Mercurial > repos > rmarenco > hubarchivecreator

annotate tool_dependencies.xml @ 1:fb5e60d4d18a draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 64cfc08088d11f6818c1b4e5514ef9e67969eaff-dirty
author rmarenco
date Wed, 13 Jul 2016 13:36:37 -0400
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children df9e12da0d13
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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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17
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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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21
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22 <!-- TODO: Tools to install -->
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23 <!-- twoBitInfo / bedToBigBed / faToTwoBit -->
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24
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25
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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">
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32 http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gff3ToGenePred
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33 </url_template>
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34 <url_template os="linux">
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35 http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gff3ToGenePred
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36 </url_template>
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37 </action>
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38 <action type="chmod">
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39 <file mode="750">$INSTALL_DIR/bin/gff3ToGenePred</file>
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40 </action>
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41 <action type="set_environment">
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42 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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43 </action>
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44 </actions>
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45 </install>
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46 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
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47 </package>
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48
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49 <!-- Package gtfToGenePred -->
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50 <package name="gtfToGenePred" version="0.0.1">
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51 <install version="1.0">
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52 <actions>
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53 <action target_directory="bin" type="download_binary">
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54 <url_template os="darwin">
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55 http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gtfToGenePred
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56 </url_template>
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57 <url_template os="linux">
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58 http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gtfToGenePred
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59 </url_template>
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60 </action>
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61 <action type="chmod">
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62 <file mode="750">$INSTALL_DIR/bin/gtfToGenePred</file>
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63 </action>
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64 <action type="set_environment">
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65 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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66 </action>
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67 </actions>
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68 </install>
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69 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
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70 </package>
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71
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72 <!-- Package genePredToBed -->
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73 <package name="genePredToBed" version="0.0.1">
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74 <install version="1.0">
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75 <actions>
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76 <action target_directory="bin" type="download_binary">
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77 <url_template os="darwin">
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78 http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/genePredToBed
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79 </url_template>
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80 <url_template os="linux">
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81 http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/genePredToBed
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82 </url_template>
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83 </action>
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84 <action type="chmod">
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85 <file mode="750">$INSTALL_DIR/bin/genePredToBed</file>
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86 </action>
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87 <action type="set_environment">
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88 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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89 </action>
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90 </actions>
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91 </install>
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92 <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
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93 </package>
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94 </tool_dependency>