Gong, Henry wrote:
> 
> 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.

Hi Henry,

Where is your srma JAR file located?  It should be
/path/to/galaxy-dist/tool-data/shared/jars/srma.jar

--nate

> 
> Cheers,
> 
> Henry
> 
> 
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