<?xml version="1.0"?>
<tool_dependency>
  <package name="boost" version="1.53.0">
    <repository changeset_revision="dbdde1a2d0c5" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
  </package>
  <package name="mugsy" version="1.2.3.1">
    <install version="1.0">
      <actions>
        <!-- checkout from svn source repository into a directory with the same name of the package, which will be automatically used as working directory -->
        <action type="shell_command">svn checkout http://svn.code.sf.net/p/mugsy/code/ mugsy</action>
        <!-- fix for Boost >= 1.42.0 -->
        <action type="shell_command">sed -i 's/boost\/property_map\.hpp/boost\/property_map\/property_map.hpp/' trunk/chaining/synchain-mugsy.cpp</action>
        <!-- fix for Boost >= 1.47.0 -->
        <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>
        <!-- fix chaining Makefile -->
        <action type="shell_command">sed -i -e 's/-static//g' -e 's/-lbgl-viz -lboost_graph-gcc41-mt//g' trunk/chaining/Makefile</action>
        <!-- fix missing include in show-diff.cc -->
        <action type="shell_command">sed -i '13 a \#include &lt;algorithm&gt;' trunk/MUMmer3.20/src/tigr/show-diff.cc</action>
        <!-- skip make of streeproto.h since it would fail because of missing skproto.x -->
        <action type="shell_command">touch trunk/MUMmer3.20/src/kurtz/streesrc/streeproto.h</action>
        <!-- fix Makefile -->
        <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>
        <!-- fix MUMmer3.20 Makefile -->
        <action type="shell_command">sed -i '/DOC_DIR/d' trunk/MUMmer3.20/Makefile</action>
        <!-- populate the environment variables from the dependent repos -->
        <action type="set_environment_for_install">
          <repository name="package_boost_1_53" owner="bgruening" toolshed="http://toolshed.g2.bx.psu.edu">
            <package name="boost" version="1.53.0" />
          </repository>
        </action>
        <!-- use $BOOST_ROOT_DIR in chaining Makefile -->
        <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 $(BOOST_ROOT_DIR)\/lib/g' trunk/chaining/Makefile trunk/mugsy-seqan/platforms/gcc/platform.mak</action>
        <!-- equivalent of make clean -->
        <action type="shell_command">rm -f trunk/chaining/synchain-mugsy trunk/mugsyWGA trunk/synchain-mugsy &amp;&amp; make -C trunk/MUMmer3.20 clean</action>
        <action type="shell_command">make -C trunk all</action>
        <action type="shell_command">make -C trunk install</action>
        <action type="move_directory_files">
          <source_directory>trunk/mugsy_x86-64-v1r2.3.1</source_directory>
          <destination_directory>$INSTALL_DIR</destination_directory>
        </action>
        <action type="set_environment">
          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
        </action>
        <action type="set_environment">
          <environment_variable action="set_to" name="MUGSY_INSTALL">$INSTALL_DIR</environment_variable>
        </action>
      </actions>
    </install>
    <readme>
    </readme>
  </package>
</tool_dependency>