Hi,
I have a Bioconductor package which depends on R 3.1.1 , so I think I cannot
use the "setup_r_environment" trick.
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.
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/>
<?xml version="1.0"?>
<tool_dependency>
<!-- see also http://wiki.galaxyproject.org/ToolShedToolFeatures for syntax help
partly based on : https://toolshed.g2.bx.psu.edu/repos/iuc/package_r_3_0_3
-->
<package name="R_bioc_metams" version="3.1.1">
<install version="1.0">
<actions_group>
<actions>
<action type="download_by_url">http://cran.r-project.org/src/base/R-3/R-3.1.1.tar.gz</action>
<action type="move_directory_files">
<source_directory>.</source_directory>
<destination_directory>$INSTALL_DIR</destination_directory>
</action>
<action type="shell_command">
cd $INSTALL_DIR; $INSTALL_DIR/configure --libdir=$INSTALL_DIR/lib --prefix=$INSTALL_DIR
</action>
<action type="shell_command">make -C $INSTALL_DIR</action>
</actions>
<action type="set_environment">
<environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/doc</environment_variable>
<environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR</environment_variable>
<environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
<environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/share</environment_variable>
<environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
<environment_variable action="set_to" name="R_HOME">$INSTALL_DIR</environment_variable>
<environment_variable action="set_to" name="RHOME">$INSTALL_DIR</environment_variable>
<environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/library</environment_variable>
<environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
</action>
<!-- the Bioconductor and metaMS part -->
<action type="shell_command">wget -P $INSTALL_DIR http://testtoolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_metabolomics_dependencies/raw-file/tip/INSTALL.r</action>
<action type="shell_command">$INSTALL_DIR/bin/Rscript $INSTALL_DIR/INSTALL.r</action>
</actions_group>
</install>
<readme>
Ensures R 3.1.1 is installed.
Ensures Bioconductor 3.0 and package metaMS, multtest and snow are installed.
R is a free software environment for statistical computing and graphics.
</readme>
</package>
</tool_dependency>___________________________________________________________
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