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:kpvinc...@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:n...@bx.psu.edu]
> Sent: Thu 6/16/2011 7:35 AM
> To: Gong, Henry
> Cc: galaxy-u...@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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