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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="3.2.0">
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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="darwin">
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7 <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.0-Linux-x86_64.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>$INSTALL_DIR</destination_directory>
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11 </action>
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12 </actions>
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13 <actions architecture="x86_64" os="linux">
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14 <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.0-Linux-x86_64.tar.gz</action>
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15 <action type="move_directory_files">
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16 <source_directory>.</source_directory>
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17 <destination_directory>$INSTALL_DIR</destination_directory>
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18 </action>
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19 <action type="set_environment">
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20 <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
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21 <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
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22 </action>
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23 </actions>
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24 <actions>
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25 <package name="readline" version="6.2">
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26 <repository changeset_revision="f4201ff5aa66" name="package_readline_6_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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27 </package>
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28 <package name="libpng" version="1.6.7">
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29 <repository changeset_revision="833849e0ddfc" name="package_libpng_1_6_7" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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30 </package>
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31 <package name="cairo" version="1.12.14">
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32 <repository changeset_revision="8f011e7388e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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33 </package>
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34 <package name="pixman" version="0.32.4">
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35 <repository changeset_revision="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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36 </package>
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37 <package name="freetype" version="2.5.2">
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38 <repository changeset_revision="34ebf47e4941" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://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="f4201ff5aa66" name="package_readline_6_2" owner="devteam" prior_installation_required="True" toolshed="http://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="http://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="8f011e7388e1" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://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="bcf53d429118" name="package_pixman_0_32_4" owner="devteam" prior_installation_required="True" toolshed="http://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="http://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 </action>
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57 <action type="shell_command">
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58 export LDFLAGS="-L$PNG_LIBS -L$READLINE_LIBS" &&
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59 export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIBS" &&
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60 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &&
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61 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PNG_LIB_PATH" &&
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62 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &&
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63 export CFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDES" &&
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64 export CXXFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDES" &&
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65 export CPPFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDES" &&
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66 ./configure --with-tcltk \
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67 --with-blas \
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68 --with-lapack \
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69 --with-readline \
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70 --with-cairo \
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71 --with-libpng \
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72 --without-x \
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73 --enable-R-shlib \
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74 --disable-R-framework \
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75 --libdir=$INSTALL_DIR/lib \
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76 --prefix=$INSTALL_DIR
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77 </action>
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78 <action type="make_install" />
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79 <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
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80 <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
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81 </actions>
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82 <action type="set_environment">
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83 <environment_variable action="set_to" name="R_DOC_DIR">$INSTALL_DIR/lib/R/doc</environment_variable>
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84 <environment_variable action="set_to" name="R_HOME_DIR">$INSTALL_DIR/lib/R</environment_variable>
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85 <environment_variable action="set_to" name="R_INCLUDE_DIR">$INSTALL_DIR/lib/R/include</environment_variable>
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86 <environment_variable action="set_to" name="R_SHARE_DIR">$INSTALL_DIR/lib/R/share</environment_variable>
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87 <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
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88 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
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89 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
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90 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
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91 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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92 </action>
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93 </actions_group>
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94 </install>
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95 <readme>
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96 The precompiled versions of this package were built 2014-03-06.
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97 R is a free software environment for statistical computing and graphics.
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98 NOTE: See custom compilation options above.
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99 </readme>
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100 </package>
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101
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102 <package name="limma" version="3.24.15">
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103 <install version="1.0">
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104 <actions>
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105 <action type="setup_r_environment">
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106 <package name="R" version="3.2.0">
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107 <repository changeset_revision="17cf1bdcf41f" name="r_3_2_0_test1" owner="deepakjadmin" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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108 </package>
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109 <action type="download_by_url">http://bioconductor.org/packages/release/bioc/src/contrib/limma_3.24.15.tar.gz</action>
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110 <action type="shell_command">R CMD INSTALL tar.gz</action>
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111 </action>
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112 </actions>
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113 </install>
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114 <readme>
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115 limma_3.24.12 installed now try edgeR
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116 </readme>
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117
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118 </package>
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119
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120 </tool_dependency>
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