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annotate tool_dependencies.xml @ 5:3bd1087db05e draft

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Add dependecies for bowtie, blat, and faToTwoBit
author Jim Johnson <jj@umn.edu>
date Fri, 04 Jan 2013 15:01:19 -0600
parents 679a5c7b1294
children 1ea6445491d4
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="defuse" version="0.5.0">
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4 <install version="1.0">
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5 <actions>
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6 <action type="download_by_url">http://sourceforge.net/projects/defuse/files/defuse/0.5/defuse-0.5.0.tar.gz</action>
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7 <action type="shell_command">cd tools &amp;&amp; make</action>
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8 <action type="move_directory_files">
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9 <source_directory>.</source_directory>
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10 <destination_directory>$INSTALL_DIR</destination_directory>
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11 </action>
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12 <action type="set_environment">
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13 <environment_variable name="DEFUSE_PATH" action="set_to">$INSTALL_DIR</environment_variable>
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14 </action>
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15 </actions>
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16 </install>
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17 <readme>
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18 </readme>
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19 </package>
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20
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21 <package name="bowtie" version="0.12.7">
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22 <install version="1.0">
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23 <actions>
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24 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip</action>
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25 <action type="shell_command">make</action>
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26 <action type="move_file">
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27 <source>bowtie</source>
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28 <destination>$INSTALL_DIR/bin</destination>
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29 </action>
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30 <action type="move_file">
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31 <source>bowtie-build</source>
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32 <destination>$INSTALL_DIR/bin</destination>
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33 </action>
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34 <action type="move_file">
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35 <source>bowtie-inspect</source>
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36 <destination>$INSTALL_DIR/bin</destination>
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37 </action>
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38 <action type="set_environment">
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39 <environment_variable name="PATH" action="prepend_to">$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>
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44 Compiling Bowtie requires libpthread to be present on your system.
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45 </readme>
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46 </package>
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47
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48 <package name="blat" version="34x10">
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49 <install version="1.0">
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50 <actions>
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51 <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/blat/blat</action>
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52 <action type="shell_command">chmod 755 blat</action>
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53 <action type="move_file">
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54 <source>blat</source>
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55 <destination>$INSTALL_DIR/bin</destination>
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56 </action>
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57 <action type="set_environment">
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58 <environment_variable name="PATH" action="prepend_to">$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>
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63 This only handles blat for a non-commercial linux system.
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64
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65 Please note that the Blat source and executables are freely available for
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66 academic, nonprofit and personal use. Commercial licensing information is
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67 available on the Kent Informatics website (http://www.kentinformatics.com/).
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68 </readme>
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69 </package>
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70
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71 <package name="fatotwobit" version="34x10">
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72 <install version="1.0">
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73 <actions>
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74 <action type="download_by_url">http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit</action>
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75 <action type="shell_command">chmod 755 faToTwoBit</action>
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76 <action type="move_file">
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77 <source>faToTwoBit</source>
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78 <destination>$INSTALL_DIR/bin</destination>
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79 </action>
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80 <action type="set_environment">
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81 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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82 </action>
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83 </actions>
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84 </install>
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85 <readme>
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86 This only handles faToTwoBit for a non-commercial linux system.
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87
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88 Please note that the source and executables are freely available for
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89 academic, nonprofit and personal use. Commercial licensing information is
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90 available on the Kent Informatics website (http://www.kentinformatics.com/).
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91 </readme>
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92 </package>
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93
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94 </tool_dependency>