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6
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <!-- UCSC Tools in -->
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4 <!-- Useful for HAC are:
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5 - twoBitInfo
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6 - sort
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7 - bedToBigBed
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8 - gff3ToGenePred
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9 - gtfToGenePred
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10 - genePredToBed
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11 - genePredToBigGenePred
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12 - faToTwoBit
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13 - samtools
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14 - pslToBigPsl
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15 -->
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16 <package name="ucsc_tools" version="312">
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17 <repository changeset_revision="ceda74761368" name="package_ucsc_tools_312" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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18 </package>
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19
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20 <package name="samtools" version="1.2">
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21 <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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22 </package>
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23
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24 <!-- TODO: Tools to install -->
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25 <!-- twoBitInfo / bedToBigBed / faToTwoBit -->
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26
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27
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28 <!-- Package gff3ToGenePred -->
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29 <package name="gff3ToGenePred" version="0.0.1">
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30 <install version="1.0">
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31 <actions>
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32 <action target_directory="bin" type="download_binary">
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33 <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gff3ToGenePred</url_template>
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34 <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gff3ToGenePred</url_template>
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35 </action>
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36 <action type="chmod">
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37 <file mode="750">$INSTALL_DIR/bin/gff3ToGenePred</file>
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38 </action>
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39 <action type="set_environment">
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40 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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41 </action>
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42 </actions>
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43 </install>
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44 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
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45 </package>
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46
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47 <!-- Package gtfToGenePred -->
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48 <package name="gtfToGenePred" version="0.0.1">
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49 <install version="1.0">
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50 <actions>
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51 <action target_directory="bin" type="download_binary">
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52 <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gtfToGenePred</url_template>
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53 <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gtfToGenePred</url_template>
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54 </action>
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55 <action type="chmod">
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56 <file mode="750">$INSTALL_DIR/bin/gtfToGenePred</file>
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57 </action>
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58 <action type="set_environment">
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59 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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60 </action>
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61 </actions>
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62 </install>
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63 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
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64 </package>
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65
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66 <!-- Package genePredToBed -->
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67 <package name="genePredToBed" version="0.0.1">
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68 <install version="1.0">
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69 <actions>
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70 <action target_directory="bin" type="download_binary">
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71 <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/genePredToBed</url_template>
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72 <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/genePredToBed</url_template>
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73 </action>
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74 <action type="chmod">
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75 <file mode="750">$INSTALL_DIR/bin/genePredToBed</file>
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76 </action>
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77 <action type="set_environment">
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78 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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79 </action>
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80 </actions>
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81 </install>
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82 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
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83 </package>
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84
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85 http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToBigGenePred
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86
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87 <!-- Package genePredToBigGenePred -->
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88 <package name="genePredToBigGenePred" version="0.0.1">
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89 <install version="1.0">
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90 <actions>
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91 <action target_directory="bin" type="download_binary">
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92 <url_template os="darwin">
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93 http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/genePredToBigGenePred
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94 </url_template>
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95 <url_template os="linux">
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96 http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/genePredToBigGenePred
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97 </url_template>
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98 </action>
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99 <action type="chmod">
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100 <file mode="750">$INSTALL_DIR/bin/genePredToBigGenePred</file>
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101 </action>
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102 <action type="set_environment">
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103 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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104 </action>
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105 </actions>
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106 </install>
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107 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
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108 </package>
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109
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110 <!-- Package pslToBigPsl -->
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111 <package name="pslToBigPsl" version="0.0.1">
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112 <install version="1.0">
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113 <actions>
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114 <action target_directory="bin" type="download_binary">
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115 <url_template os="darwin">
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116 http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/pslToBigPsl
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117 </url_template>
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118 <url_template os="linux">
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119 http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/pslToBigPsl
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120 </url_template>
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121 </action>
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122 <action type="chmod">
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123 <file mode="750">$INSTALL_DIR/bin/pslToBigPsl</file>
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124 </action>
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125 <action type="set_environment">
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126 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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127 </action>
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128 </actions>
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129 </install>
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130 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
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131 </package>
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132 </tool_dependency>
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