Note: Local install questions are normally directed to the galaxy-dev
list (CC'd)
rather than galaxy-user

On Mon, Aug 1, 2011 at 3:21 PM, Joseph Hargitai
<joseph.hargi...@einstein.yu.edu> wrote:
> Enis,
>
> a few things we came across:
>
> a, local install
>
> 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/

> 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

> permissions:
>
> the script seems to use sudo and galaxy interchangeably, which creates an
> issue with permissions writing to folders.
>
> Is there a way to install as galaxy user only?

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

> If we do need the switching between sudo and galaxy - is there a set of
> directory permissions you suggest for the original galaxy-dist install and
> the galaxyToools folder?

Good question - having manually reset permissions on a test server while
debugging driving mappings, I'd like to know what they should be.

Are you planing on using the Linux user group functionality as part of your
setup? e.g. Both your personal account and the Galaxy user account
could be part of a Galaxy admin group.

> b,
> as a second category of questions:
> are there any tools that do not work on the standard cloud install? (skipped
> over entirely or installed but do not work?)

By that do you mean of the standard tool set in the main repository?
(Because there will be lots of Galaxy tools in the Tool Shed which are
not in the standard cloud install).

Peter
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