Hi, Richard,
I see you are looking in the main toolshed. I cant speak for fcarmia's one
but it doesn't do any dependency installation. The 'digital_dge' one was
deprecated - I've now deleted it.

The differential count models package in the statistics section of the test
toolshed -
http://testtoolshed.g2.bx.psu.edu/view/fubar/differential_count_models is
ready for testing so if you have time, please try it. It installs all
dependencies including R and bioconductor automatically. Installation
through the galaxy admin interface should work automatically but be warned
- it takes a very long time to install all the dependencies including
compiling R and installing Bioconductor. You will need to generate count
matrices from bam files - there's an htseq_bams_to_count_matrix tool to do
that which also installs all dependencies - also in the statistics section.


On Thu, Aug 15, 2013 at 1:17 AM, Richard Kuo <izen...@gmail.com> wrote:

> Hello,
> I have some questions about the edgeR (fcaramia) and digital_dge (fubar)
> repositories in tool shed.
>
> What is the difference between the two respositories in terms of being
> able to run edgeR?
>
> What is the proper way to install R so that the tool wrappers can use
> edgeR?
>
> What versions of R and edgeR do each of the repositories work with?
> Similaraly why is it that the repositories do not have information about
> which versions of R and edgeR are compatible?
>
> I have tried both repositories and have installed R and loaded the edgeR
> library but the tools do not seem to work. There are no errors coming up
> but the outputs are empty. The input file works with edgeR ran the
> traditional way through R (without Galaxy).
>
> Thank you,
> Richard
>
> ____________________________________________
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