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1 <?xml version="1.0"?>
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2 <tool_dependency>
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33
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3 <package name="breakdancer" version="1.2.6">
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4 <install version="1.0">
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49
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5 <actions_group>
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51
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6 <!-- <actions architecture="i386" os="linux">
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7 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/freebayes/freebayes-0.9.6_9608597d-Linux-i686.tgz</action>
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8 <action type="move_directory_files">
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9 <source_directory>.</source_directory>
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10 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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11 </action>
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12 </actions> -->
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13 <actions>
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14 <action type="shell_command">git clone --recursive https://github.com/genome/breakdancer</action>
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15 <!-- <action type="download_by_url">https://github.com/genome/breakdancer/archive/master.zip</action> -->
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16 <action type="shell_command">mkdir build</action>
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17 <action type="change_directory">build</action>
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18 <action type="shell_command">cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local</action>
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19 <action type="shell_command">make</action>
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20 <action type="move_file">
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21 <source>bin/breakdancer-max</source>
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22 <destination>$INSTALL_DIR/bin</destination>
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23 </action>
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24 <action type="move_file">
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25 <source>../perl/bam2cfg.pl</source>
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26 <destination>$INSTALL_DIR/bin</destination>
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27 </action>
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57
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28 <!-- <action type="download_by_url">http://9ypffrj86h.1fichier.com/breakdancer2vcf.py</action> -->
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29 <action type="shell_command">wget https://github.com/ALLBio/allbiotc2/blob/master/breakdancer/breakdancer2vcf.py</action>
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30 <action type="shell_command">ls</action>
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31 <action type="shell_command">pwd</action>
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58
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32 <!-- <action type="change_directory">..</action>
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33 <action type="shell_command">ls</action>
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34 <action type="shell_command">pwd</action>
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56
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35 <action type="change_directory">..</action>
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55
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36 <action type="shell_command">ls</action>
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37 <action type="shell_command">pwd</action> -->
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38 <action type="move_file">
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39 <source>breakdancer2vcf.py</source>
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40 <destination>$INSTALL_DIR/bin</destination>
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41 </action>
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42 <!-- <action type="shell_command">ls</action>
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55
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43 <action type="shell_command">pwd</action>
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57
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44 <action type="change_directory">..</action>
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45 <action type="shell_command">ls</action>
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46 <action type="shell_command">pwd</action>
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47 <action type="change_directory">..</action>
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48 <action type="shell_command">ls</action>
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49 <action type="shell_command">pwd</action> -->
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56
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50 <!-- <action type="move_directory_files">
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54
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51 <source_directory>../../1_2_6</source_directory>
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52 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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56
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53 </action> -->
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51
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54 <action type="set_environment">
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55 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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56 </action>
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48
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57 </actions>
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58 </actions_group>
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59 </install>
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60 <readme>
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61 </readme>
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62 </package>
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63 </tool_dependency> |
