Re: [galaxy-user] SRMA on a local galaxy instance?
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: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 /path/to/galaxy-dist/tool-data/shared/jars/srma.jar --nate ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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 > > Cheers, > > Henry > > > ___ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
