Thanks for the information. 

I've added an option to the Cuffdiff tool so that the read group files can be 
output by Galaxy; this should make it possible to run Cuffdiff in Galaxy and 
then Cummerbund for replicate analysis. This change will make it out to our 
public server in a couple weeks.

Thanks,
J.

On Jul 31, 2013, at 5:39 PM, Mike Shamblott wrote:

> Thanks 
> 
> My tests confirm that cummerbund does require the run group files to do 
> replicate analyses. Therefore Galaxy cannot be used to do cuffdiff on 
> replicates when cummerbund is the next step in the workflow. 
> 
> Mike
> 
> 
> 
> Sent from my iPhone
> 
> On Jul 31, 2013, at 9:45 AM, Jeremy Goecks <jeremy.goe...@emory.edu> wrote:
> 
>> In the past, others have had success using Cummerbund with Galaxy, and 
>> there's even a Cummerbund wrapper in the tool shed: 
>> 
>> http://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund
>> 
>> That said, it appears that replicate information is largely contained in the 
>> read group tracking files, which are not currently included in Galaxy's 
>> Cuffdiff outputs. I don't know if these files are required by Cummerbund to 
>> do replicate analysis. This would be a good question for the Cummerbund 
>> developers, as well as what the p and q values mean when doing replicate 
>> analysis.
>> 
>> If you find that Galaxy's lacking something for Cummerbund to function 
>> correctly, that would be very useful information to share with the list.
>> 
>> Best,
>> J.
>> 
>> 
>> On Jul 26, 2013, at 8:50 PM, Mike Shamblott wrote:
>> 
>>> I'm trying to run Cuffdiff on a set of 10 human samples with biological 
>>> replication then download the results for further analyses in 
>>> Cummerbund(v2.1.1).  It seems like a standard workflow but I cannot get 
>>> cummerbund to acknowledge replicates.  I download and rename the 11 
>>> cuffdiff output files to the names expected by cummerbund.  Cummerbund 
>>> builds a CuffSet with no warnings and most analyses work as expected.  The 
>>> problem comes any time I try to see the results of replication.  For 
>>> example, in cummerbund, >replicates() returns an empty set and any type of 
>>> plot returns an error when replicates=T is included as an argument.
>>> 
>>> There is no evidence of replication data in any of the 11 cuffdiff output 
>>> files.  The data is presented with the group name only.  From this, I 
>>> conclude that the problem is with cuffdiff, since there is no replicate 
>>> data for cummerbund to build into its db.  I see that there are several 
>>> read group files that are produced by cuffdiff but cannot be downloaded in 
>>> Galaxy.  Is this the problem, and if so, how can Galaxy be used to generate 
>>> data with (essential) replication?  Are the p  and  q significance values 
>>> reported in the output files a result of replicate analysis?  
>>> 
>>> I have tried to ask this question in several different forums without 
>>> success.  The responses I've gotten suggest its a Galaxy issue rather than 
>>> either cuffdiff or cummerbund.   I'm hoping someone here can help answer my 
>>> questions.
>>> 
>>> Hopeful,
>>> 
>>> Mike
>>> 
>>> 
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