Hi Joe,
I just updated the code for the Galaxy installation process as part of
mi-deployment to use the user defined via env.galaxy_user. There is still a
(slightly guarded) chown called at the end of the script run due to the way
other tools are being installed. We keep talking about rewriting this code
entirely so it hasn't been generalized terribly much, which means that it is
likely that some customizations for the current deployment will be desired.
Overall, if you have suggestions and/or would like to fork the project and
issue pull requests with code changes, please do, I'd appreciate all of that
a lot.

Let me know if this change helps.

Enis

On Mon, Aug 1, 2011 at 2:44 PM, Joseph Hargitai <
joseph.hargi...@einstein.yu.edu> wrote:

>
> 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> 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]
>> *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>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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