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: 



-----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?

I'm moving this over to galaxy-dev since it has to do with a local  

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.


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

Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:


Reply via email to