Mercurial > repos > devteam > freebayes

annotate tool_dependencies.xml @ 0:e21073b0dc1f draft

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author devteam
date Wed, 11 Dec 2013 15:41:19 -0500
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="freebayes" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf">
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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 --recursive git://github.com/ekg/freebayes.git</action>
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7 <action type="shell_command">git checkout 9608597d12e127c847ae03aa03440ab63992fedf</action>
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8 <action type="shell_command">git submodule update --recursive</action>
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9 <action type="shell_command">make || ( make clean &amp;&amp; sed -i.bak -e &apos;s:LIBS = -lz -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix:LIBS = -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix -lz:g&apos; src/Makefile &amp;&amp; make )</action>
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10 <action type="move_directory_files">
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11 <source_directory>bin</source_directory>
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12 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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13 </action>
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14 <action type="set_environment">
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15 <environment_variable name="PATH" action="prepend_to">$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 FreeBayes requires g++ and the standard C and C++ development libraries.
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21 Additionally, cmake is required for building the BamTools API.
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22 </readme>
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23 </package>
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24 <package name="samtools" version="0.1.18">
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25 <install version="1.0">
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26 <actions>
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27 <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
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28 <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
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29 <action type="shell_command">make</action>
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30 <action type="move_file">
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31 <source>samtools</source>
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32 <destination>$INSTALL_DIR/bin</destination>
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33 </action>
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34 <action type="move_file">
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35 <source>misc/maq2sam-long</source>
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36 <destination>$INSTALL_DIR/bin</destination>
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37 </action>
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38 <action type="set_environment">
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39 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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40 </action>
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41 </actions>
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42 </install>
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43 <readme>
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44 Compiling SAMtools requires the ncurses and zlib development libraries.
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45 </readme>
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46 </package>
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47 </tool_dependency>