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
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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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. Cheers, Henry -----Original Message----- From: Nate Coraor [mailto:nate@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 /path/to/galaxy-dist/tool-data/shared/jars/srma.jar --nate
participants (2)
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Gong, Henry -
Nate Coraor