Hi Bjoern, Dave,
I have been trying to understand how
https://toolshed.g2.bx.psu.edu/repos/iuc/package_r_3_0_3
works .
It contains a number of package dependencies as shown in the XML below. However, none show up in the toolshed UI (next screenshot). Is this because the package entries (libpng, cairo, etc) are inside a <actions> tag while they should
be outside of this tag? Could it be these are not executed after all?
Furthermore, the installation actually seems to be a simple download of a pre-compiled R version from depot.galaxy.org . So why the ./configure and make commands further down the XML?
Thanks for your help!
Pieter
-----Original Message-----
From: Björn Grüning [mailto:bjoern.gruening@gmail.com]
Sent: donderdag 30 oktober 2014 11:25
To: galaxy-dev@lists.bx.psu.edu; Lukasse, Pieter; Dave Bouvier
Subject: Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this?
Hi Pieter,
Am 30.10.2014 um 11:15 schrieb Lukasse, Pieter:
> Hi,
>
> 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
https://github.com/bgruening/galaxytools/blob/master/packages/package_r_3_0_3/tool_dependencies.xml
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,
Bjoern
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.
> Thanks!
>
> 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
>
http://www.pri.wur.nl<http://www.pri.wur.nl/>
>
>
>
>
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