Bjoern,

FYI, I found that package_gatk_1_4 from the main Galaxy toolshed
produces Rscript files for VariantRecalibrator and other commands that
require ggplot_0.8.8 and reshape_0.8.4. This applies to GATK versions
1.4-20 and 1.4-37.

The magic incantation to get a systemwide R v3.1 setup properly is:

r <- getOption("repos");
r["CRAN"] <- "http://cran.rstudio.com/";;
options(repos=r);
install.packages(c('devtools','gsalib'));
require(devtools);
install_url('http://cran.r-project.org/src/contrib/Archive/plyr/plyr_1.7.1.tar.gz');
install_url('http://cran.r-project.org/src/contrib/Archive/reshape/reshape_0.8.4.tar.gz');
install_url('http://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_0.8.8.tar.gz');

I'm not sure gsalib is required, but it is better to play it safe IMO.

Can you add this to the package_gatk_1_4 documentation to help others
along? It would be even better if the package_gatk_1_4 could also
install those R libraries itself.

Cheers,

-E
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu


On Tue, Jul 29, 2014 at 4:22 PM, Björn Grüning
<bjoern.gruen...@gmail.com> wrote:
>
>
> Am 29.07.2014 um 22:45 schrieb Evan Bollig:
>
>> Hey Bjoern,
>>
>> I'm trying to use variant_recalibrator, xy_plot and other tools that
>> depend on package_r_2_11_0 and require ggplot2 to be installed. Since
>> CRAN support for R 2.11.0 and 2.15.0 is on the out, perhaps its a
>> better idea to update the packages the depend on those versions to R
>> 3.0 or 3.1?
>
>
> Yes, this would be a better idea!
>
>
>> The variant_recalibrator tool generates an Rscript
>> incompatible with modern versions of ggplot2, so this could be a quite
>> involved undertaking.
>
>
> Oh :( ... can we somehow get an old tarball of ggplot2? Have you looked at
> older linux disributions, debian stable for example?
>
> I found ggplot on download_store ;)
> https://github.com/bgruening/download_store/blob/master/gatk2_R_deps/ggplot2_0.9.3.1.tar.gz
>
> Is that old enough?
>
>
>> Meanwhile I'll look into the download_store option. You download all
>> of the tarballs and install them individually with R CMD INSTALL?
>
>
> Not really, we have a nice routine in the toolshed for such tasks:
> Have a look at:
> https://github.com/bgruening/galaxytools/tree/master/orphan_tool_dependencies/package_deseq2_1_2_10
>
> Note: the order of the packages are important ...
>
> Ciao,
> Bjoern
>
>
>> Cheers,
>>
>> -E
>> -Evan Bollig
>> Research Associate | Application Developer | User Support Consultant
>> Minnesota Supercomputing Institute
>> 599 Walter Library
>> 612 624 1447
>> e...@msi.umn.edu
>> boll0...@umn.edu
>>
>>
>> On Tue, Jul 29, 2014 at 2:46 PM, Björn Grüning
>> <bjoern.gruen...@gmail.com> wrote:
>>>
>>> Hi Evan,
>>>
>>> do you have somehow access to this tarball? Than we can put it on
>>>
>>> https://github.com/bgruening/download_store
>>>
>>> I use that to host R packages to save them for reproducibility.
>>>
>>>
>>>> Can I install another package_r and have packages that depend on
>>>> package_r_2_11_0 use the newer version?
>>>
>>>
>>>
>>> I don't think so. But that depends very much on your package. Is it not
>>> possible to use a newer R version? In either case you should save all
>>> tarballs somehow to archive them!
>>>
>>> Cheers,
>>> Bjoern
>>>
>>>> -Evan Bollig
>>>> Research Associate | Application Developer | User Support Consultant
>>>> Minnesota Supercomputing Institute
>>>> 599 Walter Library
>>>> 612 624 1447
>>>> e...@msi.umn.edu
>>>> boll0...@umn.edu
>>>> ___________________________________________________________
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>>>>
>>>
>

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