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.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