Hi Joe,
mi-deployment scripts are currently being used to create cloud images so
this is the correct code your looking at. However, when it comes to R and
rpy, those tools are (as you discovered) not being installed via those
scripts; they are installed from packages but, in the case of Galaxy cloud
images, they are inherited from the CloudBioLinux images that the Galaxy
cloud images build on top of so not even included in the mi-deployment
scripts. If you would like to follow suit and install those tools from
packages, these are the ones (for debian): r-base, r-base-core,
r-base-core-ra, r-base-dev, r-base-html, python-rpy

As far as the permissions issues goes, I'll look (over the next couple of
days) more closely at those and focus on consistency.

Enis

On Mon, Aug 1, 2011 at 11:04 AM, Peter Cock <p.j.a.c...@googlemail.com>wrote:

> Hi Jeseph,
>
> I see now you are talking about Enis' code for automated building of
> virtual machine
> Galaxy images, https://bitbucket.org/afgane/mi-deployment/src -
> mentioned briefly
> here: http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup
>
> I know very little about this area of Galaxy - we install any tools needed
> for
> Galaxy by hand (and try to document how we did it for future reference).
>
> On Mon, Aug 1, 2011 at 3:50 PM, Joseph Hargitai
> <joseph.hargi...@einstein.yu.edu> wrote:
> >
> >>
> >> 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
> >
>
> That was a CRAN mirror, which seems to have gone now.
> Not listed here: http://cran.r-project.org/mirrors.html
>
> >
> >> 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
>
> Regards,
>
> Peter
>
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