config_run.xml 2.98 KB
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<?xml version="1.0" encoding="UTF-8"?>
<commandSetRoot xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation='commandSet.xsd'>
    <commandSet type="serial">
        <state>incomplete</state>
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        <name>config_run compute</name>
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        <command>
            <type>RunUnixCommand</type>
            <name>create output directory</name>
            <state>incomplete</state>
            <executable>mkdir</executable>
            <arg>-p -m 777 $;OUTPUT_DIRECTORY$;</arg>
        </command>
        <command>
            <type>RunUnixCommand</type>
            <name>create temp directory</name>
            <state>incomplete</state>
            <executable>mkdir</executable>
            <arg>-p -m 777 $;TMP_DIR$;</arg>
        </command>
        <!--Processing-->
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        <command>
            <type>RunUnixCommand</type>
            <name>create raw file list</name>
            <state>incomplete</state>
            <executable>echo</executable>
            <arg>$;RAW_INPUT$; > $;RAW_LIST$;</arg>
        </command>
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        <command>
            <type>RunUnixCommand</type>
            <name>config_run</name>
            <state>incomplete</state>
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            <executable>python $;BIN_DIR$;/config_run.py</executable>
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            <arg></arg>
            <param>
                <key>--type</key>
                <value>"$;RUN_TYPE$;"</value>
            </param>
            <param>
                <key>--species</key>
                <value>"$;SPECIES$;"</value>
            </param>
            <param>
                <key>--project-name</key>
                <value>"$;PROJECT_NAME$;"</value>
            </param>
            <param>
                <key>--sequencer</key>
                <value>"$;SEQUENCER$;"</value>
            </param>
            <param>
                <key>--data_nature</key>
                <value>"$;DATA_NATURE$;"</value>
            </param>
            <param>
                <key>--project-description</key>
                <value>"$;PROJECT_DESCRIPTION$;"</value>
            </param>
            <param>
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                <key>--admin-login</key>
                <value>"$;ADMIN_LOGIN$;"</value>
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            </param>
            <param>
                <key>--date</key>
                <value>"$;DATE$;"</value>
            </param>
            <param>
                <key>--name</key>
                <value>"$;RUN_NAME$;"</value>
            </param>
            <param>
                <key>--description</key>
                <value>"$;RUN_DESCRIPTION$;"</value>
            </param>
            <param>
                <key>--cfg</key>
                <value>"$;CONFIG_FILE$;"</value>
            </param>
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            <param>  
                <key>stdout</key>
                <value>$;OUTPUT_DIRECTORY$;/$;COMPONENT_NAME$;.stdout</value>
            </param>
            <param>  
                <key>stderr</key>
                <value>$;OUTPUT_DIRECTORY$;/$;COMPONENT_NAME$;.stderr</value>
            </param>
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        </command>              
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    </commandSet>
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</commandSetRoot>