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annotate tool_dependencies.xml @ 5:949ac66308a7

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Update FreeBayes to 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf.
author Daniel Blankenberg <dan@bx.psu.edu>
date Fri, 24 Aug 2012 16:00:21 -0400
parents e54bb199a47b
children d3bf1e86b243
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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949ac66308a7 Update FreeBayes to 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf.
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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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949ac66308a7 Update FreeBayes to 0.9.6_9608597d12e127c847ae03aa03440ab63992fedf.
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7 <action type="shell_command">git reset --hard 9608597d12e127c847ae03aa03440ab63992fedf</action>
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8 <action type="shell_command">make</action>
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9 <action type="move_directory_files">
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10 <source_directory>bin</source_directory>
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11 <destination_directory>$INSTALL_DIR/bin</destination_directory>
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12 </action>
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13 <action type="set_environment">
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14 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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15 </action>
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16 </actions>
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17 </install>
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18 <readme>
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19 FreeBayes requires g++ and the standard C and C++ development libraries.
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20 Additionally, cmake is required for building the BamTools API.
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21 </readme>
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22 </package>
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23 <package name="samtools" version="0.1.18">
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24 <install version="1.0">
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25 <actions>
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26 <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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27 <action type="shell_command">sed -i .bak -e 's/-lcurses/-lncurses/g' Makefile</action>
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28 <action type="shell_command">make</action>
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29 <action type="move_file">
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30 <source>samtools</source>
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31 <destination>$INSTALL_DIR/bin</destination>
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32 </action>
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33 <action type="move_file">
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34 <source>misc/maq2sam-long</source>
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35 <destination>$INSTALL_DIR/bin</destination>
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36 </action>
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37 <action type="set_environment">
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38 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
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39 </action>
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40 </actions>
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41 </install>
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42 <readme>
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43 Compiling SAMtools requires the ncurses and zlib development libraries.
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44 </readme>
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45 </package>
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46 </tool_dependency>