Hi Bomba,

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[1], 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.

[1]http://testtoolshed.g2.bx.psu.edu/

Regards,
Carlos

On Fri, Mar 30, 2012 at 9:45 AM, Bomba Dam
<bomba....@visva-bharati.ac.in> 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
>
> Cheers.
>
> Bomba
>
> --
>
>
>
>
>
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