:: Simple Cytoscape batch script for windows/dos :: (c) Trey Ideker June 21, 2002; Owen Ozier March 06, 2003 :: :: Runs Cytoscape from its jar file with GO data loaded @echo off :: Create the Cytoscape.vmoptions file, if it doesn't exist. IF EXIST "Cytoscape.vmoptions" GOTO vmoptionsFileExists CALL gen_vmoptions.bat :vmoptionsFileExists IF EXIST "Cytoscape.vmoptions" GOTO itIsThere ; Run with defaults: echo "*** Missing Cytoscape.vmoptions, falling back to using defaults!" java -Dswing.aatext=true -Dawt.useSystemAAFontSettings=lcd -Xss10M -Xmx768M -jar cytoscape.jar -p plugins %* GOTO end :: We end up here if we have a Cytoscape.vmoptions file: :itIsThere :: Read vmoptions, one per line. setLocal EnableDelayedExpansion for /f "tokens=* delims= " %%a in (Cytoscape.vmoptions) do ( set /a N+=1 set opt!N!=%%a ) java !opt1! !opt2! !opt3! !opt4! !opt5! !opt6! !opt7! !opt8! !opt9! -jar cytoscape.jar -p plugins %* :end