Question: Database Associated With Galaxy Server
0
Jennifer Hillman Jackson ♦ 25k wrote:
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
--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org