Change genome build for multiple files
Hi is there a convenient way to change the genome build for a lot of files at once (e.g. a whole data library)? I want to ‘update’ to a newer genome build and the only way I found is to go through ‘Edit information’ for each file separately. I assume it can be changed directly in the db, but I’m not familiar with the scheme. thanks Frederik ================================================================== Frederik Coppens, Ph.D. Project Leader Applied Bioinformatics & Biostatistics IT manager Tel: 32 (0)9 3313812 Fax:32 (0)9 3313809 VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent Technologiepark 927, 9052 Gent, BELGIUM frcop@psb.ugent.be http://www.psb.ugent.be/abb ==================================================================
Hi Frederik, at least with the API this is possible! Sorry for not being helpful at all! Bjoern
Hi
is there a convenient way to change the genome build for a lot of files at once (e.g. a whole data library)?
I want to ‘update’ to a newer genome build and the only way I found is to go through ‘Edit information’ for each file separately. I assume it can be changed directly in the db, but I’m not familiar with the scheme.
thanks
Frederik
================================================================== Frederik Coppens, Ph.D. Project Leader Applied Bioinformatics & Biostatistics IT manager
Tel: 32 (0)9 3313812 Fax:32 (0)9 3313809 VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent Technologiepark 927, 9052 Gent, BELGIUM
frcop@psb.ugent.be <mailto:frcop@psb.ugent.be> http://www.psb.ugent.be/abb ==================================================================
___________________________________________________________ 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 Bjoern thanks for the reply. I previously did not find this in the API documentation but had a look now again (http://galaxy.readthedocs.org/en/master/api_doc.html#module-galaxy.webapps.g... <http://galaxy.readthedocs.org/en/master/api_doc.html#module-galaxy.webapps.galaxy.api>) and found things have changed quite a bit (or did I miss something previously?) I assume I need the lda_datasets module, but this does not contain an update functionality for the metadata (only for the permissions). An alternative would be the library_contents module which does have update but from the docs I’m not sure how to use this (e.g. what’s the trans parameter?). Any pointers to docs or examples? greetz Frederik
On 20 Aug 2015, at 19:41, Bjoern Gruening <bjoern.gruening@gmail.com> wrote:
Hi Frederik,
at least with the API this is possible!
Sorry for not being helpful at all! Bjoern
Hi
>
> is there a convenient way to change the genome build for a lot of
> files at once (e.g. a whole data library)?
>
> I want to ‘update’ to a newer genome build and the only way I found
> is to go through ‘Edit information’ for each file separately. I
> assume it can be changed directly in the db, but I’m not familiar
> with the scheme.
>
> thanks
>
> Frederik
>
> ==================================================================
> Frederik Coppens, Ph.D. Project Leader Applied Bioinformatics &
> Biostatistics IT manager
>
> Tel: 32 (0)9 3313812 Fax:32 (0)9 3313809 VIB
> DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent Technologiepark 927, 9052
> Gent, BELGIUM
>
> frcop@psb.ugent.be <mailto:frcop@psb.ugent.be> <mailto:frcop@psb.ugent.be> <mailto:frcop@psb.ugent.be>
> http://www.psb.ugent.be/abb <http://www.psb.ugent.be/abb>
> ==================================================================
>
>
>
> ___________________________________________________________ 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/ <https://lists.galaxyproject.org/>
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>
================================================================== Frederik Coppens, Ph.D. Project Leader Applied Bioinformatics & Biostatistics IT manager Tel: 32 (0)9 3313812 Fax:32 (0)9 3313809 VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent Technologiepark 927, 9052 Gent, BELGIUM frcop@psb.ugent.be http://www.psb.ugent.be/abb ==================================================================
participants (2)
-
Bjoern Gruening -
Frederik Coppens