Hello Mitali,

There is a rice genome available for use with most tools already on the public Main Galaxy server at https://main.g2.bx.psu.edu (http://usegalaxy.org). On the tool form, for the option to select a reference genome, or on the Upload or Edit Attributes form when selecting genome/build, type in the keyword "rice" to bring up:


     Rice (Oryza sativa): oryza_sativa_japanica_nipponbare_IRGSP4.0

For genomes not included as built-in native indexes (perhaps you wish to use a different strain), a Custom reference genome can be also used with most tools on Main. Instructions are here:
http://wiki.galaxyproject.org/Support#Custom_reference_genome

There are a few tools on Main that do not allow for Custom reference genomes - these have a fixed set of specified target genomes. Megablast is one such tool. To use an alternate genome with this tool and the few others like it, a local or cloud Galaxy is required. Instructions are here:
http://getgalaxy.org
http://usegalaxy.org/cloud

If you need to add a reference genome to a local Galaxy (a cloud Galaxy would already include everything currently on Main), you can create the indexes yourself, or rsync our files for use in your instance. The rsync server also lists all genomes currently indexed on Main. Instructions are here:
http://wiki.galaxyproject.org/Admin/Data%20Integration
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

Hopefully this helps,

Jen
Galaxy team
http://wiki.galaxyproject.org/Support#Mailing_Lists

On 7/17/13 11:43 PM, Mitali Merchant wrote:
hi,

i wanted to know the genome databases associated with Galaxy server. i want to perform peak calling using galxy server of the data of Oryza Sativa (rice genome) but since this genome is not available in galaxy, i want to know how can i get this genome as reference.
Kindly reply as soon as possible,it will be of great help

Mitali Merchant
IIIT,Hyderabad
India

--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

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