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/galax...
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