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Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
author devteam
date Mon, 16 Dec 2013 16:30:37 -0500
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7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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1 <?xml version="1.0"?>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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2 <tool_dependency>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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3 <package name="freebayes" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf">
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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4 <install version="1.0">
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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5 <actions_group>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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6 <actions architecture="i386" os="linux">
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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7 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/freebayes/freebayes-0.9.6_9608597d-Linux-i686.tgz</action>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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8 <action type="move_directory_files">
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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9 <source_directory>.</source_directory>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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10 <destination_directory>$INSTALL_DIR/bin</destination_directory>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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11 </action>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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12 </actions>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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13 <actions architecture="x86_64" os="linux">
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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14 <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/freebayes/freebayes-0.9.6_9608597d-Linux-x86_64.tgz</action>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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15 <action type="move_directory_files">
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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16 <source_directory>.</source_directory>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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17 <destination_directory>$INSTALL_DIR/bin</destination_directory>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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18 </action>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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19 </actions>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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20 <actions architecture="x86_64" os="darwin">
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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21 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/freebayes/freebayes-0.9.6_9608597d-Darwin-x86_64.tgz</action>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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22 <action type="move_directory_files">
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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23 <source_directory>.</source_directory>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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24 <destination_directory>$INSTALL_DIR/bin</destination_directory>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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25 </action>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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26 </actions>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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27 <actions>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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28 <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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29 <action type="shell_command">git checkout 9608597d12e127c847ae03aa03440ab63992fedf</action>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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30 <action type="shell_command">git submodule update --recursive</action>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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31 <action type="shell_command">make || ( make clean &amp;&amp; sed -i.bak -e &apos;s:LIBS = -lz -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix:LIBS = -lm -L./ -L../vcflib/tabixpp/ -L$(BAMTOOLS_ROOT)/lib -ltabix -lz:g&apos; src/Makefile &amp;&amp; make )</action>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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32 <action type="move_directory_files">
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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33 <source_directory>bin</source_directory>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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34 <destination_directory>$INSTALL_DIR/bin</destination_directory>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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35 </action>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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36 </actions>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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37 <action type="set_environment">
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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38 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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39 </action>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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40 </actions_group>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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41 </install>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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42 <readme>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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43 FreeBayes requires g++ and the standard C and C++ development libraries.
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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44 Additionally, cmake is required for building the BamTools API.
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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45 </readme>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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46 </package>
7615ee9e216d Uploaded tool dependency definition that specifies precompiled binaries for FreeBayes.
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47 </tool_dependency>