Jen;
That sounds great, thanks for your enthusiasm and help organizing this.
I'm @bradchapman on Trello so feel free to add me to the ticket and let
me know how I can help. I'm happy to set this up however you feel best:
looking forward to having a shared repository for all this formatted
genome data. Thanks again,
Brad


> Hi Brad,
>
> I really like this idea. I'm not going to open a ticket yet but talk 
> with Dan/team about some options. We have an alternate directory 
> structure modeled from last fall I'd like to get in place before we 
> start something like this ( is not yet implemented, but it or something 
> similar would be required to properly add in the hg19 GTAK-sort. will 
> involve a bit of other data shuffling w/ .loc changes to keep external 
> links functional ). There are also some other repo ideas in play.
>
> Let me get some internal feedback next week, then I'll start a Trello 
> ticket with some basics from our side that we can use to vet a plan to 
> go forward, assuming the rest of the team likes idea. I think test 
> cases/index validation would probably be part of this somehow. And 
> certainly some simplification we be welcomed in the more cluttered dirs, 
> if that can be managed while keeping enough around for reproducibility 
> needs.
>
> Very topical, thanks for bring up and offering to help out! These can be 
> great deal of work to create and makes total sense to share. I'll send 
> and update later next week, hopefully with a Trello link so we can get 
> started.
>
> Jen
> Galaxy
>
> On 2/21/13 12:43 PM, Brad Chapman wrote:
>>
>> Hi all;
>> Is there a way for community members to contribute indexes to the rsync
>> server? This resource is awesome and I'm working on migrating the
>> CloudBioLinux retrieval scripts to use this instead of the custom S3
>> buckets we'd set up previously:
>>
>> https://github.com/chapmanb/cloudbiolinux/blob/master/cloudbio/biodata/galaxy.py
>>
>> It's great to have this as a public shared resource and I'd like to be
>> able to contribute back. From an initial pass, here are the things I'd
>> like to do:
>>
>> - Include bowtie2 indexes for more genomes.
>>
>> - Include novoalign indexes for a number of commonly used genomes.
>>
>> - Clean up hg19 to include a full canonically sorted hg19, with indexes.
>>    Broad has a nice version prepped so GATK will be happy with it, and
>>    you need to stick with this ordering if you're ever going to use a
>>    GATK tool on it. Right now there is a partial hg19canon (without the
>>    random/haplotype chromosomes) and the structure is a bit complex.
>>
>> What's the best way to contribute these? Right now I have a lot of the
>> indexes on S3. For instance, the hg19 indexes are here:
>>
>> https://s3.amazonaws.com/biodata/genomes/hg19-bowtie.tar.xz
>> https://s3.amazonaws.com/biodata/genomes/hg19-bowtie2.tar.xz
>> https://s3.amazonaws.com/biodata/genomes/hg19-bwa.tar.xz
>> https://s3.amazonaws.com/biodata/genomes/hg19-novoalign.tar.xz
>> https://s3.amazonaws.com/biodata/genomes/hg19-seq.tar.xz
>> https://s3.amazonaws.com/biodata/genomes/hg19-ucsc.tar.xz
>>
>> I'm happy to format these differently or upload somewhere that would
>> make it easy to include. Thanks again for setting this up, I'm looking
>> forward to working off a shared repository of data,
>> Brad
>> ___________________________________________________________
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>
> -- 
> Jennifer Hillman-Jackson
> Galaxy Support and Training
> http://galaxyproject.org
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