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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="somatic-sniper" version="unstable">
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4 <install version="1.0">
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5 <actions>
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6 <!-- Samtools -->
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7 <action type="download_by_url">http://downloads.sourceforge.net/project/samtools/samtools/0.1.6/samtools-0.1.6.tar.bz2</action>
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8 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
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9 <action type="shell_command">sed -i.bak 's/-lz -L. -lbam/-lbam -lz -L./' Makefile</action>
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10 <action type="shell_command">make</action>
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11 <action type="move_directory_files">
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12 <source_directory>.</source_directory>
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13 <destination_directory>$INSTALL_DIR/bin/samtools</destination_directory>
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14 </action>
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15 <!-- CMake -->
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16 <action type="download_by_url">http://www.cmake.org/files/v2.8/cmake-2.8.11.1.tar.gz</action>
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17 <action type="shell_command">./bootstrap</action>
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18 <action type="shell_command">make</action>
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19 <action type="shell_command">make install</action>
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20 <action type="move_directory_files">
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21 <source_directory>.</source_directory>
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22 <destination_directory>$INSTALL_DIR/cmake</destination_directory>
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23 </action>
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24 <!-- Somatic Sniper -->
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25 <action type="download_file">https://github.com/genome/somatic-sniper/archive/master.zip</action>
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26 <action type="download_file">https://github.com/genome/build-common/tarball/master</action>
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27 <action type="shell_command">unzip master.zip</action>
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28 <action type="shell_command">tar -xzvf master</action>
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29 <action type="shell_command">rm -rf somatic-sniper-master/build-common/</action>
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30 <action type="shell_command">mv genome-build-common-077bd57/ somatic-sniper-master/build-common/</action>
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31 <action type="shell_command">cmake -D Samtools_INCLUDE_DIR:PATH=$INSTALL_DIR/bin/samtools somatic-sniper-master/ && make</action>
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32 <action type="move_directory_files">
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33 <source_directory>bin</source_directory>
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34 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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35 </action>
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36 <action type="set_environment">
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37 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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38 </action>
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39 </actions>
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40 </install>
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41 <readme>
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42 Somatic-sniper compiled version is unstable, for stable version use debian package system apt-get, this install requires cmake and zlib (for samtools)
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43 </readme>
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44 </package>
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45
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46
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47 </tool_dependency>
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