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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="samtools" version="0.1.19">
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1
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4 <repository changeset_revision="6b6b5498d9a2" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="R_3_0_1" version="3.0.1">
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1
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7 <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
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0
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8 </package>
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9 <package name="eden" version="1.1">
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1
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10 <repository changeset_revision="532625813f2e" name="package_eden_1_1" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" />
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0
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11 </package>
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12 <package name="mcl" version="12.135">
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1
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13 <repository changeset_revision="9f59d1a59999" name="package_mcl_12_135" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
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0
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14 </package>
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15 <package name="blockclust_rlibs" version="1.0">
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16 <install version="1.0">
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17 <actions>
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18 <action type="setup_r_environment">
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1
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19 <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
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20 <package name="R_3_0_1" version="3.0.1" />
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21 </repository>
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22 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ape_3.0-11.tar.gz</package>
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23 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/plyr_1.8.tar.gz</package>
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24 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/digest_0.6.4.tar.gz</package>
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25 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/gtable_0.1.2.tar.gz</package>
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26 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/dichromat_2.0-0.tar.gz</package>
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27 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/colorspace_1.2-4.tar.gz</package>
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28 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/munsell_0.4.2.tar.gz</package>
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29 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/labeling_0.2.tar.gz</package>
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5
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30 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/RColorBrewer_1.0-5.tar.gz</package>
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31 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/stringr_0.6.2.tar.gz</package>
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32 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/scales_0.2.3.tar.gz</package>
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33 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/proto_0.3-10.tar.gz</package>
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34 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/reshape2_1.2.2.tar.gz</package>
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35 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/ggplot2_0.9.3.1.tar.gz</package>
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36 <package>https://github.com/bgruening/download_store/raw/master/blockclust/r-packages/squash_1.0.1.tar.gz</package>
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37 </action>
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38 </actions>
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39 </install>
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40 <readme>
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41
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42 </readme>
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43 </package>
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44 <package name="blockclust" version="1.0">
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45 <install version="1.0">
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46 <actions>
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47 <action type="download_by_url">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-1.0.tar.gz</action>
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48 <action type="shell_command">make</action>
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49 <action type="move_file">
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50 <source>BlockClust</source>
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51 <destination>$INSTALL_DIR/bin</destination>
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52 </action>
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53 <action type="move_file">
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54 <source>BlockClustPipeLine.pl</source>
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55 <destination>$INSTALL_DIR/bin</destination>
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56 </action>
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57 <action type="move_file">
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58 <source>perf</source>
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59 <destination>$INSTALL_DIR/bin</destination>
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60 </action>
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61 <action type="move_file">
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62 <source>plotClusters.R</source>
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63 <destination>$INSTALL_DIR/bin</destination>
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64 </action>
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65 <action type="move_file">
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66 <source>blockclust.config</source>
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67 <destination>$INSTALL_DIR/data/</destination>
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68 </action>
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69 <action type="move_file">
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70 <source>rfam_map.txt</source>
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71 <destination>$INSTALL_DIR/data/</destination>
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72 </action>
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73 <action type="make_directory">$INSTALL_DIR/data/annotations</action>
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74 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/dm3.tar.gz</action>
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4
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75 <action type="shell_command">cd ..; tar xfvz dm3.tar.gz -C $INSTALL_DIR/data/annotations/</action>
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0
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76 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/hg19.tar.gz</action>
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4
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77 <action type="shell_command">cd ..; tar xfvz hg19.tar.gz -C $INSTALL_DIR/data/annotations/</action>
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0
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78 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/mm10.tar.gz</action>
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4
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79 <action type="shell_command">cd ..; tar xfvz mm10.tar.gz -C $INSTALL_DIR/data/annotations/</action>
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0
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80 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/panTro4.tar.gz</action>
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4
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81 <action type="shell_command">cd ..; tar xfvz panTro4.tar.gz -C $INSTALL_DIR/data/annotations/</action>
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0
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82 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/rheMac3.tar.gz</action>
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4
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83 <action type="shell_command">cd ..; tar xfvz rheMac3.tar.gz -C $INSTALL_DIR/data/annotations/</action>
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0
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84 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/celWS235.tar.gz</action>
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4
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85 <action type="shell_command">cd ..; tar xfvz celWS235.tar.gz -C $INSTALL_DIR/data/annotations/</action>
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0
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86 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/tair10.tar.gz</action>
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4
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87 <action type="shell_command">cd ..; tar xfvz tair10.tar.gz -C $INSTALL_DIR/data/annotations/</action>
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0
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88 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/models.tar.gz</action>
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4
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89 <action type="shell_command">cd ..; tar xfvz models.tar.gz -C $INSTALL_DIR/data/</action>
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0
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90 <action type="set_environment">
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91 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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92 <environment_variable action="set_to" name="BLOCKCLUST_DATA_PATH">$INSTALL_DIR/data</environment_variable>
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93 </action>
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94 </actions>
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95 </install>
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96 <readme>
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97
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98 </readme>
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99 </package>
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100 </tool_dependency>
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