Hello,
I'm working on a simple python script that auto-magically creates all indexes, and pre-processing necessary to add a genome to galaxy. I was wondering if anyone had a script to download all the genomes that are presented to you in the default genome drop down box?


Also I'm not to confident about what "all" preprocessing actually is (with respect to the default configuration). So far I create the create indexes for the following tools and add their appropriate entry into their tools-data config file:

sam index
bowtie, base/color
bwa, base/color
bfast, base (any advice on how to do color?)
blast (n and p)

Am I missing any tool that requires preprocessing?

Thanks,
James


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