using DataManager to add custom genomes

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using DataManager to add custom genomes

Nikhil Joshi-2
Hi all,

Is it possible to use a DataManager (or anything) to allow a user (or admin) to upload their genome of choice and have it be indexed and be used as a built-in/cached genome *without* having to go on the command-line? I.e., only using the Galaxy interface?

- Nik.

--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 (w)

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Re: using DataManager to add custom genomes

Nikhil Joshi-2
Of course this would be for a local install of galaxy.

On Thu, Apr 2, 2015 at 2:29 AM, Nikhil Joshi <[hidden email]> wrote:
Hi all,

Is it possible to use a DataManager (or anything) to allow a user (or admin) to upload their genome of choice and have it be indexed and be used as a built-in/cached genome *without* having to go on the command-line? I.e., only using the Galaxy interface?

- Nik.

--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 (w)



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)

___________________________________________________________
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/

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  http://galaxyproject.org/search/mailinglists/
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Re: using DataManager to add custom genomes

Daniel Blankenberg
Hi Nikhil,

Have a look at https://toolshed.g2.bx.psu.edu/view/devteam/data_manager_fetch_genome_dbkeys_all_fasta to add a new genome/fasta. Once you have the genome entry, then you can use additional Data Manager to make tool specific (bwa, samtools, etc) indexes.


Thanks for using Galaxy,

Dan


On Apr 2, 2015, at 5:41 AM, Nikhil Joshi <[hidden email]> wrote:

Of course this would be for a local install of galaxy.

On Thu, Apr 2, 2015 at 2:29 AM, Nikhil Joshi <[hidden email]> wrote:
Hi all,

Is it possible to use a DataManager (or anything) to allow a user (or admin) to upload their genome of choice and have it be indexed and be used as a built-in/cached genome *without* having to go on the command-line? I.e., only using the Galaxy interface?

- Nik.

--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 (w)



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)
___________________________________________________________
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/


___________________________________________________________
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/