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14
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <set_environment version="1.0">
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4 <environment_variable name="SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
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5 </set_environment>
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15
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6 <package name="samtools" version="0.1.18">
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7 <install version="1.0">
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8 <actions>
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9 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
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10 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
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11 <action type="shell_command">make</action>
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12 <action type="move_file">
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13 <source>samtools</source>
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14 <destination>$INSTALL_DIR/bin</destination>
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15 </action>
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16 <action type="move_file">
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17 <source>misc/maq2sam-long</source>
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18 <destination>$INSTALL_DIR/bin</destination>
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19 </action>
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20 <action type="set_environment">
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21 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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22 </action>
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23 </actions>
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24 </install>
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25 <readme>
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26 Compiling SAMtools requires the ncurses and zlib development libraries.
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27 </readme>
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28 </package>
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29
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14
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30 <package name="bowtie2" version="2.0.0-beta7">
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31 <install version="1.0">
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32 <actions>
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33 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.0.0-beta7/bowtie2-2.0.0-beta7-source.zip</action>
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34 <action type="shell_command">make</action>
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35 <action type="move_file">
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36 <source>bowtie2</source>
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37 <destination>$INSTALL_DIR/bin</destination>
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38 </action>
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39 <action type="move_file">
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40 <source>bowtie2-align</source>
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41 <destination>$INSTALL_DIR/bin</destination>
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42 </action>
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43 <action type="move_file">
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44 <source>bowtie2-build</source>
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45 <destination>$INSTALL_DIR/bin</destination>
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46 </action>
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47 <action type="shell_command">chmod +x $INSTALL_DIR/bin/bowtie2</action>
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48 <action type="set_environment">
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49 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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50 </action>
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51 </actions>
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52 </install>
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53 <readme>
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54 Compiling bowtie2 requires zlib and libpthread to be present on your system.
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55 </readme>
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56 </package>
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57 <package name="bowtie" version="0.12.8">
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58 <install version="1.0">
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59 <actions>
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60 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.8/bowtie-0.12.8-src.zip</action>
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61 <action type="shell_command">make</action>
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62 <action type="move_file">
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63 <source>bowtie</source>
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64 <destination>$INSTALL_DIR/bin</destination>
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65 </action>
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66 <action type="move_file">
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67 <source>bowtie-inspect</source>
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68 <destination>$INSTALL_DIR/bin</destination>
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69 </action>
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70 <action type="move_file">
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71 <source>bowtie-build</source>
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72 <destination>$INSTALL_DIR/bin</destination>
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73 </action>
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74 <action type="set_environment">
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75 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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76 </action>
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77 </actions>
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78 </install>
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79 <readme>
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80 </readme>
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81 </package>
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82 </tool_dependency>
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