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