Hi Jen,

fantastic news!

Thanks a lot!
Bjoern

> Thanks,
> 
> There have been no public data updates since the migration started
> (late last spring we froze the data). But there are some known issues
> and data that is ready to be released, in the process of becoming
> ready, etc. We expect to be able to start working on this again in the
> very near term.
> 
> To start this off, the mm9 bowtie2 indexes were restored this morning:
> https://trello.com/c/SbizUDQt
> 
> And these other finds are great, thanks Bjoern. I will add them to the
> public card. A few errors that were corrected later last spring popped
> out again, but will also be fixed. Small, but will be addressed ASAP.
> 
> Adding in any missing .2bit files in general are on our internal to-do
> list. Older genomes have other inconsistencies that will be addressed.
> The goal is to have the data filled in with complete indexes around
> the end of Nov, then filled in with newly released genomes/more
> variants for important model organisms by the end of the year. All of
> this depends on various factors, but this is where we are shooting
> for.
> 
> Thanks and if anything else off is noted, please feel free to send to
> the list or add to the card. All input is welcome - we want this to be
> a great resource for everyone - time to get back to making that happen
> now that the migration is wrapping up!
> 
> Jen
> Galaxy team
> 
> On 11/8/13 2:00 AM, Bjoern Gruening wrote:
> 
> > Hi,
> > 
> > to chime into this discussion.
> > 
> > I found some inconsistency during my rsync endeavor and I'm curious
> > if there is any way to contribute to that service.
> > 
> > --
> > xenTro3 xenTro3 Frog (Xenopus tropicalis):
> > xenTro3 /galaxy/data/xenTro3/seq/xenTro3.fa
> > but only
> > /xenTro3.fa.gz exists.
> > ---
> > ce6 /data/0/ref_genomes/ce6/ce6.2bit is missing from twobit.loc
> > ---
> > ce6 has no .fa file under seq/ but in allfasta.loc there is a
> > reference to it ce6 Caenorhabditis elegans:
> > ce6 /galaxy/data/ce6/seq/ce6.fa
> > ---
> > TAIR9 and TAIR10 is not available via rync  
> > ---
> > Bowtie2 indices are missing for ce6, xentTro3
> > 
> > 
> > Thanks,
> > Bjoern
> > 
> > > Hi Jennifer,
> > > 
> > > Today I was trying to pull some bowtie2 indices from Galaxy rsync server 
> > > for PhiX to run some tests and just got the ones for bowtie1… I'm 
> > > wondering what's the state in regards to this past thread and what we can 
> > > do to help in here.
> > > 
> > > Cheers!
> > > Roman
> > > 
> > > 7 mar 2013 kl. 20:01 skrev Jennifer Jackson <j...@bx.psu.edu>:
> > > 
> > > > Hi Brad (and Roman),
> > > > 
> > > > The team has talked about this in detail. There are a few wrinkles with 
> > > > just pulling in indexes - Dan is doing some work that could change this 
> > > > later on, but for now, the rsync will continue to point to the same 
> > > > location as Main's genome data source. This means that there are some 
> > > > limits on what we can do immediately. Setting up a submission pipe is 
> > > > one of them - there just isn't resource to do this right now or a 
> > > > common place distinct from Main to house the data. A few other ideas 
> > > > came up - we can chat later, each had side issues.
> > > > 
> > > > But I saw your tweet and think that it is great that you are pulling 
> > > > CloudBioLinux data from the rsync now, so let's get as much data in 
> > > > common as possible, so you have data to work with near term.
> > > > 
> > > > I am in the process of adding bt2 indexes - some are published to 
> > > > Main/rsync server already and some are not, but more will show up over 
> > > > the next week or so (along with more genomes and other indexes). I'll 
> > > > take a look at what you have and pull/match what I can. Genome sort 
> > > > order and variants are my concerns, both require special handling in 
> > > > processing and .locs. If it takes longer to check, I am just going to 
> > > > create here if I haven't already. The GATK-sort hg19 canonical is 
> > > > already on my list - it needed all indexes, not just bw2. When the next 
> > > > distribution goes out, I'll list what is new on the rsync in the News 
> > > > Brief.
> > > > 
> > > > For the Novoalign indexes, I'm not quite sure what to do about those 
> > > > yet. Or for any indexes associated with tools or genomes not hosted on 
> > > > Main. Do you want to open a card for those and any other cases that are 
> > > > similar? We can discuss a strategy from there, maybe at IUC, if 
> > > > Greg/Dan thinks it is appropriate. Please add me so I can follow.
> > > > 
> > > > I'll be in touch as I go through the data. Thanks for your patience on 
> > > > this!
> > > > 
> > > > Jen
> > > > Galaxy team
> > > > 
> > > > 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
> > > >> ___________________________________________________________
> > > >> Please keep all replies on the list by using "reply all"
> > > >> in your mail client.  To manage your subscriptions to this
> > > >> and other Galaxy lists, please use the interface at:
> > > >> 
> > > >>   http://lists.bx.psu.edu/
> > > > 
> > > > -- 
> > > > Jennifer Hillman-Jackson
> > > > Galaxy Support and Training
> > > > http://galaxyproject.org
> > > > 
> > > > ___________________________________________________________
> > > > Please keep all replies on the list by using "reply all"
> > > > in your mail client.  To manage your subscriptions to this
> > > > and other Galaxy lists, please use the interface at:
> > > > 
> > > > http://lists.bx.psu.edu/
> > > 
> > > 
> > > ___________________________________________________________
> > > Please keep all replies on the list by using "reply all"
> > > in your mail client.  To manage your subscriptions to this
> > > and other Galaxy lists, please use the interface at:
> > >   http://lists.bx.psu.edu/
> > > 
> > > To search Galaxy mailing lists use the unified search at:
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> > 
> > 
> 
> -- 
> Jennifer Hillman-Jackson
> http://galaxyproject.org



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