Cool,

one question remains:

since the cloud instance works and installs - there needs to be a script that 
is fully functional -

a - installs dependencies
b - installs tools
c - creates indexes
d - points tools to indexes


j

________________________________
From: Enis Afgan [eaf...@emory.edu]
Sent: Monday, August 01, 2011 12:54 PM
To: Joseph Hargitai
Cc: Galaxy Dev
Subject: Re: [galaxy-user] mi-tools- tools_fabfile.py permissions requirements 
(local install)

Well, you can give it a shot like that and see if it still works. I quit using 
(and thus updating) the R-installation methods a while ago now so not sure if 
the process was changed. There is high likelihood that R will work (you should 
probably update the version number in the method itself). rpy however, will 
probably not work - rpy was very hard to install to begin with and that is why 
we moved away from this approach.
Alternatively, you can add packages I listed in my last email to the list of 
packages under _required_packages method.

Enis

On Mon, Aug 1, 2011 at 12:49 PM, Joseph Hargitai 
<joseph.hargi...@einstein.yu.edu<mailto:joseph.hargi...@einstein.yu.edu>> wrote:
Hi,

so for local install i can uncomment the R and rpy from your script as far as 
at the _install_R.. part?

j

________________________________
From: Enis Afgan [eaf...@emory.edu<mailto:eaf...@emory.edu>]
Sent: Monday, August 01, 2011 12:37 PM
To: Joseph Hargitai
Cc: Galaxy Dev
Subject: Re: [galaxy-user] mi-tools- tools_fabfile.py permissions requirements 
(local install)

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<mailto: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<mailto: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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