[galaxy-dev] [galaxy-user] mi-tools- tools_fabfile.py permissions requirements (local install)

[Peter Cock]

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.hargitai at 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