Hi Bjoern,

I tried your suggestion, but it didn't work. So now I have split up the R part from the Bioconductor part (blue and yellow below, respectively). But the problem is that the <install> part executes before the <package> part is finished and the $R_ROOT_DIR reference also doesn’t seem to work as I get the following error : “ /bin/sh: 1: /bin/Rscript: not found “ . This R_ROOT_DIR is set by the <package> script in my other tool_dependency.xml but is not visible in the tool_dependency.xml below. But maybe I misunderstood what you meant by “You can now access R_ROOT_DIR from any other tool_dependency file ...”?

<tool_dependency>

<!-- see also http://wiki.galaxyproject.org/ToolShedToolFeatures for syntax help

-->

<actions_group>

<action type="shell_command">wget -P $INSTALL_DIR http://testtoolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_metabolomics/raw-file/tip/INSTALL.r</action>

<action type="shell_command">$R_ROOT_DIR/bin/Rscript $INSTALL_DIR/INSTALL.r</action>

</actions_group>

</install>

</package>

This dependency:

Ensures R 3.1.1 installation is triggered (via dependency).

Ensures Bioconductor 3.0 and package metaMS, multtest and snow are installed.

</readme>

</tool_dependency>

Thanks,

Pieter

-----Original Message-----
From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter
Sent: donderdag 6 november 2014 10:02
To: 'Björn Grüning'; galaxy-dev@lists.bx.psu.edu; Dave Bouvier
Subject: Re: [galaxy-dev] Tool shed environment dependency - HOW TO do this?

Hi Bjoern,

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 ;)

Regards,

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/>