Oh,

I forgot to mention it:

hg18.fa.fai is already in tool-data/shared/ucsc/hg18/sam_index/ as a link to tool-data/shared/ucsc/hg18/seq

Replacing the link with the actual file did not help (not suprising).

regards, Andreas

On 01.11.2012 17:56, Dave Bouvier wrote:
Andreas,

I recommend moving hg18.fa.fai into tool-data/shared/ucsc/hg18/sam_index/, and 
then samtools should
work. Also, if you're using picard tools, you'll want hg18.fa.fai and hg18.dict 
in
tool-data/shared/ucsc/hg18/srma_index/, as well as links to hg18.fa in both 
directories.


    --Dave B.

On 11/1/12 11:59:24.000, Andreas Kuntzagk wrote:
Dave,

In the meantime I found that out by myself howto generate the FASTA and
also to rum "samtools faidx" on it. The info about "all_fasta.loc" was
missing. But it's still not working.

Let me summarize what I did so far:

- tool-data/shared/ucsc/hg18/seq/ contains these files:
hg18.2bit  hg18.fa    hg18.fa.fai

where hg18.2bit was downloaded from the rsync server and the other two
generated from it.

- tool-data/shared/ucsc/builds.txt contains this line:

hg18    Human Mar. 2006 (NCBI36/hg18) (hg18)

- tool-data/all_fasta.loc contains this line:

hg18    hg18    Human (Homo sapiens): hg18
tool-data/shared/ucsc/hg18/seq/hg18.fa

- tool-data/sam_fa_indices.loc contains this line:

index    hg18    tool-data/shared/ucsc/hg18/sam_index/hg18.fa

- tool-data/srma_index.loc contains this line:

hg18    hg18    hg18    tool-data/shared/ucsc/hg18/srma_index/hg18.fa


So any ideas where to look further?


regards, Andreas

On 01.11.2012 15:36, Dave Bouvier wrote:
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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--
Andreas Kuntzagk

SystemAdministrator

Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str. 10, 13125 Berlin, Germany

http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich
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