Andreas,

When setting up the rsync server, we decided that .fa files would be excluded from the listing, since the 2bit format contains the same data but takes up to 75% less space. I would recommend downloading the relevant .2bit file and converting it back to FASTA with twoBitToFa, then updating your all_fasta.loc file to point to the resulting .fa file.

   --Dave B.

On 11/1/12 06:27:49.000, Andreas Kuntzagk wrote:
Hi,

It's still not working. I just noticed that the sam_index dir only
contains links to some files in ../seq which is mostly empty except some
2bit files.
I could not find any documentation how to obtain these data files.

regards, Andreas

On 31.10.2012 17:50, Carlos Borroto wrote:
On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk
<andreas.kuntz...@mdc-berlin.de> wrote:
Hi,

I'm still setting up a local galaxy. Currently I'm testing the setup
of NGS
tools. If I try "SAM to BAM" for a BAM file that has "hg18" set as
build I
get a message that
"Sequences are not currently available for the specified build." I guess
that I have either to manipulate one of the .loc files (but which?)
or have
to download additional data from rsync server.
(I already have the tool-data/shared/hg18 completely)


The .loc file you want to modify is 'tool-data/sam_fa_indices.loc'.
You can find information about this subject in the wiki[1]. Although
the table there is not complete, so you could always find the right
xml under 'tools' and poke inside to find a line like this one:
<validator type="dataset_metadata_in_file"
filename="sam_fa_indices.loc" metadata_name="dbkey"
metadata_column="1" message="Sequences are not currently available for
the specified build." line_startswith="index" />

[1]http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup

And I agree, dealing with .loc files is quite cumbersome.

Hope it helps,
Carlos


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