Well is not my page, I'm not directly related to Galaxy. Still, I think Galaxy Project would be happy to receive updates to the wiki, maybe a complete table can be added to the page you are mentioning.
On Thu, Nov 1, 2012 at 4:27 AM, Andreas Kuntzagk andreas.kuntzagk@mdc-berlin.de wrote:
Hi,
thank you for the pointer. I was only looking at this wiki page: http://wiki.g2.bx.psu.edu/Admin/Data%20Integration
Maybe this should point to your page?
regards, Andreas
On 31.10.2012 17:50, Carlos Borroto wrote:
On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk andreas.kuntzagk@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
-- Andreas Kuntzagk
SystemAdministrator
Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany