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.commailto: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.frmailto: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.bedhttp://www.galaxy-igbmc.fr/display_application/f1cb3a6ff6a93c01/ucsc_interval_as_bed/main/bea5029fce8b957e/data/galaxy.bed:

While it should be :

http://www.galaxy-igbmc.fr/display_at(%C5%A0)/galaxy.bedhttp://www.galaxy-igbmc.fr/display_at(%C5%A0)/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 73tel:%2B33%20%280%293%2088%2065%2032%2073 Tel. Solexa : +33 (0)3 88 65 32 97tel:%2B33%20%280%293%2088%2065%2032%2097

Le 18/03/13 19:20, « Julien SEILER » <seilerj@igbmc.frmailto: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 ___________________________________________________________ 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/

___________________________________________________________ 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/

Hi Dan,

I just updated our sources and… it works !

Thanks a lot,

Regards,

Julien

Le 21 mars 2013 à 16:30, Daniel Blankenberg <dan@bx.psu.edumailto:dan@bx.psu.edu> a écrit :

Hi Julien,

This was fixed in changeset 6cd4058d7b32 (https://bitbucket.org/galaxy/galaxy-dist/commits/6cd4058d7b32/). Can you update your Galaxy instance and see if the issue is resolved for you?

Thanks for using Galaxy,

Dan

On Mar 20, 2013, at 4:53 AM, Julien SEILER wrote:

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.commailto: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.frmailto: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.bedhttp://www.galaxy-igbmc.fr/display_application/f1cb3a6ff6a93c01/ucsc_interval_as_bed/main/bea5029fce8b957e/data/galaxy.bed:

While it should be :

http://www.galaxy-igbmc.fr/display_at(%C5%A0)/galaxy.bedhttp://www.galaxy-igbmc.fr/display_at(%C5%A0)/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 73tel:%2B33%20%280%293%2088%2065%2032%2073 Tel. Solexa : +33 (0)3 88 65 32 97tel:%2B33%20%280%293%2088%2065%2032%2097

Le 18/03/13 19:20, « Julien SEILER » <seilerj@igbmc.frmailto: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 ___________________________________________________________ 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/

___________________________________________________________ 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/