Hi Franziska,

Both species are available for NGS mapping tools (excluding megablast, which is not intended to host individual genomes on the public instance). To locate these, including /A. thaliana/, type in 'Arab' into the "Select a reference genome:" box to perform a search. Perhaps default sort order of the builds list when viewed by scrolling is what made it appear that only /A. lyrata/ was available (it is the first in the list and has a different legacy name structure)?


Many people use the main public instance to do NGS mapping every day. There are significant resources dedicated to this service, but there are usage quotas, limits on job size (72 hr job runtime limit), and delays during peak usage times (we are experiencing one right now). Your needs will determine the best type of Galaxy instance for your purposes.

This wiki has details about Galaxy options:
http://wiki.g2.bx.psu.edu/Big%20Picture/Choices

Hopefully this helps,

Jen
Galaxy team


On 4/25/12 2:02 PM, Franziska Turck wrote:
Dear Jennifer,

actually I wanted it for NGS mapping and it wasn`t in the drop down
menue although Arabidopsis lyrata was. Is NGS mapping with GALAXY even
realistic or does it take too much cpu time on the cluster.

Best,
Franziska

----- Original Message -----
From: Jennifer Jackson <j...@bx.psu.edu>
Date: Wednesday, April 25, 2012 22:46
Subject: Re: [galaxy-user] Arabidopsis thaliana genome
To: Franziska Turck <tu...@mpipz.mpg.de>
Cc: galaxy-u...@bx.psu.edu

 > Hello Franziska,
 >
 > TAIR9 and TAIR10 are available for most tools, with the notable
 > exception of the new 'NGS: GATK Tools (beta)' tool set. Is this
 > where
 > you wanted to have the genomes added? For now, only one genome
 > is
 > available while in beta and using the custom reference genome
 > feature
 > for other genomes is the current option.
 >
 > Our plans are to add genomes to the GATK tool set and fill in
 > genomes
 > for other tools in the near term. I can make sure that the
 > Arabidopsis
 > genome is included. Normally, we would put as a priority the
 > most
 > current build, which would be TAIR10. Are other builds of
 > interest?
 > Links and other information would be great. The source we have
 > used in
 > the past is (below), please send additions/corrections, help is
 > always
 > appreciated! The core input is a fasta version of the genome,
 > with
 > additional related data such as Mitochrondrial, Chloroplast,
 > Plasmid,
 > etc. as appropriate.
 > ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/
 >
 > Until this is completed, here are instructions for using a
 > custom
 > reference genome (available with most tools):
 > http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome
 >
 > Best,
 >
 > Jen
 > Galaxy team
 >
 > On 4/25/12 8:06 AM, Franziska Turck wrote:
 > > Dear Galaxy team!
 > >
 > > Could you put the Arabidopsis thaliana genome in the drop down list?
 > > What kind of data would you need for that, I can help find all
 > the links
 > > from TAIR
 > >
 > > Best,
 > > Franziska
 > >
 > > Dr. Franziska Turck
 > > Max Planck Institute for Plant Breeding Research
 > > Department Plant Developmental Biology
 > > Group Transcription Control by Chromatin Structure
 > >
 > > Carl von Linné Weg 10
 > > 50829 Köln
 > > Germany
 > >
 > > Tel: +49 221 5062 246
 > > Fax:+49 221 5062 207
 > >
 > >
 > > ___________________________________________________________
 > > The Galaxy User list should be used for the discussion of
 > > Galaxy analysis and other features on the public server
 > > at usegalaxy.org. Please keep all replies on the list by
 > > using "reply all" in your mail client. For discussion of
 > > local Galaxy instances and the Galaxy source code, please
 > > use the Galaxy Development list:
 > >
 > > http://lists.bx.psu.edu/listinfo/galaxy-dev
 > >
 > > To manage your subscriptions to this and other Galaxy lists,
 > > please use the interface at:
 > >
 > > http://lists.bx.psu.edu/
 >
 > --
 > Jennifer Jackson
 > http://galaxyproject.org

Dr. Franziska Turck
Max Planck Institute for Plant Breeding Research
Department Plant Developmental Biology
Group Transcription Control by Chromatin Structure

Carl von Linné Weg 10
50829 Köln
Germany

Tel: +49 221 5062 246
Fax:+49 221 5062 207

--
Jennifer Jackson
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

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