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1
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="samtools-mpileup-parallel" version="1.0.19">
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4 <install version="1.0">
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5 <actions>
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8
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6 <action type="shell_command">svn checkout https://github.com/mydatascience/parallel-mpileup/trunk samtools-mpileup-parallel && cd samtools-mpileup-parallel && cd $(ls |grep samtools-) && make && cp samtools ../samtools-mpileup-parallel</action>
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7 <action type="move_file">
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9
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8 <source>samtools-mpileup-parallel</source>
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9 <destination>$INSTALL_DIR/bin</destination>
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10 </action>
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11 <action type="set_environment">
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12 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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13 <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>
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14 </action>
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15 </actions>
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16 </install>
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17 <readme>
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18 Downloads and installs a modified version of samtools, able to paralellize the mpileup function.
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19 </readme>
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20 </package>
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21 <package name="VarScan" version="2.3.6">
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22 <install version="1.0">
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23 <actions>
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4
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24 <action type="download_by_url">http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.6.jar</action>
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25 <action type="move_file">
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26 <source>VarScan.v2.3.6.jar</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 <environment_variable name="PATH" action="prepend_to">$REPOSITORY_INSTALL_DIR</environment_variable>
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32 </action>
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33 </actions>
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34 </install>
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35 <readme>
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36 Downloads VarScan2.
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37 </readme>
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38 </package>
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39 </tool_dependency>
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