Installing a database on local instance Galaxy

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Installing a database on local instance Galaxy

goutham sarovaram
Hello,
My name is Goutham I'm currently doing RNA-Seq analysis on a local instance
of Galaxy installed on a workstation at our research center.
As I have been tasked with adminstrative duties for this system I would
like to know how I can install databases on to the local instance
(Databases download from Uniprot and Pfam etc.) For running blast+ and
other tools associated with the trinotate pipeline which I'm trying to
operate through Galaxy.
Best regards.
(The instance is hosted on a Kubuntu 18 LTS with a dual Xeon E series and
64 DDR4 memory, any suggestions for better optimizations are welcome)
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Re: Installing a database on local instance Galaxy

Björn Grüning-3
Hi,

this will help you hopefully for the blast tools:

https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus#configuration

In short you need to download the UniProt blast DB and edit a file
called: blastdb_p.loc

Keep in mind Galaxy is framework in which you can run thousands of
community maintained tools ... it can happen that those tools needs some
manual work to make them work. This really depends on the tools you have
installed.

Ciao,
Bjoern

Am 27.07.19 um 10:00 schrieb goutham sarovaram:

> Hello,
> My name is Goutham I'm currently doing RNA-Seq analysis on a local instance
> of Galaxy installed on a workstation at our research center.
> As I have been tasked with adminstrative duties for this system I would
> like to know how I can install databases on to the local instance
> (Databases download from Uniprot and Pfam etc.) For running blast+ and
> other tools associated with the trinotate pipeline which I'm trying to
> operate through Galaxy.
> Best regards.
> (The instance is hosted on a Kubuntu 18 LTS with a dual Xeon E series and
> 64 DDR4 memory, any suggestions for better optimizations are welcome)
> ___________________________________________________________
> 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:
>    %(web_page_url)s
>
> 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:
  %(web_page_url)s

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/