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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="velvet" version="1.2.10">
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4 <install version="1.0">
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5 <actions>
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6 <action type="shell_command">git clone git://github.com/dzerbino/velvet.git velvet</action>
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7 <action type="shell_command">git reset --hard 5cea317b4ec5c3f0fd2931321bc7231d8a250682</action>
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8 <action type="shell_command">make -i CATEGORIES=4 MAXKMERLENGTH=191 OPENMP=1</action>
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9 <action type="shell_command">mkdir scripts</action>
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10 <action type="shell_command">find contrib/[a-z]* -type f -name '*.p?' -exec cp -p {} scripts ";"</action>
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11 <action type="shell_command">cp -rp contrib/VelvetOptimiser*/VelvetOpt* scripts</action>
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12 <action type="shell_command">ls scripts</action>
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13 <action type="move_file">
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14 <source>velvetg</source>
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15 <destination>$INSTALL_DIR/bin</destination>
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16 </action>
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17 <action type="move_file">
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18 <source>velveth</source>
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19 <destination>$INSTALL_DIR/bin</destination>
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20 </action>
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21 <action type="move_directory_files">
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22 <source_directory>scripts</source_directory>
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23 <destination_directory>$INSTALL_DIR/scripts</destination_directory>
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24 </action>
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25 <action type="set_environment">
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26 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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27 </action>
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28 <action type="set_environment">
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29 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/scripts</environment_variable>
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30 </action>
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31 <action type="set_environment">
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32 <environment_variable name="MAXKMERLENGTH" action="set_to">191</environment_variable>
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33 </action>
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34 <action type="set_environment">
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35 <environment_variable name="CATEGORIES" action="set_to">4</environment_variable>
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36 </action>
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37 </actions>
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38 </install>
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39 <readme>
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40 Velvet is a sequence assembler for very short reads.
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41 http://www.ebi.ac.uk/~zerbino/velvet/
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42 This installs the velvet assembler version 1.2.10 and contributed scripts including VelvetOptimiser.pl
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43 </readme>
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44 </package>
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45 </tool_dependency>
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