Mercurial > repos > pieterlukasse > prims_metabolomics_r_dependencies

comparison tool_dependencies.xml @ 0:d57322d79cfe

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author pieter.lukasse@wur.nl
date Thu, 06 Nov 2014 16:04:57 +0100
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children 16ad47f8751f
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-1:000000000000 0:d57322d79cfe
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <!-- see also http://wiki.galaxyproject.org/ToolShedToolFeatures for syntax help
4 partly based on : https://toolshed.g2.bx.psu.edu/repos/iuc/package_r_3_0_3
5 -->
6 <package name="R_bioc_metams" version="3.1.1">
7 <install version="1.0">
8 <actions_group>
9 <actions>
10 <action type="download_by_url">http://cran.r-project.org/src/base/R-3/R-3.1.1.tar.gz</action>
11 <action type="move_directory_files">
12 <source_directory>.</source_directory>
13 <destination_directory>$INSTALL_DIR</destination_directory>
14 </action>
15 <action type="shell_command">
16 cd $INSTALL_DIR; $INSTALL_DIR/configure --libdir=$INSTALL_DIR/lib --prefix=$INSTALL_DIR
17 </action>
18 <action type="shell_command">make -C $INSTALL_DIR</action>
19 </actions>
20 <action type="set_environment">
21 <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/doc</environment_variable>
22 <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR</environment_variable>
23 <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
24 <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/share</environment_variable>
25 <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
26 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR</environment_variable>
27 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR</environment_variable>
28 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/library</environment_variable>
29 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
30 </action>
31 <!-- the Bioconductor and metaMS part -->
32 <action type="shell_command">wget -P $INSTALL_DIR http://toolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_metabolomics_r_dependencies/raw-file/tip/INSTALL.r</action>
33 <action type="shell_command">$INSTALL_DIR/bin/Rscript $INSTALL_DIR/INSTALL.r</action>
34 </actions_group>
35 </install>
36 <readme>
37 Ensures R 3.1.1 is installed.
38 Ensures Bioconductor 3.0 and package metaMS, multtest and snow are installed.
39 R is a free software environment for statistical computing and graphics.
40 </readme>
41 </package>
42
43
44 </tool_dependency>