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