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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="0.1.6">
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4 <install version="1.0">
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5 <actions>
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6 <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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7 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
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8 <action type="shell_command">sed -i.bak 's/-lz -L. -lbam/-lbam -lz -L./' Makefile</action>
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9 <action type="shell_command">make</action>
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10 <action type="move_file">
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11 <source>samtools</source>
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12 <destination>$INSTALL_DIR/bin</destination>
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13 </action>
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14 <action type="set_environment">
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15 <environment_variable name="SAMTOOLS_ROOT" action="set_to">$INSTALL_DIR/bin</environment_variable>
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16 </action>
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17 </actions>
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18 </install>
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19 <readme>
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20 Somatic-sniper only builds with samtools version 0.1.6
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21 </readme>
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22 </package>
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23
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24 <package name="somatic-sniper" version="unstable">
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25 <install version="1.0">
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26 <actions>
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9
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27 <action type="download_file">https://github.com/genome/somatic-sniper/archive/master.zip</action>
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28 <action type="download_file">https://github.com/genome/build-common/tarball/master</action>
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29 <action type="shell_command">unzip master.zip</action>
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11
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30 <action type="shell_command">tar -xzvf master</action>
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9
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31 <action type="shell_command">rm -rf somatic-sniper-master/build-common</action>
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10
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32 <action type="shell_command">echo $SAMTOOLS_PATH</action>
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9
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33 <action type="move_directory_files">
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34 <source_directory>genome-build-common-077bd57</source_directory>
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35 <destination_directory>somatic-sniper-master/build-common</destination_directory>
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36 </action>
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37
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38
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39 <action type="shell_command">cmake somatic-sniper-master/</action>
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40 <action type="shell_command">make somatic-sniper-master/</action>
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4
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41 <action type="move_file">
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9
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42 <source>somatic-sniper-master/bin/bam-somaticsniper</source>
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4
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43 <destination>$INSTALL_DIR/bin</destination>
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44 </action>
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45 <action type="set_environment">
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46 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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47 </action>
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48 </actions>
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49 </install>
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50 <readme>
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51 Somatic-sniper compiled version is unstable, for stable version use debian package system apt-get
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52 </readme>
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53 </package>
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54
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55
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56 </tool_dependency>
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