I'm also quite interested on getting cummeRbund into Galaxy. I was able to start developing a tool to use it, but with tough time constraints at work and school, I haven't been able to get it to a point where I'm happy publishing it in the Main Toolshed. It is however in the Test Toolshed, you could find it by searching. If you have a local or cloud instance you should be able to install it and start playing with it. I got to the point where you can generate most kind of plots and you can select what kind of feature you want to plot, genes/isoform/TSS/CDS.
There is a lot to do still. For example I think it is a most to be able to use a list of genes as input for some of the graphs, like scatterplots and heatmaps, right now you can do this but you have to enter the genes one by one. There is no support for any non-plotting function, like getSig() or getSigTable(). Hopefully I will find the time in the near future to get it in shape for submission to the Main Toolshed. This however doesn't mean it would appear in the Main Galaxy sever, that's a decision only Galaxy developers can make.
Lastly, if there is interest in contributing to this effort, please let me know as I'll be happy to collaborate with other interested party developing this tool.
On Fri, Mar 30, 2012 at 9:45 AM, Bomba Dam firstname.lastname@example.org wrote:
Hi Galaxy team,
Are there any plans to add the CummeRband tool in the Galaxy platform.
It would be very nice to have it within Galaxy, this will help people like us (Biologists, without much programming knowledge) to do the complete RNA-seq analysis and visualize the data in graphical forms
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