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_...
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.nlhttp://www.pri.wur.nl/
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