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


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