Bjoern and Dave,
That sounds great. Of course my next question will be "how much is a
little bit" ;) It just that I have to move on for now and make things at
least work, so I might try it with using the default R instance now, but
as soon as a 3.1.0 package is out I will definitely pick it up!
Stef
----- Original message -----
From: Björn Grüning <bjoern.gruen...@gmail.com>
To: Stef van Lieshout <stefvanliesh...@fastmail.fm>,
galaxy-dev@lists.bx.psu.edu, Dave Bouvier <d...@bx.psu.edu>
Subject: Re: [galaxy-dev] R bioconductor dependencies when creating
toolshed installation
Date: Tue, 17 Jun 2014 17:37:24 +0200
Hi Stef,
Am 17.06.2014 15:40, schrieb Stef van Lieshout:
> Hi Bjoern,
>
> That looks much better indeed ;) The only problem I still have then is
> that I need R 3.1.0 for a bioconductor 2.14 package (have send a new
> mailing list msg for that). Looking at the xml of other versions it's
> not something I will easily do myself.
If you can wait a little bit we (the IUC, or more concrete Dave Bouvier)
will take care of that and create such a repository.
> What will happen if I do not specify the R dependency ("package_r_3_0_3"
> in your example code) but do specify the download/install of packages,
> guess these get installed in the "default" R instance?
Puh, to be honest, I do not know. I never tested it without a real
instance. I guess it will pick the default version.
> Related to that, how can I call a specific instance of R in de tool.xml
> without specifying the full path to the tool. Eg, in the tool.xml I now
> do:
>
> <command>
> /path/to/lib/R/R-3.1.0/bin/Rscript
> /path/to/galaxy-dist/tools/testdir/tool.R $config
> </command>
>
> Where normally you can do:
>
> <command interpreter="Rscript">
> tool.R $config
> </command>
You should always use the latter version, without a path to R. Setting
the correct path or assuming the default should be handled by Galaxy.
The correct R version will be created with the <requirement> tag. You
can specify 3.1 as soon as we have it :)
You can thank Dave for the new R packages, he spend much time in
creating a big R binary that can run on almost all architectures.
Cheers,
Bjoern
> Thanks again!
> Stef
>
>
> ----- Original message -----
> From: Björn Grüning <bjoern.gruen...@gmail.com>
> To: Stef van Lieshout <stefvanliesh...@fastmail.fm>,
> galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] R bioconductor dependencies when creating
> toolshed installation
> Date: Tue, 17 Jun 2014 15:17:36 +0200
>
> Hi Stef,
>
> for R packages we have a special installation routine that will
> (hapefully) make your life easier.
>
>> I'm running into some difficulties on how to setup the installation
>> procedure for a galaxy tool which executes an R script and has certain
>> dependencies (mainly bioconductor packages). R can deal with
>> dependencies, packages can be installed with install.packages (has a
>> "dependencies" argument) or biocLite() for bioconductor packages.
>>
>> Yet, now I want my tool to be available at toolsheds. To do this I see
>> several options:
>
> Great!
>
>> 1) setting up tool_dependencies.xml with "R CMD INSTALL" for all
>> packages. BUT: need to download all dependencies before install, and can
>> older versions still be downloaded? Maybe need to upload them to
>> toolshed too..
>
> It is all a matter of how reproducible you want to have your tool.
> If you want 100% reproducibility, you need to mirror the source packages
> somehow, because bioc will not store older versions. At least that is
> not guaranteed.
>
> I'm using a special github repository for that purpose:
> https://github.com/bgruening/download_store
>
> R CMD INSTALL is not needed, see below.
>
>> 2) setting up tool_dependencies.xml to call an installation script with
>> Rscript (where I could use install.packages), BUT: Dependencies are
>> taken care of. But how do I select specific (older) versions, because if
>> I dont, installing at different time can give different version.
>
> Older versions is not possible as far as I know.
>
>> 3) creating a repository for each package and have all of them as
>> requirement in my galaxy tool. BUT: a lot of work for a lot of
>> dependencies
>
> Imho, we should have one R repository with a handful of standard
> packages included in the toolshed.
> Like packages_r_3_0_1. You should depend on that repository and
> additionally define one second dependency. Lets say your tool is called
> deseq2 than create one additional tool_dependencies.xml file called
> package_deseq2_1_2_10. In that definition you will install every
> dependency you need in addition to R.
>
> Here is one example:
> https://github.com/bgruening/galaxytools/blob/master/deseq2/tool_dependencies.xml
> https://github.com/bgruening/galaxytools/blob/master/orphan_tool_dependencies/package_deseq2_1_2_10/tool_dependencies.xml
>
> The really nice part is the "setup_r_environment" function from the
> toolshed. It will install source packages for you automatically. All you
> need to do is to name the package or, as shown in the example, specify
> the location of the source package.
>
> The only downside is that the order of these packages is important. If
> you are interested we have a script that will give you the correct
> dependency tree of a given package.
>
> Hope that helps,
> Bjoern
>
>
>> All have pros and cons, how do people deal with this?
>>
>> Stef
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>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
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>
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>
___________________________________________________________
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