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" />


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

Hope it helps,
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