Cummerbund is available in the Galaxy toolshed for use in local or cloud Galaxies:
http://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund We haven't put it on our public server yet because there are testing and compatibility challenges that need to be addressed. Best, J. On Feb 11, 2013, at 7:49 PM, Mike Shamblott wrote: > I have been using cufflinks on Galaxy Main. I have downloaded the files > generated but they do not correspond to the file names expected by > cummeRbund. > > For example: > cummeRbund expects 4 tracking files (e.g isoforms.fpkm_tracking) , 4 .diff > files (e.g isoform_exp.diff). > > Here is a trimmed version of the output I download, grouped by what Im > guessing is the tracking, diff and usage files: > > > TRACKING > ...Galaxy109_transcript_FPKM_tracking.tabular > ...Galaxy107_gene_FPKM_tracking.tabular > ...Galaxy105_TSS_groups_FPKM_tracking.tabular > ...Galaxy103_CDS_FPKM_tracking.tabular > > .DIFF > > ...Galaxy108_transcript_differential_expression_testing.tabular > ...Galaxy106_gene_differential_expression_testing.tabular > ...Galaxy102_CDS_FPKM_differential_expression_testing.tabular > > USAGE > ...Galaxy99_splicing_differential_expression_testing.tabular > ...Galaxy100_promoters_differential_expression_testing.tabular > ...Galaxy101_CDS_overloading_differential_expression_testing.tabular > > > Given that cummeRbund is a common next step in the workflow, is there an > option to save the output in the expected format, perhaps with a galaxy > history number prepend? I'm not sure which files are to be renamed and to > what name and it seems that one file is missing. > > If there were a cummeRbund implementation on Main it probably wouldn't matter > as much but until that happens, I (and i'm guessing other newcomers) would > appreciate the help! > > Thanks, > > mike > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. 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/
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. 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/