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annotate tool_dependencies.xml @ 11:d05236b15f81 draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3760d0c8353b924ecf994131a5c2eb381aa81fb2
author rmarenco
date Wed, 27 Jul 2016 10:10:49 -0400
parents df9e12da0d13
children cbd8982c9f51
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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 - faToTwoBit
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12 - samtools
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13 -->
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14 <package name="ucsc_tools" version="312">
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15 <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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16 </package>
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18 <package name="samtools" version="1.2">
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19 <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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20 </package>
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22 <!-- TODO: Tools to install -->
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23 <!-- twoBitInfo / bedToBigBed / faToTwoBit -->
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26 <!-- Package gff3ToGenePred -->
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27 <package name="gff3ToGenePred" version="0.0.1">
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28 <install version="1.0">
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29 <actions>
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30 <action target_directory="bin" type="download_binary">
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31 <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gff3ToGenePred</url_template>
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32 <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gff3ToGenePred</url_template>
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33 </action>
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34 <action type="chmod">
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35 <file mode="750">$INSTALL_DIR/bin/gff3ToGenePred</file>
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36 </action>
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37 <action type="set_environment">
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38 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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39 </action>
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40 </actions>
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41 </install>
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42 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
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43 </package>
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45 <!-- Package gtfToGenePred -->
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46 <package name="gtfToGenePred" version="0.0.1">
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47 <install version="1.0">
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48 <actions>
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49 <action target_directory="bin" type="download_binary">
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50 <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gtfToGenePred</url_template>
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51 <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gtfToGenePred</url_template>
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52 </action>
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53 <action type="chmod">
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54 <file mode="750">$INSTALL_DIR/bin/gtfToGenePred</file>
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55 </action>
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56 <action type="set_environment">
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57 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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58 </action>
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59 </actions>
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60 </install>
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61 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
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62 </package>
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63
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64 <!-- Package genePredToBed -->
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65 <package name="genePredToBed" version="0.0.1">
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66 <install version="1.0">
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67 <actions>
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68 <action target_directory="bin" type="download_binary">
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69 <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/genePredToBed</url_template>
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70 <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/genePredToBed</url_template>
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71 </action>
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72 <action type="chmod">
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73 <file mode="750">$INSTALL_DIR/bin/genePredToBed</file>
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74 </action>
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75 <action type="set_environment">
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76 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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77 </action>
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78 </actions>
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79 </install>
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80 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
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81 </package>
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82 </tool_dependency>