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
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http://galaxyproject.org
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