Question: Srma On A Local Galaxy Instance?
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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
