>
> R - not the correct download url,

Which URL are you talking about? The wiki page on dependencies
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
correctly links to the R project as http://www.r-project.org/

you are correct, however the tools_fabfile.py has

   version = "2.11.1"
    url = "http://mira.sunsite.utk.edu/CRAN/src/base/R-2/R-%s.tar.gz"; % version




> rpy - will this be fixed?

What needs to be fixed? Moving Galaxy to rpy2?
https://bitbucket.org/galaxy/galaxy-central/issue/103/upgrade-rpy-to-latest-version


again script has a comment:

def _install_rpy():
    # *Does not work in reality*



> Do you mean installing Galaxy without admin rights (i.e. without using sudo)?

either way - but should work. The fab script for instance adds some jar files 
to the galaxy-dist structure - then more added via the same script as sudo, and 
when it wants to change permissions for the entire folder for the next 
application the script fails. Hence just curious what a smoother solution would 
be.   


In general - is the cloud install using the mi- script to install the tools? If 
so, where is it located? I'd like to compare it to the one i use for the local 
install. If it uses another script where/what is it?

thanks,
joe





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