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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