2
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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16
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3 <set_environment version="1.0">
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4 <environment_variable name="JAR_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
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5 </set_environment>
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6
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7 <set_environment version="1.0">
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8 <environment_variable name="CIRCOS_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
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9 </set_environment>
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10
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21
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11
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16
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12 <package name="circos" version="0.64">
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10
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13 <install version="1.0">
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16
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14 <actions>
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15 <!-- Downloads the Circos software from its website and unpacks it -->
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16 <action type="download_by_url">http://circos.ca/distribution/circos-0.64.tgz </action>
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17 <action type="move_directory_files">
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18 <source_directory>.</source_directory>
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19 <destination_directory>$INSTALL_DIR/</destination_directory>
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20 </action>
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21 <action type="set_environment">
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22 <environment_variable name="CIRCOS_PATH" action="set_to">$INSTALL_DIR</environment_variable>
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23 </action>
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24 </actions>
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10
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25 </install>
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15
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26 <readme>
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16
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27 Downloads and installs Circos (v.0.64) for use in visualization. Requires perl to be installed.
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15
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28 </readme>
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16
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29 </package>
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30
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31 <set_environment version="1.0">
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32 <environment_variable name="R_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
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33 </set_environment>
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34
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21
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35 <package name="R_3_0_2" version="3.0.2">
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36 <install version="1.0">
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37 <actions_group>
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38 <actions architecture="x86_64" os="darwin">
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39 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/R/R-3.0.2-Darwin-x86_64.tgz</action>
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40 <action type="move_directory_files">
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41 <source_directory>.</source_directory>
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42 <destination_directory>$INSTALL_DIR</destination_directory>
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43 </action>
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44 </actions>
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45 <actions architecture="x86_64" os="linux">
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46 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/R/R-3.0.2-Linux-x86_64.tgz</action>
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47 <action type="move_directory_files">
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48 <source_directory>.</source_directory>
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49 <destination_directory>$INSTALL_DIR</destination_directory>
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50 </action>
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51 <action type="set_environment">
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52 <environment_variable action="set_to" name="TCL_LIBRARY">$INSTALL_DIR/lib/libtcl8.4.so</environment_variable>
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53 <environment_variable action="set_to" name="TK_LIBRARY">$INSTALL_DIR/lib/libtk8.4.so</environment_variable>
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54 </action>
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55 </actions>
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56 <actions>
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57 <package name="readline" version="6.2">
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58 <repository changeset_revision="246f31787ca1" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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59 </package>
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60 <package name="libpng" version="1.6.7">
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61 <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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62 </package>
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63 <package name="cairo" version="1.12.14">
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64 <repository changeset_revision="4f7c800b1050" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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65 </package>
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66 <package name="pixman" version="0.32.4">
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67 <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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68 </package>
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69 <package name="freetype" version="2.5.2">
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70 <repository changeset_revision="86bbb06ec11b" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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71 </package>
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72 <action type="download_by_url">http://cran.rstudio.com/src/base/R-3/R-3.0.2.tar.gz</action>
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73 <action type="set_environment_for_install">
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74 <repository changeset_revision="246f31787ca1" name="package_readline_6_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
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75 <package name="readline" version="6.2" />
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76 </repository>
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77 <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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78 <package name="libpng" version="1.6.7" />
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79 </repository>
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80 <repository changeset_revision="4f7c800b1050" name="package_cairo_1_12_14" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
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81 <package name="cairo" version="1.12.14" />
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82 </repository>
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83 <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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84 <package name="pixman" version="0.32.4" />
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85 </repository>
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86 <repository changeset_revision="86bbb06ec11b" name="package_freetype_2_5_2" owner="devteam" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
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87 <package name="freetype" version="2.5.2" />
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88 </repository>
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89 </action>
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90 <action type="shell_command">
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91 export LDFLAGS="-L$PNG_LIBS -L$READLINE_LIB_PATH" &&
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92 export LDFLAGS="$LDFLAGS -Wl,-rpath,$READLINE_LIB_PATH" &&
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93 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PIXMAN_LIB_PATH" &&
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94 export LDFLAGS="$LDFLAGS -Wl,-rpath,$PNG_LIB_PATH" &&
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95 export LDFLAGS="$LDFLAGS -Wl,-rpath,$FREETYPE_LIB_PATH" &&
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96 export CFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &&
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97 export CXXFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &&
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98 export CPPFLAGS="-I$PNG_INCLUDES -I$READLINE_INCLUDE_PATH" &&
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99 ./configure --with-tcltk \
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100 --with-blas \
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101 --with-lapack \
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102 --with-readline \
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103 --with-cairo \
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104 --with-libpng \
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105 --without-x \
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106 --enable-R-shlib \
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107 --disable-R-framework \
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108 --libdir=$INSTALL_DIR/lib \
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109 --prefix=$INSTALL_DIR
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110 </action>
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111 <action type="make_install" />
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112 <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/bin/R</action>
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113 <action type="shell_command">sed -i.bak 's;$INSTALL_DIR;\${R_ROOT_DIR};g' $INSTALL_DIR/lib/R/bin/R</action>
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114 </actions>
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115 <action type="set_environment">
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116 <environment_variable action="set_to" name="R_ROOT_DIR">$INSTALL_DIR</environment_variable>
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117 <environment_variable action="set_to" name="R_HOME">$INSTALL_DIR/lib/R</environment_variable>
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118 <environment_variable action="set_to" name="RHOME">$INSTALL_DIR/lib/R</environment_variable>
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119 <environment_variable action="set_to" name="R_LIBS">$INSTALL_DIR/lib/R/library</environment_variable>
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120 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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121 </action>
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122 </actions_group>
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123 </install>
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124 <readme>
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125 The precompiled versions were built 2014-03-07.
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126 R is a free software environment for statistical computing and graphics. http://www.r-project.org/
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127 </readme>
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128 </package>
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129
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2
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130 </tool_dependency>
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