Hi Carrie,

I'll start this off by stating that I am not as familiar with this wrapper as many of the others. I am bringing in the repository owner (Jim Johnson) to the thread so that he can offer help. You can also reach him (or any other repository owner) when logged in under the "Repository Actions" menu under "Contact Repository Owner".

Just from a quick look, I am wondering if the R package dependencies are installed with all necessary components and available to the "Galaxy user". Or, if the ones you tried are the correct ones to be using with this tool. The "attributes" warning is one that is given by R.

Going forward, using the galaxy-...@bx.psu.edu mailing list will be best for questions like this one. This list is being retired on Friday (replaced by Galaxy Biostar). Please join us there for usage questions (although there is some cross-over in questions and we are open to both, the community is still actively using galaxy-dev for primary local install help and you will reach more developers there): https://wiki.galaxyproject.org/Support#Biostar

Hopefully Jim will see this thread, but also try contacting him direct if no reply is sent here.

Sorry I could not help more,

Jen
Galaxy team

On 6/2/14 2:57 PM, Ganote, Carrie L wrote:
Hi list,

Is the cummeRbund wrapper on Galaxy yet functional? I've got some replicates 
that I'm trying to test for a user on our local Galaxy, but I just can't get 
the program to behave.

Using cuffdiff v2.2.0 604fa75232a2
cummeRbund version 0.0.7, 137aab1d9ac1
R 2.15.2 and 3.0.1 (tried both)
Last galaxy-dist/stable changeset: 7a7985a007fb

I ran cuffdiff like so:
Transcripts     83: Cuffmerge on data 6, data 67, and others: merged 
transcripts        
Name    control         
Add replicate   44: Tophat2 on data 1 and data 6: accepted_hits (ran as 
single-end fastq)
Add replicate   54: Tophat2 on data 2 and data 6: accepted_hits (ran as 
single-end fastq)
Name    sample  
Add replicate   59: Tophat2 on data 3 and data 6: accepted_hits (ran as 
single-end fastq)
Add replicate   64: Tophat2 on data 4 and data 6: accepted_hits (ran as 
single-end fastq)
Library normalization method    geometric       
Dispersion estimation method    pooled  
False Discovery Rate    0.05    
Min Alignment Count     10      
Use multi-read correct  No      
Perform Bias Correction         No      
Include Read Group Datasets     No      
Set Additional Parameters? (not recommended for paired-end reads)       No

Here's what I get when I run cummeRbund:
(From Galaxy, with R 2.15.2)
Creating database //path/job_working_directory/005/5051/galaxy_dataset_16602.dat
Reading //path/dataset_files/009/dataset_9861.dat
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading //path/dataset_files/009/dataset_9861.dat
Error in function (classes, fdef, mtable)  :
   unable to find an inherited method for function 'make.db.names' for signature 
'"SQLiteConnection", "NULL"'
Calls: readCufflinks ... make.db.names -> .valueClassTest -> is -> <Anonymous>
Execution halted

(From R interpreter on command line, R = 3.0.1)
Reading //path/dataset_files/009/dataset_9842.dat
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading //path/dataset_files/009/dataset_9842.dat
Error in (function (classes, fdef, mtable)  :
   unable to find an inherited method for function 'make.db.names' for signature 
'"SQLiteConnection", "NULL"'
In addition: Warning message:
attributes are not identical across measure variables; they will be dropped

I tried changing the group names in cuffdiff but no luck. No spaces or funny 
characters.

Thanks for any insight,

Carrie Ganote


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Posts to this list will be disabled in May 2014.  In the
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___________________________________________________________
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at https://biostar.usegalaxy.org/

Posts to this list will be disabled in May 2014.  In the
meantime, you are encouraged to post all new questions to
Galaxy Biostar.

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/

To search Galaxy mailing lists use the unified search at:

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