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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="R" version="3.1.2">
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4 <install version="1.0">
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5 <actions_group>
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6 <actions architecture="x86_64" os="linux">
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7 <action sha256sum="586dde39d6821bcc5079004450f5d19f836a26d4554083c7add3933f071451e0" type="download_by_url">https://depot.galaxyproject.org/software/r/r_3.1.2_linux_x64.tar.gz</action>
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8 <action type="move_directory_files">
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9 <source_directory>.</source_directory>
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10 <destination_directory>$INSTALL_DIR</destination_directory>
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11 </action>
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12 <action type="set_environment">
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13 <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
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14 <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
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15 </action>
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16 </actions>
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17 <actions>
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18 <action sha256sum="bcd150afcae0e02f6efb5f35a6ab72432be82e849ec52ce0bb89d8c342a8fa7a" type="download_by_url">https://cran.rstudio.com/src/base/R-3/R-3.1.2.tar.gz</action>
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19 <package name="readline" version="6.2">
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20 <repository changeset_revision="1007a3015bdb" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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21 </package>
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22 <package name="libpng" version="1.6.7">
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23 <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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24 </package>
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25 <package name="cairo" version="1.12.14">
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26 <repository changeset_revision="f1cf1dd60867" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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27 </package>
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28 <package name="pixman" version="0.32.4">
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29 <repository changeset_revision="7056a708062b" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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30 </package>
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31 <package name="freetype" version="2.5.2">
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32 <repository changeset_revision="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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33 </package>
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34 <package name="ncurses" version="5.9">
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35 <repository changeset_revision="ad27910a950c" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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36 </package>
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37 <package name="fontconfig" version="2.11.1">
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38 <repository changeset_revision="66bcc0972d16" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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39 </package>
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40 <action type="set_environment_for_install">
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41 <repository changeset_revision="1007a3015bdb" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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42 <package name="readline" version="6.2" />
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43 </repository>
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44 <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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45 <package name="libpng" version="1.6.7" />
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46 </repository>
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47 <repository changeset_revision="f1cf1dd60867" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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48 <package name="cairo" version="1.12.14" />
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49 </repository>
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50 <repository changeset_revision="7056a708062b" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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51 <package name="pixman" version="0.32.4" />
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52 </repository>
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53 <repository changeset_revision="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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54 <package name="freetype" version="2.5.2" />
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55 </repository>
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56 <repository changeset_revision="ad27910a950c" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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57 <package name="ncurses" version="5.9" />
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58 </repository>
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59 <repository changeset_revision="66bcc0972d16" name="package_fontconfig_2_11_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
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60 <package name="fontconfig" version="2.11.1" />
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61 </repository>
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62 </action>
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63 <action type="autoconf">--with-tcltk --with-blas --with-lapack --with-readline --with-cairo --with-libpng --without-x --without-aqua --enable-R-shlib --disable-R-framework --libdir=$INSTALL_DIR/lib</action>
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64 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
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65 <action type="shell_command">sed -i.bak -e 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
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66 </actions>
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67 <action type="set_environment">
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68 <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable>
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69 <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable>
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70 <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable>
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71 <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable>
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72 <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
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73 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
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74 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
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75 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
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76 <!-- Include library with local rJava installation -->
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77 <environment_variable action="prepend_to" name="R_LIBS">/usr/lib/R/site-library</environment_variable>
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78 <!-- Set JAVA_HOME & LD_LIBRARY_PATH -->
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79 <environment_variable action="set_to" name="JAVA_HOME">/usr/lib/jvm/java-8-openjdk-amd64/jre</environment_variable>
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80 <environment_variable action="set_to" name="LD_LIBRARY_PATH">/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server</environment_variable>
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81 <!-- Set FONTCONFIG_PATH for R png output -->
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82 <environment_variable action="set_to" name="FONTCONFIG_PATH">$INSTALL_DIR/etc/fonts</environment_variable>
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83 <environment_variable action="set_to" name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
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84 <environment_variable action="set_to" name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig</environment_variable>
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85 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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86 <!-- Append java bin to PATH -->
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87 <environment_variable action="append_to" name="PATH">$JAVA_HOME/bin</environment_variable>
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88 </action>
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89 </actions_group>
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90 </install>
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91 <readme>
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92 The precompiled versions of this package were built 2014-12-21.
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93 R is a free software environment for statistical computing and graphics.
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94 NOTE: See custom compilation options above.
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95 </readme>
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96 </package>
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97 </tool_dependency>
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