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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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2
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10 <package name="readline" version="6.2">
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11 <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
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12 </package>
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13 <package name="libpng" version="1.6.7">
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14 <repository changeset_revision="db14a391648d" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
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15 </package>
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16 <package name="cairo" version="1.12.14">
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17 <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
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18 </package>
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19 <package name="pixman" version="0.32.4">
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20 <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
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21 </package>
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22 <package name="freetype" version="2.5.2">
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23 <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
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24 </package>
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25 <action type="set_environment_for_install">
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26 <repository changeset_revision="052e8df231ac" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
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27 <package name="readline" version="6.2" />
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28 </repository>
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29 <repository changeset_revision="db14a391648d" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
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30 <package name="libpng" version="1.6.7" />
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31 </repository>
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32 <repository changeset_revision="b39299b4b6e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
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33 <package name="cairo" version="1.12.14" />
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34 </repository>
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35 <repository changeset_revision="3d44a209a6b9" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
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36 <package name="pixman" version="0.32.4" />
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37 </repository>
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38 <repository changeset_revision="58782940c411" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu">
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39 <package name="freetype" version="2.5.2" />
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40 </repository>
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41 </action>
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42 <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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43 <action type="move_directory_files">
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44 <source_directory>.</source_directory>
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45 <destination_directory>$INSTALL_DIR</destination_directory>
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46 </action>
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47 <action type="shell_command">
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2
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48 cd $INSTALL_DIR;
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49 export LDFLAGS="-L$PNG_LIBS -L$READLINE_LIB_PATH" &&
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50 export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" &&
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51 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &&
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52 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PNG_LIB_PATH" &&
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53 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &&
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54 export CFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &&
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55 export CXXFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &&
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56 export CPPFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &&
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57 $INSTALL_DIR/configure --with-tcltk \
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58 --with-blas \
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59 --with-lapack \
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60 --with-readline \
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61 --with-cairo \
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62 --with-libpng \
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63 --without-x \
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64 --enable-R-shlib \
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65 --disable-R-framework \
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66 --libdir=$INSTALL_DIR/lib \
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67 --prefix=$INSTALL_DIR
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68 </action>
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69 <action type="shell_command">make -C $INSTALL_DIR</action>
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70 </actions>
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71 <action type="set_environment">
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72 <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/doc</environment_variable>
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73 <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR</environment_variable>
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74 <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/include</environment_variable>
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75 <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/share</environment_variable>
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76 <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
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77 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR</environment_variable>
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78 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR</environment_variable>
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79 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/library</environment_variable>
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80 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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81 </action>
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82 <!-- the Bioconductor and metaMS part -->
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83 <action type="shell_command">wget -P $INSTALL_DIR http://toolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_metabolomics_r_dependencies/raw-file/tip/INSTALL.r</action>
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84 <action type="shell_command">$INSTALL_DIR/bin/Rscript $INSTALL_DIR/INSTALL.r</action>
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85 </actions_group>
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86 </install>
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87 <readme>
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88 Ensures R 3.1.1 is installed.
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89 Ensures Bioconductor 3.0 and package metaMS, multtest and snow are installed.
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90 R is a free software environment for statistical computing and graphics.
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91 </readme>
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92 </package>
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93
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94
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95 </tool_dependency> |
