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view tool_dependencies.xml @ 36:1d15cd0bd913 draft

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author davidvanzessen
date Tue, 24 Sep 2013 10:15:19 -0400
parents 31dae1214002
children 215aa111db64
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<?xml version="1.0"?>
<tool_dependency>
	<set_environment version="1.0">            
    </set_environment>
    
	<package name="igBlastn" version="1.0.0"> 
        <install version="1.0">
            <actions>
            	<action type="download_by_url" target_filename="ncbi-igblast-1.0.0-x64-linux.tar.gz">
            		ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.0.0/ncbi-igblast-1.0.0-x64-linux.tar.gz
            	</action>
            	
            	
            	<action type="move_directory_files">
		    		<source_directory>ncbi-igblast-1.0.0</source_directory>
			   		<destination_directory>$INSTALL_DIR/ncbi-igblast-1.0.0</destination_directory>
	       		</action>
                <action type="set_environment">
                	<environment_variable name="IGDATA" action="set_to">$INSTALL_DIR/ncbi-igblast-1.0.0</environment_variable>
                </action>
                
                <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human.ndm.imgt</action>
                <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human.ndm.kabat</action>
                <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human.pdm.imgt</action>
                <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human.pdm.kabat</action>

				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.nhr</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.nin</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.nog</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.nsd</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.nsi</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.nsq</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.phr</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.pin</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.pog</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.psd</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.psi</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.psq</action>
                
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.nhr</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.nin</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.nog</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.nsd</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.nsi</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.nsq</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.phr</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.pin</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.pog</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.psd</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.psi</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.psq</action>
				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V_prot</action>

                <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data</action>
                <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</action>
                
                <action type="move_file">
				    <source>human_V</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_V.nhr</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_V.nin</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_V.nog</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_V.nsd</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_V.nsi</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_V.nsq</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_V.phr</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_V.pin</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_V.pog</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_V.psd</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_V.psi</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_V.psq</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_V_prot</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>


                <action type="move_file">
				    <source>human.ndm.imgt</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human.ndm.kabat</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human.pdm.imgt</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human.pdm.kabat</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>

                <action type="move_file">
				    <source>human_TR_V.nhr</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_TR_V.nin</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_TR_V.nog</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_TR_V.nsd</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_TR_V.nsi</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_TR_V.nsq</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_TR_V.phr</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_TR_V.pin</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_TR_V.pog</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_TR_V.psd</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_TR_V.psi</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>
                <action type="move_file">
				    <source>human_TR_V.psq</source>
				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
                </action>

            </actions>
        </install>
        <readme>
			Downloads igBlast with the human_V internal data file.
        </readme>
    </package>
</tool_dependency>