<commit_before><?xml version="1.0"?>
<tool_dependency>
    <package name="mrbayes" version="3.2.6">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://downloads.sourceforge.net/project/mrbayes/mrbayes/3.2.6/mrbayes-3.2.6.tar.gz</action>
		<action type="make_directory">$INSTALL_DIR/documentation</action>
		<action type="make_directory">$INSTALL_DIR/examples</action>
    <action type="make_directory">$INSTALL_DIR/src</action>
		<action type="move_directory_files">
		  <source_directory>documentation</source_directory>
		  <destination_directory>$INSTALL_DIR/documentation</destination_directory>
		</action>
                <action type="move_directory_files">
		  <source_directory>examples</source_directory>
		  <destination_directory>$INSTALL_DIR/examples</destination_directory>
		</action>
                <action type="move_directory_files">
      <source_directory>src</source_directory>
      <destination_directory>$INSTALL_DIR/src</destination_directory>
    </action>
                <action type="set_environment">
                <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/src</environment_variable>
                </action>

                <action type="shell_command">(cd $INSTALL_DIR/src; autoconf)</action>
                <action type="shell_command">(cd $INSTALL_DIR/src; ./configure --prefix=$INSTALL_DIR --with-beagle=no)</action>
                <action type="shell_command">make -C $INSTALL_DIR/src</action>
                <action type="shell_command">make install -C $INSTALL_DIR/src</action>
            </actions>
        </install>
        <readme>
This installs MrBayes 3.2.6.

See manual here http://mrbayes.sourceforge.net/mb3.2_manual.pdf
See also here http://mrbayes.sourceforge.net/manual.php
        </readme><commit_msg>Changed file organization, removed examples and docs folders (inaccessible anyway), change make to use built in action<commit_after><?xml version="1.0"?>
<tool_dependency>
    <package name="mrbayes" version="3.2.6">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://downloads.sourceforge.net/project/mrbayes/mrbayes/3.2.6/mrbayes-3.2.6.tar.gz</action>
                <action type="change_directory">src</action>
                <action type="set_environment">
                  <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/src</environment_variable>
                </action>

                <action type="shell_command">autoconf</action>
                <action type="shell_command">./configure --prefix=$INSTALL_DIR --with-beagle=no</action>
                <action type="make_install"/>
            </actions>
        </install>
        <readme>
This installs MrBayes 3.2.6.

See manual here http://mrbayes.sourceforge.net/mb3.2_manual.pdf
See also here http://mrbayes.sourceforge.net/manual.php
        </readme>
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