[Genome] gbdb folder in UCSC browser mirror

[Galt Barber]

The leading slash in "/gbdb/dm2/multiz15way/anno/maf/chr2L.maf"
indicates that it is starting from the root "/".

You will either need to move gbdb dir to be
directly under the root, or make a symlink /gbdb to it.

You could also change the entries in tables
like "extFile" to  add ".." to the path, but
this is not as simple or desirable as the
other two solutions.

-Galt


On Wed, 24 Jan 2007, Thomas Sandmann wrote:

> Dear UCSC browser team,
>
> I am trying to set up a local mirror of the UCSC genome browser on
> Mac OS X. After following the instructions posted on your website and
> the WIKI, I think I am almost there:
> the table browser is working and the (empty) hg18 database can be
> accessed via the Genome browser itself. I am only interested in the
> dm2 data, so I have downloaded all dm2 mysql databases and the
> corresponding dm2 gbdb files. Nevertheless, entering Drosophila
> melanogaster coordinates yields the following error:
>
> External file /gbdb/dm2/multiz15way/anno/maf/chr2L.maf cannot be
> opened or has wrong size. Old size 590189055, new size -1, error No
> such file or directory
>
> The same happens with any other coordinate. The file is in found in
> the specified location and its size is correct, too. It is accessible
> by any user.  Maybe I placed the gbdb folder in the wrong location ?
> Currently my folder tree looks like this:
>
> www-genome-browser/
> html               cgi-bin	         goldenPath                 trash
> 		gbdb
>
> Any advice would be highly appreciated !
> Cheers, Thomas
>
> -------------------------------------------
>
> Thomas Sandmann
> EMBL Heidelberg
> Developmental Biology Unit
> Furlong group
> Meyerhofstr 1,
> D-69117, Heidelberg
> Germany
> -------------------------------------------
> email:sandmann at embl.de
> tel: +49 6221 387 8154
> fax: +49 6221 387 166
>
>
>
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