Re: [galaxy-dev] [galaxy-user] SRMA on a local galaxy instance?
Henry, I'm moving this over to galaxy-dev since it has to do with a local instance. It definitely sounds like you've got things set up right. You don't say what the result of your run is--is it "successful" (green) but an empty file? Or is there an error? If it's empty, it's possible your data just didn't yield any results. If there's an error, please share that with us. There are a couple of other things you could do to start figure out where the problem is. Have you tried running the functional tests for SRMA? There are two and you could comment out the first one in the xml since it relies on hg18chr21 being in the loc file, but if the second one passes then we'd know SRMA is installed correctly but there is something with your data (the command is: sh run_functional_tests.sh - id srma_wrapper). You also could try running your data through on our test server's (test.g2.bx.psu.edu) version of SRMA to see if if produces any results. Let us know if you need further assistance. Thanks, Kelly On Thu Jun 16, at 12:49 PM, Gong, Henry wrote:
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
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Hi Kelly and others, Thanks for the move. The SRMA run doesn't seem to go to completion; instead, it stays yellow and produces no output (the corresponding dataset is 0KB). I did try the second test in srma_wrapper, and here is the error I got: Traceback (most recent call last): File "/Users/user/galaxy-dist/eggs/nose-0.11.1-py2.4.egg/nose/failure.py", line 39, in runTest raise self.exc_class(self.exc_val) OSError: No such file /Users/user/galaxy-dist/- I'm not sure what that file is supposed to be. Here's the whole output on pastebin, just in case it helps: http://pastebin.com/yUE0LmGL Thanks! Henry -----Original Message----- From: Kelly Vincent [mailto:kpvincent@bx.psu.edu] Sent: Thu 6/16/2011 10:20 AM To: Gong, Henry Cc: Nate Coraor; Shieh, Joseph; Galaxy Dev Subject: Re: [galaxy-user] SRMA on a local galaxy instance? Henry, I'm moving this over to galaxy-dev since it has to do with a local instance. It definitely sounds like you've got things set up right. You don't say what the result of your run is--is it "successful" (green) but an empty file? Or is there an error? If it's empty, it's possible your data just didn't yield any results. If there's an error, please share that with us. There are a couple of other things you could do to start figure out where the problem is. Have you tried running the functional tests for SRMA? There are two and you could comment out the first one in the xml since it relies on hg18chr21 being in the loc file, but if the second one passes then we'd know SRMA is installed correctly but there is something with your data (the command is: sh run_functional_tests.sh - id srma_wrapper). You also could try running your data through on our test server's (test.g2.bx.psu.edu) version of SRMA to see if if produces any results. Let us know if you need further assistance. Thanks, Kelly On Thu Jun 16, at 12:49 PM, Gong, Henry wrote:
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 -
Kelly Vincent