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

[Enis Afgan]

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.hargitai at 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 [eafgan at 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.cock at 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.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
>>
>
>
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