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4
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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 <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="pindel" version="0.2.5">
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7 <install version="1.0">
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8 <actions>
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6
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9 <action type="download_by_url" target_filename="pindel-master.zip">https://github.com/genome/pindel/archive/master.zip</action>
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7
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10 <!--<action type="shell_command">unzip pindel-master.zip -d pindel</action>-->
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11 <action type="shell_command">cd pindel-master</action>
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6
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12 <action type="shell_command">make SAMTOOLS=~/samtools</action>
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13 <action type="move_file">
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14 <source>pindel</source>
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15 <destination>$INSTALL_DIR/</destination>
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7
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16 </action>
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4
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17 <action type="set_environment">
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18 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</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 </readme>
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24 </package>
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25 </tool_dependency>
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