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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="python" version="2.7">
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4 <readme>
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5 Contra requires Python >= 2.6
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6 </readme>
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7 </package>
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8 <package name="R" version="1.0">
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9 <readme>
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10 Contra requires any version of R
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11 </readme>
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12 </package>
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13
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14
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15 <package name="samtools" version="0.1.18">
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16 <install version="1.0">
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17 <actions>
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18 <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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19 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
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20 <action type="shell_command">make</action>
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21 <action type="move_file">
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22 <source>samtools</source>
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23 <destination>$INSTALL_DIR/bin</destination>
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24 </action>
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25 <action type="move_file">
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26 <source>misc/maq2sam-long</source>
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27 <destination>$INSTALL_DIR/bin</destination>
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28 </action>
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29 <action type="set_environment">
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30 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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31 </action>
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32 </actions>
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33 </install>
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34 <readme>
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35 Compiling SAMtools requires the ncurses and zlib development libraries.
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36 </readme>
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37 </package>
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38
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39
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40 <package name="bedtools" version="2.17.0">
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41 <install version="1.0">
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42 <actions>
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43 <action type="download_by_url" target_filename="bedtools-2.17.0.tar.gz" >http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action>
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44 <action type="shell_command">make all</action>
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45 <action type="set_environment">
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46 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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47 </action>
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48 </actions>
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49 </install>
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50 <readme>
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51 GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools
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52 </readme>
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53 </package>
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54 <package name="contra" version="2.0.4">
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55 <install version="1.0">
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56 <actions>
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57 <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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58 <action type="shell_command">rm -rf bedtools_installation_guide.txt</action>
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59 <action type="shell_command">rm -rf BEDTools-User-Manual.v4.pdf</action>
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60 <action type="shell_command">rm -rf BEDTools.v2.11.2.tar.gz</action>
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61 <action type="shell_command">rm -rf CONTRA_User_Guide.2.0.pdf</action>
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62 <action type="set_environment">
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63 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
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64 </action>
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65 </actions>
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66 </install>
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67 <readme>
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68 Contra requires Samtools, Bedtools, Python and R
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69 </readme>
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70 </package>
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71 </tool_dependency>
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72
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73
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