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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___________________________________________________________
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in your mail client. To manage your subscriptions to this
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