<?xml version="1.0"?>
<tool_dependency>
<!-- see also http://wiki.galaxyproject.org/ToolShedToolFeatures for syntax help -->
    <package name="xtandem" version="12.10011">
        <install version="1.0">
            <actions>
                <action type="download_by_url">ftp://ftp.thegpm.org/projects/tandem/source/2012-10-01/tandem-linux-12-10-01-1.zip</action>
                <!--<action type="shell_command">make clean</action>
                <action type="shell_command">make</action>-->
                <action type="move_directory_files">
					<source_directory>../tandem-linux-12-10-01-1</source_directory>
					<destination_directory>$INSTALL_DIR/tandem-linux-12-10-01-1</destination_directory>
				</action>
				<action type="shell_command">chmod 755 $INSTALL_DIR/tandem-linux-12-10-01-1/bin/tandem.exe</action>
				<!--<action type="chmod"><file mode="755">$INSTALL_DIR/tandem-linux-12-10-01-1/bin/tandem.exe</file><action>-->
                <action type="set_environment">
                    <environment_variable name="XTANDEM_12_10_01_PATH" action="set_to">$INSTALL_DIR/tandem-linux-12-10-01-1</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
Ensures XTandem is installed. 
        </readme>
    </package>
    <package name="proteowizard" version="3.05622">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://toolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_masscomb/raw-file/tip/pwiz-bin-linux-x86_64-gcc48-release-3_0_5622.tar.bz2</action>
                <action type="move_directory_files">
					<source_directory>.</source_directory>
					<destination_directory>$INSTALL_DIR/pwiz_3_0_5622</destination_directory>
				</action>
				<action type="set_environment">
                    <environment_variable name="PWIZ_3_0_5622_PATH" action="set_to">$INSTALL_DIR/pwiz_3_0_5622</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
Ensures ProteoWizard binaries are installed. 
        </readme>
    </package>
	<set_environment version="1.0">
        <environment_variable name="PWIZ_3_0_5622_PATH" action="set_to">$INSTALL_DIR/pwiz_3_0_5622</environment_variable>   
    </set_environment>
</tool_dependency>