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 <nate@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 ___________________________________________________________ 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:

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