Applied Biosystems 7900HT Fast Real-Time PCR System and SDS ...

Appendix ASoftware ReferenceOperating the SDS Software from a Command LineOverviewRunning theSoftware from aCommand LineExample Code A-17The SDS software allows you to use batch files to analyze and export results from thecommand line. Use of the command line interface is intended for advanced users(such as systems administrators, bioinformaticians, and laboratory networkadministrators) who choose to drive the application using a scripting language.Note: If you are unfamiliar with Microsoft DOS, Applied Biosystems recommendsrunning the application from the user interface.1. In the desktop, double-click My Computer > AppliedBiosystems > SDS2.2.1.2. Create a copy of the SDS 2,bat file and rename it (such as SDS_RESULTS.bat).3. Using the Notepad application, edit the contents of the batch file as follows.SDS2.bat Batch FileThe text of the batch file appears as follows:set classpath=./service/config;./service/Lib/audit.jar;./service/Lib/rtc.jar;./service/Lib/ab-reqres.jar;./service/Lib/translation.jar;./service/Lib/apv.jar;./service/lib/coreutil.jar;./service/JMS/lib/fmprtl.zip;./service/Lib/coregui.jar;./service/lib/EmlException.jar;./service/lib/emlhandler.jar;./service/lib/esig.jar;./service/lib/esig/exception.jar;./service/lib/Coreutil.jar;set path=./lib/algorithm/bin/win32;./lib;%path%jre\bin\java -Dab.home=C:\AppliedBiosystems\SDS2.2\service -Dcom.apldbio.sds.global.approot=.-Dcom.apldbio.sds.global.config= .\config\config.properties -Xms110m -Xmx300m-Dsource=batchfile -Ddefport=8080 -classpath %classpath%;lib\SDS2.jar;lib\common.jar;lib\sdsdb.jar;lib\ojdbc14.jar;lib\accesscontrol.jar;lib\sdsdb.jar;lib\activation.jar;lib\mail.jar;lib\accesscontrol.jar;lib\Coreutil.jar;lib\EmlException.jarcom.apldbio.sds.shell.SDSMainIn the last line, replacecom.apldbio.sds.shell.SDSMainwith one of the following, to generate:• Multicomponent data for an SDS plate document file, enter:com.apldbio.sds.MulticompAnalyzerMain %*• Analyzed data for an SDS plate document file, enter:com.apldbio.sds.SDSResultsAnalyzerMain %*• Multicomponent and analyzed data for a plate document file, enter:com.apldbio.sds.MulticompAndResultsAnalyzerMain %*4. Save and close the batch file.5. Invoke the file at the command line by entering:SDS_RESULTS.bat sdsfile.sds sdsresultsfile.txtwhere:• SDS_RESULTS.bat – Is the name of the batch file you created.• sdsfile.sds – Is the SDS plate document file that you have targeted foranalysis.• sdsresultsfile.txt – Is the name of the exported results file.A-18 Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User GuideDRAFTSeptember 1, 2004 11:39 am, App_SWReference.fm