James;

> 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?

Really great you are interested in this are. We've been working on
this problem as part of the cloudbiolinux project:

https://github.com/chapmanb/cloudbiolinux

and have a fabric install file:

https://github.com/chapmanb/cloudbiolinux/blob/master/data_fabfile.py

the pulls genomes and index types specified by a configuration file:

https://github.com/chapmanb/cloudbiolinux/blob/master/config/biodata.yaml

This has two ways of installing the indexes. The first,
install_data, will download the genomes from UCSC/Ensembl/NCBI
and then build the indexes locally. The second, install_data_s3,
has pre-prepared and indexed genomes stored in Amazon S3 buckets.
This lets you fetch and unpack ready to go genomes without having
the overhead of indexing; this works from anywhere -- local or
Amazon cloud machines. After download, both methods update the
appropriate *.loc files to integrate with Galaxy.

As you mentioned, there are a lot of different targets and genomes,
and we're definitely interested in expanding out to include them.

It sounds like this approach is similar to what you were working on.
If you're interested, we'd be very happy to have you involved. We've
been working with Enis on this but it's not an official Galaxy 
team project; rather it's a community supplement to the great install
automation they already provide.

Hope this helps,
Brad
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