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view tool_dependencies.xml @ 0:b1ac138f0287 draft

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author hammock
date Mon, 26 Jan 2015 06:24:21 -0500
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children 4db310b7e37c
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<?xml version="1.0"?>
<tool_dependency>
        <package name="clustalomega" version="1.2.0">
            <install version="1.0">
				<actions_group>
					<actions architecture="x86_64" os="linux">
                        <action type="download_by_url">http://www.clustal.org/omega/clustalo-1.2.0-Ubuntu-x86_64</action>
						<action type="shell_command">chmod 755 clustalo-1.2.0-Ubuntu-x86_64</action>
						<action type="move_file">
       	            		<source>clustalo-1.2.0-Ubuntu-x86_64</source>
       	            		<destination>$INSTALL_DIR</destination>
       		         	</action>
						<action type="shell_command">sed -i "s%#clustalOmegaCommand=%clustalOmegaCommand=$INSTALL_DIR/clustalo-1.2.0-Ubuntu-x86_64%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
					</actions>
					<actions architecture="x86_64" os="darwin">
						<action type="download_by_url">http://www.clustal.org/omega/clustal-omega-1.2.0-macosx</action>
						<action type="shell_command">chmod 755 clustalo-1.2.0-Ubuntu-x86_64</action>
						<action type="move_file">
                   			<source>clustalo-1.2.0-Ubuntu-x86_64</source>
                 	  		<destination>$INSTALL_DIR</destination>
                		</action>
						<action type="shell_command">sed -i "s%#clustalOmegaCommand=%clustalOmegaCommand=$INSTALL_DIR/clustalo-1.2.0-Ubuntu-x86_64%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
					</actions>
				</actions_group>
			</install>
		</package>

        <package name="hmmer" version="3.1b1">
            <install version="1.0">
				<actions_group>
                    <actions architecture="x86_64" os="linux">
                        <action type="download_by_url">http://selab.janelia.org/software/hmmer3/3.1b1/hmmer-3.1b1-linux-intel-x86_64.tar.gz</action>
						<action type="move_file">
                    		<source>binaries/hmmbuild</source>
                    		<destination>$INSTALL_DIR</destination>
                		</action>
						<action type="move_file">
                    		<source>binaries/hmmsearch</source>
                    		<destination>$INSTALL_DIR</destination>
                		</action>
						<action type="shell_command">sed -i "s%#hmmbuildCommand=%hmmbuildCommand=$INSTALL_DIR/hmmbuild%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
						<action type="shell_command">sed -i "s%#hmmsearchCommand=%hmmsearchCommand=$INSTALL_DIR/hmmsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
					</actions>
                    <actions architecture="x86_64" os="darwin">
                        <action type="download_by_url">http://selab.janelia.org/software/hmmer3/3.1b1/hmmer-3.1b1-macosx-intel.tar.gz</action>
						<action type="move_file">
                    		<source>binaries/hmmbuild</source>
                    		<destination>$INSTALL_DIR</destination>
                		</action>
						<action type="move_file">
                    		<source>binaries/hmmsearch</source>
                    		<destination>$INSTALL_DIR</destination>
                		</action>
						<action type="shell_command">sed -i "s%#hmmbuildCommand=%hmmbuildCommand=$INSTALL_DIR/hmmbuild%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
						<action type="shell_command">sed -i "s%#hmmsearchCommand=%hmmsearchCommand=$INSTALL_DIR/hmmsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
					</actions>
				</actions_group>
			</install>
		</package>

        <package name="hhsuite" version="2.0.16">
            <install version="1.0">
				<actions_group>
                    <actions architecture="x86_64" os="linux">
                        <action type="download_by_url">ftp://toolkit.genzentrum.lmu.de/pub/HH-suite/releases/hhsuite-2.0.16-linux-x86_64.tar.gz</action>
						<action type="move_file">
                    		<source>bin/hhmake</source>
                    		<destination>$INSTALL_DIR</destination>
                		</action>
						<action type="move_file">
                    		<source>bin/hhsearch</source>
                    		<destination>$INSTALL_DIR</destination>
                		</action>
						<action type="move_file">
                    		<source>lib</source>
                    		<destination>$INSTALL_DIR</destination>
                		</action>
						<action type="shell_command">sed -i "s%#hhmakeCommand=%hhmakeCommand=$INSTALL_DIR/hhmake%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
						<action type="shell_command">sed -i "s%#hhsearchCommand=%hhsearchCommand=$INSTALL_DIR/hhsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
						<action type="shell_command">sed -i "s%#reformatCommand=%reformatCommand=$INSTALL_DIR/lib/hh/scripts/reformat.pl%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
						<action type="set_environment">
							<environment_variable name="HHLIB" action="set_to">$INSTALL_DIR/lib/hh</environment_variable>   
						</action>
					</actions>
                    <actions architecture="x86_64" os="darwin">
                        <action type="download_by_url">ftp://toolkit.genzentrum.lmu.de/pub/HH-suite/releases/hhsuite-2.0.16-macosx.tar.gz</action>
						<action type="move_file">
                    		<source>bin/hhmake</source>
                    		<destination>$INSTALL_DIR</destination>
                		</action>
						<action type="move_file">
                    		<source>bin/hhsearch</source>
                    		<destination>$INSTALL_DIR</destination>
                		</action>
						<action type="move_file">
                    		<source>lib</source>
                    		<destination>$INSTALL_DIR</destination>
                		</action>
						<action type="shell_command">sed -i "s%#hhmakeCommand=%hhmakeCommand=$INSTALL_DIR/hhmake%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
						<action type="shell_command">sed -i "s%#hhsearchCommand=%hhsearchCommand=$INSTALL_DIR/hhsearch%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
						<action type="shell_command">sed -i "s%#reformatCommand=%reformatCommand=$INSTALL_DIR/lib/hh/scripts/reformat.pl%g" $REPOSITORY_INSTALL_DIR/Hammock/settings/settings.prop</action>
						<action type="set_environment">
							<environment_variable name="HHLIB" action="set_to">$INSTALL_DIR/lib/hh</environment_variable>   
						</action>
					</actions>
				</actions_group>
			</install>
		</package>



    <set_environment version="1.0">
		<environment_variable name="HAMMOCK_JAR" action="set_to">$REPOSITORY_INSTALL_DIR/Hammock/dist/Hammock.jar</environment_variable>
		<environment_variable name="MATRIX_PATH" action="set_to">$REPOSITORY_INSTALL_DIR/Hammock/matrices/</environment_variable>  
    </set_environment>
</tool_dependency>