Does anyone know how to get SRMA to work properly in galaxy? I've used the 
pre-built 0.1.15 jar as well as a 0.1.16 jar I built from source, but the 
result of an SRMA re-alignment job in both instances is a python process which 
only takes a few percent CPU (or less, since it only seems to be outputting 
timestamps to the terminal). Here are my system's specs if they're important: 
2.8Ghz Intel i5, 4 core; 4GB 1333MHz DDR3; 1TB HDD (430GB free). The OS is OS X 
10.6.7. I've also built the required indices and placed them in 
path/to/galaxy-dist/hg19/srma_path/hg19.dict, hg19.fa.fai, and hg19.fa; the 
hg19 is a concatenated version of the various chromosome and contig files, and 
I've followed the sample files in adding these locations to the .loc files 
(both srma and picard tools).

The NGS installation page seems to suggest that SRMA does work, so I'm not sure 
if I'm overreacting, but I'd really appreciate any advice on this, since I 
imagine others have had similar problems.

Cheers,

Henry


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to