Applied Biosystems 7900HT - Operating the SDS Software from a Command Line

DRAFT
September 1, 2004 11:39 am, App_SWReference.fm
Appendix A Software Reference
A-18 Applied Biosystems 7900HT Fast Real-Time PCR System and SDS Enterprise Database User Guide
Operating the SDS Software from a Command Line
Overview
The SDS software allows you to use batch files to analyze and export results from the
command line. Use of the command line interface is intended for advanced users
(such as systems administrators, bioinformaticians, and laboratory network
administrators) who choose to drive the application using a scripting language.
Note: If you are unfamiliar with Microsoft DOS, Applied Biosystems recommends
running the application from the user interface.
Running the
Software from a
Command Line
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.
4. Save and close the batch file.
5. Invoke the file at the command line by entering:
SDS_RESULTS.bat sdsfile.sds sdsresultsfile.txt
where:
• SDS_RESULTS.bat – Is the name of the batch file you created.
•
sdsfile.sds – Is the SDS plate document file that you have targeted for
analysis.
•
sdsresultsfile.txt – Is the name of the exported results file.
Example Code A-17 SDS2.bat Batch File
The 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.jar
com.apldbio.sds.shell.SDSMain
In the last line, replace
com.apldbio.sds.shell.SDSMain
with 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 %*