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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="boost" version="1.53.0">
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4 <repository changeset_revision="dbdde1a2d0c5" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="mugsy" version="1.2.3.1">
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7 <install version="1.0">
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8 <actions>
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9 <!-- checkout from svn source repository into a directory with the same name of the package, which will be automatically used as working directory -->
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10 <action type="shell_command">svn checkout http://svn.code.sf.net/p/mugsy/code/ mugsy</action>
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11 <!-- fix for Boost >= 1.42.0 -->
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12 <action type="shell_command">sed -i 's/boost\/property_map\.hpp/boost\/property_map\/property_map.hpp/' trunk/chaining/synchain-mugsy.cpp</action>
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13 <!-- fix for Boost >= 1.47.0 -->
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14 <action type="shell_command">sed -i 's/boost\/graph\/kolmogorov_max_flow\.hpp/boost\/graph\/boykov_kolmogorov_max_flow.hpp/' trunk/chaining/synchain-mugsy.cpp trunk/mugsy-seqan/projects/library/apps/mugsy/mugsy.cpp</action>
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15 <!-- fix chaining Makefile -->
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16 <action type="shell_command">sed -i -e 's/-static//g' -e 's/-lbgl-viz -lboost_graph-gcc41-mt//g' trunk/chaining/Makefile</action>
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17 <!-- fix missing include in show-diff.cc -->
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18 <action type="shell_command">sed -i '13 a \#include <algorithm>' trunk/MUMmer3.20/src/tigr/show-diff.cc</action>
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19 <!-- skip make of streeproto.h since it would fail because of missing skproto.x -->
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20 <action type="shell_command">touch trunk/MUMmer3.20/src/kurtz/streesrc/streeproto.h</action>
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21 <!-- fix Makefile -->
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22 <action type="shell_command">sed -i -e 's/install synchain-mugsy/install chaining\/synchain-mugsy/' -e 's/install mugsyWGA \(.*\)/install mugsy-seqan\/projects\/library\/apps\/mugsy\/gcc\/mugsy \1\/mugsyWGA/' trunk/Makefile</action>
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23 <!-- fix MUMmer3.20 Makefile -->
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24 <action type="shell_command">sed -i '/DOC_DIR/d' trunk/MUMmer3.20/Makefile</action>
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25 <!-- populate the environment variables from the dependent repos -->
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26 <action type="set_environment_for_install">
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27 <repository name="package_boost_1_53" owner="bgruening" toolshed="http://toolshed.g2.bx.psu.edu">
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28 <package name="boost" version="1.53.0" />
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29 </repository>
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30 </action>
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31 <!-- use $BOOST_ROOT_DIR in chaining Makefile -->
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32 <action type="shell_command">sed -i -e 's/-I \/usr\/local\/projects\/angiuoli\/boost\/include\/boost-1_38/-I $(BOOST_ROOT_DIR)\/include/g' -e 's/-L \/usr\/local\/projects\/angiuoli\/boost\/lib\//-L $(BOOST_ROOT_DIR)\/lib/g' trunk/chaining/Makefile trunk/mugsy-seqan/platforms/gcc/platform.mak</action>
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33 <!-- equivalent of make clean -->
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34 <action type="shell_command">rm -f trunk/chaining/synchain-mugsy trunk/mugsyWGA trunk/synchain-mugsy && make -C trunk/MUMmer3.20 clean</action>
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35 <action type="shell_command">make -C trunk all</action>
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36 <action type="shell_command">make -C trunk install</action>
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37 <action type="move_directory_files">
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38 <source_directory>trunk/mugsy_x86-64-v1r2.3.1</source_directory>
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39 <destination_directory>$INSTALL_DIR</destination_directory>
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40 </action>
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41 <action type="set_environment">
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42 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
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43 </action>
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44 <action type="set_environment">
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45 <environment_variable action="set_to" name="MUGSY_INSTALL">$INSTALL_DIR</environment_variable>
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46 </action>
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47 </actions>
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48 </install>
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49 <readme>
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50 </readme>
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51 </package>
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52 </tool_dependency>
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