Mercurial > repos > fcaramia > somatic_sniper

annotate tool_dependencies.xml @ 0:e81f5649bd4d draft default tip

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author fcaramia
date Thu, 20 Jun 2013 00:06:01 -0400
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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
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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>$INSTALL_DIR/bin/samtools</destination_directory>
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14 </action>
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15
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16 <action type="download_file">https://github.com/genome/somatic-sniper/archive/master.zip</action>
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17 <action type="download_file">https://github.com/genome/build-common/tarball/master</action>
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18 <action type="shell_command">unzip master.zip</action>
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19 <action type="shell_command">tar -xzvf master</action>
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20 <action type="shell_command">rm -rf somatic-sniper-master/build-common/</action>
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21 <action type="shell_command">mv genome-build-common-077bd57/ somatic-sniper-master/build-common/</action>
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22 <action type="shell_command">cmake -D Samtools_INCLUDE_DIR:PATH=$INSTALL_DIR/bin/samtools somatic-sniper-master/ &amp;&amp; make</action>
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23 <action type="move_directory_files">
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24 <source_directory>bin</source_directory>
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25 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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26 </action>
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27 <action type="set_environment">
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28 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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29 </action>
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30 </actions>
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31 </install>
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32 <readme>
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33 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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34 </readme>
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35 </package>
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36
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38 </tool_dependency>