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annotate tool_dependencies.xml @ 52:c66803bff0cc draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit adc1ac50269e02570e7ce12c732637bdd3f9a547-dirty
author yating-l
date Thu, 11 May 2017 17:21:15 -0400
parents 364b8db8de17
children 44059c9e7c02
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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="samtools" version="1.2">
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17 <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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18 </package>
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19
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20 <package name="ucsc_tools_340" version="1.0">
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21 <install version="1.0">
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22 <actions_group>
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23 <actions architecture="x86_64" os="linux">
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24 <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/ucsc_tools_340.tar.gz</action>
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25 <action type="move_directory_files">
52
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26 <source_directory>.</source_directory>
51
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27 <destination_directory>$INSTALL_DIR/bin</destination_directory>
52
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28 </action>
51
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29 </actions>
0
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30 <action type="set_environment">
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31 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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32 </action>
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33 </actions_group>
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34 </install>
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35 <readme>The well known UCSC tools from Jim Kent.</readme>
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36 </package>
52
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37
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38 <!-- package ucsc_bigwig is created by Wilson Leung -->
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39 <package name="ucsc_bigwig" version="340">
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40 <install version="1.0">
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41 <actions_group>
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42 <actions architecture="x86_64" os="darwin">
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43 <action sha256sum="a34c57a9fb3c36a984b8fa879a99697c994cd981a1277663d372638e4dec8bb2" type="download_by_url">
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44 http://old-gep.wustl.edu/~wilson/packages/ucsc_bigwig/ucsc_bigwig_340_macOS_x86_64.tar.gz
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45 </action>
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46 <action type="move_directory_files">
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47 <source_directory>bin</source_directory>
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48 <destination_directory>$INSTALL_DIR</destination_directory>
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49 </action>
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50 </actions>
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51
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52 <actions architecture="x86_64" os="linux">
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53 <action sha256sum="0d2bd886e312980e0ae58ae912315beeeac612fd1783c959b4eabd62cffd8512" type="download_by_url">
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54 http://old-gep.wustl.edu/~wilson/packages/ucsc_bigwig/ucsc_bigwig_340_linux_x86_64.tar.gz
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55 </action>
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56 <action type="move_directory_files">
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57 <source_directory>bin</source_directory>
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58 <destination_directory>$INSTALL_DIR</destination_directory>
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59 </action>
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60 </actions>
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61
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62 <!-- Display error message for unsupported OS and CPU architecture -->
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63 <actions>
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64 <action type="shell_command">
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65 echo "ERROR: This package only supports 64-bit systems running macOS or Linux"
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66 </action>
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67 <action type="shell_command">false</action>
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68 </actions>
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69
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70 <!-- update $PATH environment variable -->
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71 <action type="set_environment">
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72 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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73 </action>
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74 </actions_group>
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75 </install>
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76 <readme>
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77
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78 This package contains the utilities for constructing
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79 `bigWig files &lt;https://genome.ucsc.edu/goldenpath/help/bigWig.html&gt;`_.
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80 The utilities were created by the
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81 `Genome Bioinformatics Group &lt;https://genome.ucsc.edu/staff.html&gt;`_
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82 at the UCSC Genomics Institute.
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83
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84 The bigWig file format is designed to store dense continuous datasets
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85 and it is compatible with many genome browsers (e.g., UCSC Genome Browser,
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86 JBrowse, IGV).
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87
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88 </readme>
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89 </package>
0
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90 </tool_dependency>