
> Uploading with FTP fails on our Galaxy, because the /tmp directory has not
> enough space. How can I hack in the Galaxy code base that the temporary
> directory needs to be /mnt/gal
Excuses for the repost, but I really need to solve this.
Uploading with FTP fails on our Galaxy, because the /tmp directory has
not enough space. How can I hack in the Galaxy code base that the
temporary directory needs to be /mnt/galaxydb/tmp ? Another solution:
how can I provide a symlink to
Dear devs,
Question about FTP upload: is it correct that Galaxy copies the data
from the FTP upload directory to galaxy database instead of symlinking?
Can I set somewhere the option to symlink instead of copying?
I run galaxy in a small virtual machine. The Galaxy database is on a
network s
it shouldn't copy the file, it should move it, so there's no duplication.
what's the ownership and permission of the file after upload?
and don't use the database/files/ folder!
On Thu, Oct 13, 2011 at 9:09 AM, alessandro albiero <
alessandroalbi...@gmail.com> wrote:
> galaxy copy the file in the
Dear all,
I've a question about FTP upload of data.
The data uploaded via ftp are placed in the directory ftp_upload_dir defined
in universe_wgsi.uni
After the uploading, when a user select the data to import in its history,
galaxy copy the file in the dir file_path (defined in universe_wgsi.uni).
; --- On Tue, 4/19/11, vasu punj wrote:
>
> From: vasu punj
> Subject: Re: [galaxy-dev] FTP upload of data
> To: "Dannon Baker"
> Date: Tuesday, April 19, 2011, 8:37 AM
>
> Dannon,
>
> I used winSCP to upload the files but dont see in Galaxy in history
To be clear, you were able to connect to the galaxy server using WinSCP in
plain FTP mode, and had no errors uploading the files?
-Dannon
On Apr 19, 2011, at 9:37 AM, vasu punj wrote:
> Dannon,
>
> I used winSCP to upload the files but dont see in Galaxy in history of
> uploaded files or eve
Vasu,
No, a paid service is not at all required. jjw14's solution in that thread
predates native FTP transfer to galaxy, and that sort of intermediate paid host
is not necessary.
Find detailed instructions here:
https://bitbucket.org/galaxy/galaxy-central/wiki/UploadViaFTP
-Dannon
On Apr
Hi All,
I was wondering if there are instructions for uploading data files (large) to
Galaxy via FTP and if this is a paid service as per link :
http://seqanswers.com/forums/showthread.php?t=5328
Thnaks.
Vasu___
Please keep all repli
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