Question: Srma On A Local Galaxy Instance?
7.5 years ago by
Gong, Henry • 20
Gong, Henry • 20 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. Cheers, Henry
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