|
0
|
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> |
