On Feb 13, 2013, at 6:42 PM, Gaueko Erge wrote:

> Hi Nate,
> 
> Thank you for your reply. After a lot of trying I was able to figure this out
> 
> Entries in my alignsec.loc file were pointing to:
> 
> seq     AaegL1  /db/galaxydb/AaegL1/seq/
> seq     AgamP3  /db/galaxydb/AgamP3/seq/
> 
> and not to:
> 
> seq     AaegL1  /db/galaxydb/AaegL1/seq/AaegL1.2bit
> seq     AgamP3  /db/galaxydb/AgamP3/seq/AgamP3.2bit
> 
> As required for this this work
> 
> I guess, I was confused and/or did not understand the instructions well. 
> Also, I was confused because I thought that the '2bit' files had to be 
> present in the 'twobit.loc' file and not in alignsec.loc
> 
> Honestly, I am still trying to mentally sort out what datasets are used by 
> ucsc browser (local installation) and what datasets are used only by galaxy. 
> AND how to proceed to upload my own genomes to both galaxy and to my local 
> deployment of ucsc browser

Hi Gaueko,

I'm glad to hear it's working.  If you have any suggestions on how to improve 
our documentation for this, please let us know.

--nate

> 
> Thanks
> 
> --G
> 
> 
> On Wed, Feb 13, 2013 at 1:27 PM, Nate Coraor <n...@bx.psu.edu> wrote:
> On Feb 12, 2013, at 10:49 AM, Gaueko Erge wrote:
> 
> > Hi,
> >
> > I have followed, carefully, the instructions posted 
> > in:http://wiki.galaxyproject.org/Admin/Data%20Integration
> >
> > Yet, despite my best efforts when I get, say all exons from hg19 build and 
> > try to their fetch sequences, galaxy tells me that the sequences for hg19 
> > are not there
> >
> > I find this surprising because I have downloaded:
> >
> > rsync://datacache.g2.bx.psu.edu/indexes/
> > rsync://hgdownload.cse.ucsc.edu/gbdb/
> > rsync://hgdownload.cse.ucsc.edu/goldenPath/vicPac1/bigZips
> >
> > databases and added the correct paths to the 'alignseq.loc' file
> 
> Hi Gaueko,
> 
> It'd be helpful if you could provide us with the entry from your alignseq.loc 
> file.  Also, you may want to verify that your alignseq.loc contains only tabs 
> between the fields, not spaces.
> 
> --nate
> 
> >
> > Any ideas will be appreciated
> >
> > Thanks
> >
> > --G
> > ___________________________________________________________
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> 


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