Hello Carl,

We are using galaxy-dist on revision a4113cc1cb5e.

When we talk about private dataset, we mean datasets that have been uploaded to a user history through the Upload file tool. The access permission is allowed only to the current user role for these datasets.

Anonymous user are not allowed on our galaxy instance.

Regards,

Julien

Le 19 mars 2013 à 22:45, Carl Eberhard <carlfeberhard@gmail.com> a écrit :

Hello, Stephanie and Julien

What revision are you using IGBMC? 

Can you clarify what you mean by a private dataset? Are non-owners importing into a history via a shared history, or are they being passed a direct link to the UCSC display viewer from the owner?

Thanks for the information,

Carl

On Tue, Mar 19, 2013 at 1:27 PM, Stephanie LE GRAS <slegras@igbmc.fr> wrote:

Hi all,

Here is an update regarding the problem we are facing with Julien with our
local instance of Galaxy.

As Julien said
"we are encountering a problem when trying to use UCSC display application
on private dataset.
UCSC is giving us the following error message :
Unrecognized format line 2 of http://.../galaxy.bed
(note: chrom names are case sensitive)"

We have worked for hours on it today and we have identified that datasets
that can be uploaded to UCSC are actually public datasets and that Julien
can upload all his datasets to UCSC because they are all public by default.


What is interesting now is that we've seen that the path to the data in
the UCSC error message is :

http://www.galaxy-igbmc.fr/display_application/f1cb3a6ff6a93c01/ucsc_interv
al_as_bed/main/bea5029fce8b957e/data/galaxy.bed:


While it should be :

http://www.galaxy-igbmc.fr/display_at(Š)/galaxy.bed

Because the right function to use in order to check whether the dataset
can be uploaded to UCSC should be display_at but not display_application.

Any ideas of what could cause Galaxy not to use the right function?

Thank you in advance,


Stephanie
--
Stephanie Le Gras
Bioinformatics engineer
High throughput sequencing platform
IGBMC
1, rue Laurent Fries
67404 ILLKIRCH Cedex
France
Tel. : +33 (0)3 88 65 32 73
Tel. Solexa : +33 (0)3 88 65 32 97









Le 18/03/13 19:20, « Julien SEILER » <seilerj@igbmc.fr> a écrit :

>Hi all,
>
>We have installed a local galaxy server and we are encountering a problem
>when trying to use UCSC display application on private dataset.
>UCSC is giving us the following error message :
>Unrecognized format line 2 of http://.../galaxy.bed
>(note: chrom names are case sensitive)
>
>Curiously, it works fine with my personal account but it doesn't for all
>other users. It also works for displaying tracks based on a public
>dataset for all users.
>
>Could anybody explain us what's happening ?
>
>Thanks in advance for any help,
>
>Julien
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___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:

 http://lists.bx.psu.edu/