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1 <?xml version="1.0"?>
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2 <tool_dependency>
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2
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3 <package name="samtools" version="0.1.19">
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4 <repository changeset_revision="cb87eae7fc3e" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
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1
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5 </package>
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6 <set_environment version="1.0">
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1
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7 <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
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8 </set_environment>
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9 <package name="bowtie2" version="2.1.0">
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10 <install version="1.0">
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11 <actions>
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12 <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip</action>
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13 <action type="shell_command">make</action>
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14 <action type="move_file">
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15 <source>bowtie2</source>
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16 <destination>$INSTALL_DIR/bin</destination>
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17 </action>
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18 <action type="move_file">
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19 <source>bowtie2-align</source>
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20 <destination>$INSTALL_DIR/bin</destination>
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21 </action>
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22 <action type="move_file">
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23 <source>bowtie2-build</source>
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24 <destination>$INSTALL_DIR/bin</destination>
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25 </action>
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26 <action type="shell_command">chmod +x $INSTALL_DIR/bin/bowtie2</action>
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27 <action type="set_environment">
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1
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28 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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29 </action>
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30 </actions>
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31 </install>
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32 <readme>
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33 Compiling bowtie2 requires zlib and libpthread to be present on your system.
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34 </readme>
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35 </package>
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36 <package name="bowtie" version="0.12.8">
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37 <install version="1.0">
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38 <actions>
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39 <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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40 <action type="shell_command">make</action>
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41 <action type="move_file">
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42 <source>bowtie</source>
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43 <destination>$INSTALL_DIR/bin</destination>
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44 </action>
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45 <action type="move_file">
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46 <source>bowtie-inspect</source>
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47 <destination>$INSTALL_DIR/bin</destination>
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48 </action>
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49 <action type="move_file">
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50 <source>bowtie-build</source>
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51 <destination>$INSTALL_DIR/bin</destination>
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52 </action>
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53 <action type="set_environment">
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1
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54 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
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0
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55 </action>
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56 </actions>
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57 </install>
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58 <readme>
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59 </readme>
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60 </package>
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61 </tool_dependency>
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