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