I may have just sent an empty reply email; if so, my apologies.

Yes, I have the srma jar in that folder, without the version number exactly 
like that.


-----Original Message-----
From: Nate Coraor [mailto:n...@bx.psu.edu]
Sent: Thu 6/16/2011 7:35 AM
To: Gong, Henry
Cc: galaxy-user@lists.bx.psu.edu; Shieh, Joseph
Subject: Re: [galaxy-user] SRMA on a local galaxy instance?
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


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