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.



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