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/> > > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
