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 ___________________________________________________________ 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: http://galaxyproject.org/search/mailinglists/
