Carrie,

We've had issues when gene ids contain a '#' character, which is the R comment character. We've had issues when the group names in a plot weren't exactly the same as those used in the cuffdiff inputs.

Are you linking in all the individual output files from cuffdiff? I included a cuffdiff tool in the cummeRbund toolshed respository because the original cuffdiff galaxy tool didn't output all 21 files that cummeRbund prefers. Are you also including the "genome reference and Feature file". The gtf may be needed for some functions.

JJ

On 6/3/14, 11:54 AM, Jennifer Jackson wrote:

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-dev@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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