[galaxy-dev] Data manager for ncbi_blast_plus in the main tool shed?

[David Kovalic]

Peter,
Thanks.
Dan,
What is your opinion (what work needs to be done to make this
production-worthy)? Maybe if my chops are up to it I can take a crack…
David


David Kovalic Ph.D.President,Analomephone:+314.496.8808web:www.analome.comemail:

kova...@analome.com






On Fri, Aug 11, 2017 4:58 AM, Peter Cock p.j.a.c...@googlemail.com  wrote:
Hi David,
Daniel Blankenberg wrote one (CC'd):
https://github.com/peterjc/galaxy_blast/tree/master/data_managers/ncbi_blastdb

http://testtoolshed.g2.bx.psu.edu/view/blankenberg/data_manager_example_blastdb_ncbi_update_blastdb

I've never used it in production and don't have enough understandingof it and
the Data Manager framework to understand what if anythingneeds working on.
Locally we have mirrors of the NCBI blast databases (updated with cron),local
databases for organisms of interest - these are all listed in the *.locfiles by
hand.
Separately, our users can and do make their own databases withinGalaxy using
makeblastdb.
Regards,
Peter
On Thu, Aug 10, 2017 at 10:32 PM, David Kovalic   wrote:
Hi,
Does anyone know if a data manager exists in the tool shed for creating and
integrating NCBI BLAST+ indices within galaxy?
I can't seem to find it in the tools shed or searching the internet Surly such a
tool must exist.
Any info would be greatly appreciated.
Thanks,
David


David Kovalic Ph.D.President,Analomephone:+314.496.8808web:www.analome.comemail:

kova...@analome.com

___
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/___
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/

Re: [galaxy-dev] Data manager for ncbi_blast_plus in the main tool shed?

[Peter Cock]

Hi David,

Daniel Blankenberg wrote one (CC'd):

https://github.com/peterjc/galaxy_blast/tree/master/data_managers/ncbi_blastdb

http://testtoolshed.g2.bx.psu.edu/view/blankenberg/data_manager_example_blastdb_ncbi_update_blastdb

I've never used it in production and don't have enough understanding
of it and the Data Manager framework to understand what if anything
needs working on.

Locally we have mirrors of the NCBI blast databases (updated with cron),
local databases for organisms of interest - these are all listed in the
*.loc
files by hand.

Separately, our users can and do make their own databases within
Galaxy using makeblastdb.

Regards,

Peter

On Thu, Aug 10, 2017 at 10:32 PM, David Kovalic  wrote:

> Hi,
>
> Does anyone know if a data manager exists in the tool shed for creating
> and integrating NCBI BLAST+ indices within galaxy?
>
> I can't seem to find it in the tools shed or searching the internet  Surly
> such a tool must exist.
>
> Any info would be greatly appreciated.
>
> Thanks,
>
> David
>
>
>
> David Kovalic Ph.D.   President, Analome
> phone: +314.496.8808
> web: www.analome.com
> email: kova...@analome.com
> 
>
>
> ___
> 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/
>
___
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/

[galaxy-dev] Data manager for ncbi_blast_plus in the main tool shed?

[David Kovalic]

Hi,
Does anyone know if a data manager exists in the tool shed for creating and
integrating NCBI BLAST+ indices within galaxy?
I can't seem to find it in the tools shed or searching the internet Surly such a
tool must exist.
Any info would be greatly appreciated.
Thanks,
David


David Kovalic Ph.D.President,Analomephone:+314.496.8808web:www.analome.comemail:

kova...@analome.com___
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/