Hi all, I have uploaded a gff annotation to a shared library and when I try to load it into trackster it tries consistently to load an older dataset that does not exist anymore and does not correspond to the real gff dataset file. If I load the gff into a history, then this file is correctly loaded into trackster. Any ideas what is going on? Any workaround so that we can load visualisations without creating histories with all the data beforehand? Cheers,Cristian
Hi Cristian
This problem sounds familiar. Have the new and the old file the same name? If so, try renaming your new gff file.
Hans-Rudolf
On Jun 10, 2015, at 10:34 AM, C. Ch. tuto345@hotmail.com wrote:
Hi all,
I have uploaded a gff annotation to a shared library and when I try to load it into trackster it tries consistently to load an older dataset that does not exist anymore and does not correspond to the real gff dataset file. If I load the gff into a history, then this file is correctly loaded into trackster.
Any ideas what is going on? Any workaround so that we can load visualisations without creating histories with all the data beforehand?
Cheers, Cristian ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Hans, Actually the older dataset has nothing to do with the actual GFF file name-wise or other. Trackster tries to load database/files/004/dataset_4402.dat (a dataset created in 01/2013 and which has been deleted and purged) whereas the GFF file corresponds to database/files/044/dataset_44835.dat.In another test, trackster tries to load database/files/003/dataset_3905.dat (12/2012, deleted and purged) when the real dataset file for the GFF is database/files/030/dataset_30088.dat. Cheers,CristianSubject: Re: [galaxy-dev] Trackster bug From: hansrudolf.hotz@fmi.ch Date: Wed, 10 Jun 2015 10:38:58 +0200 CC: galaxy-dev@lists.galaxyproject.org To: tuto345@hotmail.com
Hi Cristian This problem sounds familiar. Have the new and the old file the same name? If so, try renaming your new gff file. Hans-Rudolf
On Jun 10, 2015, at 10:34 AM, C. Ch. tuto345@hotmail.com wrote:Hi all, I have uploaded a gff annotation to a shared library and when I try to load it into trackster it tries consistently to load an older dataset that does not exist anymore and does not correspond to the real gff dataset file. If I load the gff into a history, then this file is correctly loaded into trackster. Any ideas what is going on? Any workaround so that we can load visualisations without creating histories with all the data beforehand? Cheers,Cristian___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
just double checking: and what about the 'name' in the History panel?
Hans-Rudolf
On Jun 10, 2015, at 11:43 AM, C. Ch. tuto345@hotmail.com wrote:
Hi Hans,
Actually the older dataset has nothing to do with the actual GFF file name-wise or other. Trackster tries to load database/files/004/dataset_4402.dat (a dataset created in 01/2013 and which has been deleted and purged) whereas the GFF file corresponds to database/files/044/dataset_44835.dat. In another test, trackster tries to load database/files/003/dataset_3905.dat (12/2012, deleted and purged) when the real dataset file for the GFF is database/files/030/dataset_30088.dat.
Cheers, Cristian Subject: Re: [galaxy-dev] Trackster bug From: hansrudolf.hotz@fmi.ch Date: Wed, 10 Jun 2015 10:38:58 +0200 CC: galaxy-dev@lists.galaxyproject.org To: tuto345@hotmail.com
Hi Cristian
This problem sounds familiar. Have the new and the old file the same name? If so, try renaming your new gff file.
Hans-Rudolf
On Jun 10, 2015, at 10:34 AM, C. Ch. tuto345@hotmail.com wrote:
Hi all,
I have uploaded a gff annotation to a shared library and when I try to load it into trackster it tries consistently to load an older dataset that does not exist anymore and does not correspond to the real gff dataset file. If I load the gff into a history, then this file is correctly loaded into trackster.
Any ideas what is going on? Any workaround so that we can load visualisations without creating histories with all the data beforehand?
Cheers, Cristian ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Nope, the name of the gff file is unique except for the fact that I uploaded different versions of it in the data library. The second test I did has only one version and has the same problem. Remember that the file imported from the data library into the history works but the file directly from the data library fails.I've been looking in the database to see where the dataset 4402 might come from, but till now I really don't see how trackster associates this information with dataset 44835. Cheers,Cristian
Subject: Re: [galaxy-dev] Trackster bug From: hansrudolf.hotz@fmi.ch Date: Wed, 10 Jun 2015 11:54:07 +0200 CC: galaxy-dev@lists.galaxyproject.org To: tuto345@hotmail.com
just double checking: and what about the 'name' in the History panel?
Hans-Rudolf
On Jun 10, 2015, at 11:43 AM, C. Ch. tuto345@hotmail.com wrote:Hi Hans, Actually the older dataset has nothing to do with the actual GFF file name-wise or other. Trackster tries to load database/files/004/dataset_4402.dat (a dataset created in 01/2013 and which has been deleted and purged) whereas the GFF file corresponds to database/files/044/dataset_44835.dat.In another test, trackster tries to load database/files/003/dataset_3905.dat (12/2012, deleted and purged) when the real dataset file for the GFF is database/files/030/dataset_30088.dat. Cheers,CristianSubject: Re: [galaxy-dev] Trackster bug From: hansrudolf.hotz@fmi.ch Date: Wed, 10 Jun 2015 10:38:58 +0200 CC: galaxy-dev@lists.galaxyproject.org To: tuto345@hotmail.com
Hi Cristian This problem sounds familiar. Have the new and the old file the same name? If so, try renaming your new gff file. Hans-Rudolf
On Jun 10, 2015, at 10:34 AM, C. Ch. tuto345@hotmail.com wrote:Hi all, I have uploaded a gff annotation to a shared library and when I try to load it into trackster it tries consistently to load an older dataset that does not exist anymore and does not correspond to the real gff dataset file. If I load the gff into a history, then this file is correctly loaded into trackster. Any ideas what is going on? Any workaround so that we can load visualisations without creating histories with all the data beforehand? Cheers,Cristian___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
I am not really familiar about the linking of the datasets in the database (especially, when it comes down to visualization), but as a last suggestion: Have you tried using a new visualization ?
Hans-Rudolf
On Jun 10, 2015, at 12:36 PM, C. Ch. tuto345@hotmail.com wrote:
Nope, the name of the gff file is unique except for the fact that I uploaded different versions of it in the data library. The second test I did has only one version and has the same problem. Remember that the file imported from the data library into the history works but the file directly from the data library fails. I've been looking in the database to see where the dataset 4402 might come from, but till now I really don't see how trackster associates this information with dataset 44835.
Cheers, Cristian
Subject: Re: [galaxy-dev] Trackster bug From: hansrudolf.hotz@fmi.ch Date: Wed, 10 Jun 2015 11:54:07 +0200 CC: galaxy-dev@lists.galaxyproject.org To: tuto345@hotmail.com
just double checking: and what about the 'name' in the History panel?
Hans-Rudolf
On Jun 10, 2015, at 11:43 AM, C. Ch. tuto345@hotmail.com wrote:
Hi Hans,
Actually the older dataset has nothing to do with the actual GFF file name-wise or other. Trackster tries to load database/files/004/dataset_4402.dat (a dataset created in 01/2013 and which has been deleted and purged) whereas the GFF file corresponds to database/files/044/dataset_44835.dat. In another test, trackster tries to load database/files/003/dataset_3905.dat (12/2012, deleted and purged) when the real dataset file for the GFF is database/files/030/dataset_30088.dat.
Cheers, Cristian Subject: Re: [galaxy-dev] Trackster bug From: hansrudolf.hotz@fmi.ch Date: Wed, 10 Jun 2015 10:38:58 +0200 CC: galaxy-dev@lists.galaxyproject.org To: tuto345@hotmail.com
Hi Cristian
This problem sounds familiar. Have the new and the old file the same name? If so, try renaming your new gff file.
Hans-Rudolf
On Jun 10, 2015, at 10:34 AM, C. Ch. tuto345@hotmail.com wrote:
Hi all,
I have uploaded a gff annotation to a shared library and when I try to load it into trackster it tries consistently to load an older dataset that does not exist anymore and does not correspond to the real gff dataset file. If I load the gff into a history, then this file is correctly loaded into trackster.
Any ideas what is going on? Any workaround so that we can load visualisations without creating histories with all the data beforehand?
Cheers, Cristian ___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Hi Hans, This happens when I try to create new visualisations. I'll try to have a look at the trackster code... but not feeling very confident about that :-( Thanks anyways,Cristian
Subject: Re: [galaxy-dev] Trackster bug From: hansrudolf.hotz@fmi.ch Date: Wed, 10 Jun 2015 13:21:09 +0200 CC: galaxy-dev@lists.galaxyproject.org To: tuto345@hotmail.com
I am not really familiar about the linking of the datasets in the database (especially, when it comes down to visualization), but as a last suggestion: Have you tried using a new visualization ? Hans-Rudolf On Jun 10, 2015, at 12:36 PM, C. Ch. tuto345@hotmail.com wrote:Nope, the name of the gff file is unique except for the fact that I uploaded different versions of it in the data library. The second test I did has only one version and has the same problem. Remember that the file imported from the data library into the history works but the file directly from the data library fails.I've been looking in the database to see where the dataset 4402 might come from, but till now I really don't see how trackster associates this information with dataset 44835. Cheers,Cristian
Subject: Re: [galaxy-dev] Trackster bug From: hansrudolf.hotz@fmi.ch Date: Wed, 10 Jun 2015 11:54:07 +0200 CC: galaxy-dev@lists.galaxyproject.org To: tuto345@hotmail.com
just double checking: and what about the 'name' in the History panel?
Hans-Rudolf
On Jun 10, 2015, at 11:43 AM, C. Ch. tuto345@hotmail.com wrote:Hi Hans, Actually the older dataset has nothing to do with the actual GFF file name-wise or other. Trackster tries to load database/files/004/dataset_4402.dat (a dataset created in 01/2013 and which has been deleted and purged) whereas the GFF file corresponds to database/files/044/dataset_44835.dat.In another test, trackster tries to load database/files/003/dataset_3905.dat (12/2012, deleted and purged) when the real dataset file for the GFF is database/files/030/dataset_30088.dat. Cheers,CristianSubject: Re: [galaxy-dev] Trackster bug From: hansrudolf.hotz@fmi.ch Date: Wed, 10 Jun 2015 10:38:58 +0200 CC: galaxy-dev@lists.galaxyproject.org To: tuto345@hotmail.com
Hi Cristian This problem sounds familiar. Have the new and the old file the same name? If so, try renaming your new gff file. Hans-Rudolf
On Jun 10, 2015, at 10:34 AM, C. Ch. tuto345@hotmail.com wrote:Hi all, I have uploaded a gff annotation to a shared library and when I try to load it into trackster it tries consistently to load an older dataset that does not exist anymore and does not correspond to the real gff dataset file. If I load the gff into a history, then this file is correctly loaded into trackster. Any ideas what is going on? Any workaround so that we can load visualisations without creating histories with all the data beforehand? Cheers,Cristian___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
galaxy-dev@lists.galaxyproject.org
-
C. Ch. -
Hans-Rudolf Hotz