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annotate tool_dependencies.xml @ 19:0152500d9acd draft

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author rmarenco
date Thu, 13 Oct 2016 22:49:01 -0400
parents d786bca6a75d
children 40469b265ddb
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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 -->
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15 <package name="ucsc_tools" version="312">
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16 <repository changeset_revision="2d6bafd63401" name="package_ucsc_tools_312" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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17 </package>
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19 <package name="samtools" version="1.2">
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20 <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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21 </package>
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23 <!-- TODO: Tools to install -->
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24 <!-- twoBitInfo / bedToBigBed / faToTwoBit -->
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27 <!-- Package gff3ToGenePred -->
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28 <package name="gff3ToGenePred" version="0.0.1">
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29 <install version="1.0">
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30 <actions>
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31 <action target_directory="bin" type="download_binary">
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32 <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gff3ToGenePred</url_template>
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33 <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gff3ToGenePred</url_template>
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34 </action>
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35 <action type="chmod">
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36 <file mode="750">$INSTALL_DIR/bin/gff3ToGenePred</file>
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37 </action>
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38 <action type="set_environment">
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39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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40 </action>
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41 </actions>
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42 </install>
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43 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
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44 </package>
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46 <!-- Package gtfToGenePred -->
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47 <package name="gtfToGenePred" version="0.0.1">
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48 <install version="1.0">
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49 <actions>
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50 <action target_directory="bin" type="download_binary">
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51 <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gtfToGenePred</url_template>
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52 <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gtfToGenePred</url_template>
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53 </action>
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54 <action type="chmod">
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55 <file mode="750">$INSTALL_DIR/bin/gtfToGenePred</file>
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56 </action>
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57 <action type="set_environment">
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58 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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59 </action>
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60 </actions>
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61 </install>
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62 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
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63 </package>
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64
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65 <!-- Package genePredToBed -->
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66 <package name="genePredToBed" version="0.0.1">
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67 <install version="1.0">
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68 <actions>
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69 <action target_directory="bin" type="download_binary">
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70 <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/genePredToBed</url_template>
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71 <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/genePredToBed</url_template>
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72 </action>
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73 <action type="chmod">
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74 <file mode="750">$INSTALL_DIR/bin/genePredToBed</file>
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75 </action>
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76 <action type="set_environment">
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77 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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78 </action>
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79 </actions>
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80 </install>
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81 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
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82 </package>
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84 http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToBigGenePred
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86 <!-- Package genePredToBigGenePred -->
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87 <package name="genePredToBigGenePred" version="0.0.1">
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88 <install version="1.0">
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89 <actions>
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90 <action target_directory="bin" type="download_binary">
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91 <url_template os="darwin">
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92 http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/genePredToBigGenePred
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93 </url_template>
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94 <url_template os="linux">
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95 http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/genePredToBigGenePred
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96 </url_template>
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97 </action>
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98 <action type="chmod">
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99 <file mode="750">$INSTALL_DIR/bin/genePredToBigGenePred</file>
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100 </action>
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101 <action type="set_environment">
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102 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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103 </action>
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104 </actions>
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105 </install>
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106 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
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107 </package>
1
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108 </tool_dependency>