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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="0.1.18">
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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/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
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7 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
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8 <action type="shell_command">make</action>
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9 <action type="move_file">
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10 <source>samtools</source>
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11 <destination>$INSTALL_DIR/bin</destination>
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12 </action>
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13 <action type="move_file">
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14 <source>misc/maq2sam-long</source>
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15 <destination>$INSTALL_DIR/bin</destination>
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16 </action>
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17 <action type="set_environment">
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18 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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19 </action>
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20 </actions>
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21 </install>
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22 <readme>
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23 Compiling SAMtools requires the ncurses and zlib development libraries.
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24 </readme>
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25 </package>
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26
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27
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28 <package name="bedtools" version="2.17.0">
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29 <install version="1.0">
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30 <actions>
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31 <action type="download_by_url" target_filename="bedtools-2.17.0.tar.gz" >http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action>
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32 <action type="shell_command">make all</action>
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10
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33 <action type="make_directory">$INSTALL_DIR/bin</action>
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9
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34 <action type="move_directory_files">
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12
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35 <source_directory>bin</source_directory>
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36 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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9
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37 </action>
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38 <action type="set_environment">
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39 <environment_variable name="PATH" action="prepend_to">$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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8
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44 GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools. g++ required
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45 </readme>
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46 </package>
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47 <package name="contra" version="2.0.4">
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48 <install version="1.0">
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49 <actions>
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50 <action type="download_by_url">http://downloads.sourceforge.net/project/contra-cnv/CONTRA.V2.0/CONTRA.v2.0.4.tar.gz</action>
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51 <action type="shell_command">rm -rf bedtools_installation_guide.txt</action>
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52 <action type="shell_command">rm -rf BEDTools-User-Manual.v4.pdf</action>
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53 <action type="shell_command">rm -rf BEDTools.v2.11.2.tar.gz</action>
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8
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54 <action type="shell_command">rm -rf CONTRA_User_Guide.2.0.pdf</action>
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10
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55 <action type="make_directory">$INSTALL_DIR/bin</action>
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12
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56 <action type="make_directory">$INSTALL_DIR/bin/scripts</action>
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10
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57 <action type="move_file">
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11
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58 <source>contra.py</source>
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59 <destination>$INSTALL_DIR/bin</destination>
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60 </action>
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61 <action type="move_file">
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62 <source>baseline.py</source>
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63 <destination>$INSTALL_DIR/bin</destination>
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64 </action>
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8
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65 <action type="move_directory_files">
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12
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66 <source_directory>scripts</source_directory>
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67 <destination_directory>$INSTALL_DIR/bin/scripts</destination_directory>
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10
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68 </action>
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0
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69 <action type="set_environment">
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8
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70 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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71 </action>
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72 </actions>
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73 </install>
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74 <readme>
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75 Contra requires Samtools, Bedtools, Python and R
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76 </readme>
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77 </package>
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78 </tool_dependency>
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79
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80
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