Thanks for this reply. I will have to try referring to the R_ROOT_DIR from
another tool_dependency. If it doesn't work I'll come back ;)
From: Björn Grüning [mailto:bjoern.gruen...@gmail.com]
Sent: donderdag 30 oktober 2014 11:25
To: firstname.lastname@example.org; Lukasse, Pieter; Dave Bouvier
Subject: Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this?
Am 30.10.2014 um 11:15 schrieb Lukasse, Pieter:
> I have a Bioconductor package which depends on R 3.1.1 , so I think I cannot
> use the "setup_r_environment" trick.
Why? Do you need a new release? The latest current release in the Tool Shed is
R 3.1.0. If this is not enough we need to poke Dave to build a new package. But
this way would be the preferred way.
> I already got a tool_dependency.xml working that installs R 3.1.1 and the
> necessary Bioconductor packages using bioclite method (see attachment). Now
> my question is:
> * I would like to split up this into two steps as I don't want to
> trigger the compilation of new R environment every time I when I need to just
> update the
>Bioconductor package....the question is: how to do such things in general? How
>can I access the INSTALL_DIR of another tool from within another
>tool_dependency.xml? If I can do this, then my problem is solved.
If you really want to build your R packages by your own. Have a look at
You will find an exhaustive installation instruction how to build R properly.
Also note that we export a variable called R_ROOT_DIR that is set to
$INSTALL_DIR. You can now access R_ROOT_DIR from any other tool_dependency file
Hope this helps,
P.S. Do you mind asking this question on biostar again, I think this is a very
nice question that can be of interest to a lot more people.
> Pieter Lukasse
> Wageningen UR, Plant Research International Department of
> Bioinformatics (Bioscience) Wageningen Campus, Building 107,
> Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
> T: +31-317481122;
> M: +31-628189540;
> skype: pieter.lukasse.wur
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