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Improved scripts to be independent of jar file addition.

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This commit is contained in:
cjmyers 2011-05-14 01:31:21 +00:00
parent 7bb33c3c15
commit 40c97ab130
16 changed files with 126 additions and 37 deletions
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6
bin/ATACSGUI.bat
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@ -1 +1,5 @@
java -Xmx512M -classpath "%ATACSGUI%\gui\dist\classes";"%ATACSGUI%\gui\lib\jcommon-1.0.16.jar";"%ATACSGUI%\gui\lib\jfreechart-1.0.13.jar";"%ATACSGUI%\gui\lib\iText-2.1.5.jar";"%ATACSGUI%\gui\lib\batik-anim.jar";"%ATACSGUI%\gui\lib\batik-awt-util.jar";"%ATACSGUI%\gui\lib\batik-bridge.jar";"%ATACSGUI%\gui\lib\batik-codec.jar";"%ATACSGUI%\gui\lib\batik-css.jar";"%ATACSGUI%\gui\lib\batik-dom.jar";"%ATACSGUI%\gui\lib\batik-ext.jar";"%ATACSGUI%\gui\lib\batik-extension.jar";"%ATACSGUI%\gui\lib\batik-gui-util.jar";"%ATACSGUI%\gui\lib\batik-gvt.jar";"%ATACSGUI%\gui\lib\batik-parser.jar";"%ATACSGUI%\gui\lib\batik-script.jar";"%ATACSGUI%\gui\lib\batik-svg-dom.jar";"%ATACSGUI%\gui\lib\batik-svggen.jar";"%ATACSGUI%\gui\lib\batik-swing.jar";"%ATACSGUI%\gui\lib\batik-transcoder.jar";"%ATACSGUI%\gui\lib\batik-util.jar";"%ATACSGUI%\gui\lib\batik-xml.jar";"%ATACSGUI%\gui\lib\js.jar";"%ATACSGUI%\gui\lib\pdf-transcoder.jar";"%ATACSGUI%\gui\lib\xalan-2.6.0.jar";"%ATACSGUI%\gui\lib\xerces_2_5_0.jar";"%ATACSGUI%\gui\lib\xml-apis.jar";"%ATACSGUI%\gui\lib\xml-apis-ext.jar";"%ATACSGUI%\gui\lib\epsgraphics.jar";"%ATACSGUI%\gui\lib\sbmlj.jar";"%ATACSGUI%\gui\lib\org-jdesktop-layout.jar";"%ATACSGUI%\gui\lib\swing-layout-1.0.3.jar";"%ATACSGUI%\gui\lib\activation.jar";"%ATACSGUI%\gui\lib\mail.jar";"%ATACSGUI%\gui\lib\biomodelswslib-standalone-1.11.jar";"%ATACSGUI%\gui\lib\grappa1_2.jar";"%ATACSGUI%\gui\lib\jgraphx.jar";"%ATACSGUI%\gui\lib\gson-1.6.jar" main.Gui -atacs
setlocal ENABLEDELAYEDEXPANSION
set CLASSPATH="%ATACSGUI%\gui\dist\classes"
for /f %%a IN ('dir /b "%ATACSGUI%\gui\lib\*.jar"') do call set CLASSPATH=!CLASSPATH!;"%ATACSGUI%\gui\lib\%%a"
java -Xmx512M -classpath %CLASSPATH% main.Gui -atacs

14
bin/ATACSGUI.linux
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@ -1,5 +1,11 @@
#!/bin/sh
#
# run-time wrapper for ATACSGUI gui
export LD_LIBRARY_PATH=$ATACSGUI/lib:$LD_LIBRARY_PATH
exec java -Xmx512M -classpath $ATACSGUI/gui/dist/classes:$ATACSGUI/gui/lib/jcommon-1.0.16.jar:$ATACSGUI/gui/lib/jfreechart-1.0.13.jar:$ATACSGUI/gui/lib/iText-2.1.5.jar:$ATACSGUI/gui/lib/batik-anim.jar:$ATACSGUI/gui/lib/batik-awt-util.jar:$ATACSGUI/gui/lib/batik-bridge.jar:$ATACSGUI/gui/lib/batik-codec.jar:$ATACSGUI/gui/lib/batik-css.jar:$ATACSGUI/gui/lib/batik-dom.jar:$ATACSGUI/gui/lib/batik-ext.jar:$ATACSGUI/gui/lib/batik-extension.jar:$ATACSGUI/gui/lib/batik-gui-util.jar:$ATACSGUI/gui/lib/batik-gvt.jar:$ATACSGUI/gui/lib/batik-parser.jar:$ATACSGUI/gui/lib/batik-script.jar:$ATACSGUI/gui/lib/batik-svg-dom.jar:$ATACSGUI/gui/lib/batik-svggen.jar:$ATACSGUI/gui/lib/batik-swing.jar:$ATACSGUI/gui/lib/batik-transcoder.jar:$ATACSGUI/gui/lib/batik-util.jar:$ATACSGUI/gui/lib/batik-xml.jar:$ATACSGUI/gui/lib/js.jar:$ATACSGUI/gui/lib/pdf-transcoder.jar:$ATACSGUI/gui/lib/xalan-2.6.0.jar:$ATACSGUI/gui/lib/xerces_2_5_0.jar:$ATACSGUI/gui/lib/xml-apis.jar:$ATACSGUI/gui/lib/xml-apis-ext.jar:$ATACSGUI/gui/lib/epsgraphics.jar:$ATACSGUI/gui/lib/libsbmlj.jar:$ATACSGUI/gui/lib/org-jdesktop-layout.jar:$ATACSGUI/gui/lib/swing-layout-1.0.3.jar:$ATACSGUI/gui/lib/activation.jar:$ATACSGUI/gui/lib/mail.jar:$ATACSGUI/gui/lib/biomodelswslib-standalone-1.11.jar:$ATACSGUI/gui/lib/grappa1_2.jar:$ATACSGUI/gui/lib/jgraphx.jar:$ATACSGUI/gui/lib/gson-1.6.jar main.Gui -atacs
export DYLD_LIBRARY_PATH=$BIOSIM/lib:$DYLD_LIBRARY_PATH
CLASSPATH=$BIOSIM/gui/dist/classes
for jarFile in $BIOSIM/gui/lib/*.jar
do
CLASSPATH=$CLASSPATH:$jarFile
done
exec java -Xmx512M -classpath $CLASSPATH main.Gui -atacs

14
bin/ATACSGUI.linux64
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@ -1,5 +1,11 @@
#!/bin/sh
#
# run-time wrapper for ATACSGUI gui
export LD_LIBRARY_PATH=$ATACSGUI/lib64:$LD_LIBRARY_PATH
exec java -Xmx512M -classpath $ATACSGUI/gui/dist/classes:$ATACSGUI/gui/lib/jcommon-1.0.16.jar:$ATACSGUI/gui/lib/jfreechart-1.0.13.jar:$ATACSGUI/gui/lib/iText-2.1.5.jar:$ATACSGUI/gui/lib/batik-anim.jar:$ATACSGUI/gui/lib/batik-awt-util.jar:$ATACSGUI/gui/lib/batik-bridge.jar:$ATACSGUI/gui/lib/batik-codec.jar:$ATACSGUI/gui/lib/batik-css.jar:$ATACSGUI/gui/lib/batik-dom.jar:$ATACSGUI/gui/lib/batik-ext.jar:$ATACSGUI/gui/lib/batik-extension.jar:$ATACSGUI/gui/lib/batik-gui-util.jar:$ATACSGUI/gui/lib/batik-gvt.jar:$ATACSGUI/gui/lib/batik-parser.jar:$ATACSGUI/gui/lib/batik-script.jar:$ATACSGUI/gui/lib/batik-svg-dom.jar:$ATACSGUI/gui/lib/batik-svggen.jar:$ATACSGUI/gui/lib/batik-swing.jar:$ATACSGUI/gui/lib/batik-transcoder.jar:$ATACSGUI/gui/lib/batik-util.jar:$ATACSGUI/gui/lib/batik-xml.jar:$ATACSGUI/gui/lib/js.jar:$ATACSGUI/gui/lib/pdf-transcoder.jar:$ATACSGUI/gui/lib/xalan-2.6.0.jar:$ATACSGUI/gui/lib/xerces_2_5_0.jar:$ATACSGUI/gui/lib/xml-apis.jar:$ATACSGUI/gui/lib/xml-apis-ext.jar:$ATACSGUI/gui/lib/epsgraphics.jar:$ATACSGUI/gui/lib/libsbmlj.jar:$ATACSGUI/gui/lib/org-jdesktop-layout.jar:$ATACSGUI/gui/lib/swing-layout-1.0.3.jar:$ATACSGUI/gui/lib/activation.jar:$ATACSGUI/gui/lib/mail.jar:$ATACSGUI/gui/lib/biomodelswslib-standalone-1.11.jar:$ATACSGUI/gui/lib/grappa1_2.jar:$ATACSGUI/gui/lib/jgraphx.jar:$ATACSGUI/gui/lib/gson-1.6.jar main.Gui -atacs
export DYLD_LIBRARY_PATH=$BIOSIM/lib64:$DYLD_LIBRARY_PATH
CLASSPATH=$BIOSIM/gui/dist/classes
for jarFile in $BIOSIM/gui/lib/*.jar
do
CLASSPATH=$CLASSPATH:$jarFile
done
exec java -Xmx512M -classpath $CLASSPATH main.Gui -atacs

11
bin/ATACSGUI.mac
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@ -1,5 +1,12 @@
#!/bin/sh
#
# run-time wrapper for BioSim gui
export DYLD_LIBRARY_PATH=$ATACSGUI/lib:$DYLD_LIBRARY_PATH
exec java -Xmx512M -classpath $ATACSGUI/gui/dist/classes:$ATACSGUI/gui/lib/jcommon-1.0.16.jar:$ATACSGUI/gui/lib/jfreechart-1.0.13.jar:$ATACSGUI/gui/lib/iText-2.1.5.jar:$ATACSGUI/gui/lib/batik-anim.jar:$ATACSGUI/gui/lib/batik-awt-util.jar:$ATACSGUI/gui/lib/batik-bridge.jar:$ATACSGUI/gui/lib/batik-codec.jar:$ATACSGUI/gui/lib/batik-css.jar:$ATACSGUI/gui/lib/batik-dom.jar:$ATACSGUI/gui/lib/batik-ext.jar:$ATACSGUI/gui/lib/batik-extension.jar:$ATACSGUI/gui/lib/batik-gui-util.jar:$ATACSGUI/gui/lib/batik-gvt.jar:$ATACSGUI/gui/lib/batik-parser.jar:$ATACSGUI/gui/lib/batik-script.jar:$ATACSGUI/gui/lib/batik-svg-dom.jar:$ATACSGUI/gui/lib/batik-svggen.jar:$ATACSGUI/gui/lib/batik-swing.jar:$ATACSGUI/gui/lib/batik-transcoder.jar:$ATACSGUI/gui/lib/batik-util.jar:$ATACSGUI/gui/lib/batik-xml.jar:$ATACSGUI/gui/lib/js.jar:$ATACSGUI/gui/lib/pdf-transcoder.jar:$ATACSGUI/gui/lib/xalan-2.6.0.jar:$ATACSGUI/gui/lib/xerces_2_5_0.jar:$ATACSGUI/gui/lib/xml-apis.jar:$ATACSGUI/gui/lib/xml-apis-ext.jar:$ATACSGUI/gui/lib/epsgraphics.jar:$ATACSGUI/gui/lib/libsbmlj.jar:$ATACSGUI/gui/lib/org-jdesktop-layout.jar:$ATACSGUI/gui/lib/swing-layout-1.0.3.jar:$ATACSGUI/gui/lib/activation.jar:$ATACSGUI/gui/lib/mail.jar:$ATACSGUI/gui/lib/biomodelswslib-standalone-1.11.jar:$ATACSGUI/gui/lib/grappa1_2.jar:$ATACSGUI/gui/lib/jgraphx.jar:$ATACSGUI/gui/lib/gson-1.6.jar -Dapple.laf.useScreenMenuBar=true -Xdock:name="ATACS" -Xdock:icon=$ATACSGUI/gui/icons/ATACS.png main.Gui -atacs
export DYLD_LIBRARY_PATH=$BIOSIM/lib:$DYLD_LIBRARY_PATH
CLASSPATH=$ATACSGUI/gui/dist/classes
for jarFile in $ATACSGUI/gui/lib/*.jar
do
CLASSPATH=$CLASSPATH:$jarFile
done
exec java -Xmx512M -classpath $CLASSPATH -Dapple.laf.useScreenMenuBar=true -Xdock:name="ATACSGUI" -Xdock:icon=$ATACSGUI/gui/icons/ATACS.png main.Gui -atacs

11
bin/ATACSGUI.mac64
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@ -1,5 +1,12 @@
#!/bin/sh
#
# run-time wrapper for BioSim gui
export DYLD_LIBRARY_PATH=$ATACSGUI/lib64:$DYLD_LIBRARY_PATH
exec java -Xmx512M -classpath $ATACSGUI/gui/dist/classes:$ATACSGUI/gui/lib/jcommon-1.0.16.jar:$ATACSGUI/gui/lib/jfreechart-1.0.13.jar:$ATACSGUI/gui/lib/iText-2.1.5.jar:$ATACSGUI/gui/lib/batik-anim.jar:$ATACSGUI/gui/lib/batik-awt-util.jar:$ATACSGUI/gui/lib/batik-bridge.jar:$ATACSGUI/gui/lib/batik-codec.jar:$ATACSGUI/gui/lib/batik-css.jar:$ATACSGUI/gui/lib/batik-dom.jar:$ATACSGUI/gui/lib/batik-ext.jar:$ATACSGUI/gui/lib/batik-extension.jar:$ATACSGUI/gui/lib/batik-gui-util.jar:$ATACSGUI/gui/lib/batik-gvt.jar:$ATACSGUI/gui/lib/batik-parser.jar:$ATACSGUI/gui/lib/batik-script.jar:$ATACSGUI/gui/lib/batik-svg-dom.jar:$ATACSGUI/gui/lib/batik-svggen.jar:$ATACSGUI/gui/lib/batik-swing.jar:$ATACSGUI/gui/lib/batik-transcoder.jar:$ATACSGUI/gui/lib/batik-util.jar:$ATACSGUI/gui/lib/batik-xml.jar:$ATACSGUI/gui/lib/js.jar:$ATACSGUI/gui/lib/pdf-transcoder.jar:$ATACSGUI/gui/lib/xalan-2.6.0.jar:$ATACSGUI/gui/lib/xerces_2_5_0.jar:$ATACSGUI/gui/lib/xml-apis.jar:$ATACSGUI/gui/lib/xml-apis-ext.jar:$ATACSGUI/gui/lib/epsgraphics.jar:$ATACSGUI/gui/lib/libsbmlj.jar:$ATACSGUI/gui/lib/org-jdesktop-layout.jar:$ATACSGUI/gui/lib/swing-layout-1.0.3.jar:$ATACSGUI/gui/lib/activation.jar:$ATACSGUI/gui/lib/mail.jar:$ATACSGUI/gui/lib/biomodelswslib-standalone-1.11.jar:$ATACSGUI/gui/lib/grappa1_2.jar:$ATACSGUI/gui/lib/jgraphx.jar:$ATACSGUI/gui/lib/gson-1.6.jar -Dapple.laf.useScreenMenuBar=true -Xdock:name="ATACS" -Xdock:icon=$ATACSGUI/gui/icons/ATACS.png main.Gui -atacs
export DYLD_LIBRARY_PATH=$BIOSIM/lib64:$DYLD_LIBRARY_PATH
CLASSPATH=$ATACSGUI/gui/dist/classes
for jarFile in $ATACSGUI/gui/lib/*.jar
do
CLASSPATH=$CLASSPATH:$jarFile
done
exec java -Xmx512M -classpath $CLASSPATH -Dapple.laf.useScreenMenuBar=true -Xdock:name="ATACSGUI" -Xdock:icon=$ATACSGUI/gui/icons/ATACS.png main.Gui -atacs

6
bin/LEMA.bat
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@ -1,2 +1,6 @@
java -Xmx512M -classpath "%LEMA%\gui\dist\classes";"%LEMA%\gui\lib\jcommon-1.0.16.jar";"%LEMA%\gui\lib\jfreechart-1.0.13.jar";"%LEMA%\gui\lib\iText-2.1.5.jar";"%LEMA%\gui\lib\batik-anim.jar";"%LEMA%\gui\lib\batik-awt-util.jar";"%LEMA%\gui\lib\batik-bridge.jar";"%LEMA%\gui\lib\batik-codec.jar";"%LEMA%\gui\lib\batik-css.jar";"%LEMA%\gui\lib\batik-dom.jar";"%LEMA%\gui\lib\batik-ext.jar";"%LEMA%\gui\lib\batik-extension.jar";"%LEMA%\gui\lib\batik-gui-util.jar";"%LEMA%\gui\lib\batik-gvt.jar";"%LEMA%\gui\lib\batik-parser.jar";"%LEMA%\gui\lib\batik-script.jar";"%LEMA%\gui\lib\batik-svg-dom.jar";"%LEMA%\gui\lib\batik-svggen.jar";"%LEMA%\gui\lib\batik-swing.jar";"%LEMA%\gui\lib\batik-transcoder.jar";"%LEMA%\gui\lib\batik-util.jar";"%LEMA%\gui\lib\batik-xml.jar";"%LEMA%\gui\lib\js.jar";"%LEMA%\gui\lib\pdf-transcoder.jar";"%LEMA%\gui\lib\xalan-2.6.0.jar";"%LEMA%\gui\lib\xerces_2_5_0.jar";"%LEMA%\gui\lib\xml-apis.jar";"%LEMA%\gui\lib\xml-apis-ext.jar";"%LEMA%\gui\lib\epsgraphics.jar";"%LEMA%\gui\lib\sbmlj.jar";"%LEMA%\gui\lib\org-jdesktop-layout.jar";"%LEMA%\gui\lib\swing-layout-1.0.3.jar";"%LEMA%\gui\lib\activation.jar";"%LEMA%\gui\lib\mail.jar";"%LEMA%\gui\lib\biomodelswslib-standalone-1.11.jar";"%LEMA%\gui\lib\grappa1_2.jar";"%LEMA%\gui\lib\jgraphx.jar";"%LEMA%\gui\lib\gson-1.6.jar" main.Gui -lema
setlocal ENABLEDELAYEDEXPANSION
set CLASSPATH="%LEMA%\gui\dist\classes"
for /f %%a IN ('dir /b "%LEMA%\gui\lib\*.jar"') do call set CLASSPATH=!CLASSPATH!;"%LEMA%\gui\lib\%%a"
java -Xmx512M -classpath %CLASSPATH% main.Gui -lema

14
bin/LEMA.linux
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@ -1,5 +1,11 @@
#!/bin/sh
#
# run-time wrapper for BioSim gui
export LD_LIBRARY_PATH=$LEMA/lib:$LD_LIBRARY_PATH
exec java -Xmx512M -classpath $LEMA/gui/dist/classes:$LEMA/gui/lib/jcommon-1.0.16.jar:$LEMA/gui/lib/jfreechart-1.0.13.jar:$LEMA/gui/lib/iText-2.1.5.jar:$LEMA/gui/lib/batik-anim.jar:$LEMA/gui/lib/batik-awt-util.jar:$LEMA/gui/lib/batik-bridge.jar:$LEMA/gui/lib/batik-codec.jar:$LEMA/gui/lib/batik-css.jar:$LEMA/gui/lib/batik-dom.jar:$LEMA/gui/lib/batik-ext.jar:$LEMA/gui/lib/batik-extension.jar:$LEMA/gui/lib/batik-gui-util.jar:$LEMA/gui/lib/batik-gvt.jar:$LEMA/gui/lib/batik-parser.jar:$LEMA/gui/lib/batik-script.jar:$LEMA/gui/lib/batik-svg-dom.jar:$LEMA/gui/lib/batik-svggen.jar:$LEMA/gui/lib/batik-swing.jar:$LEMA/gui/lib/batik-transcoder.jar:$LEMA/gui/lib/batik-util.jar:$LEMA/gui/lib/batik-xml.jar:$LEMA/gui/lib/js.jar:$LEMA/gui/lib/pdf-transcoder.jar:$LEMA/gui/lib/xalan-2.6.0.jar:$LEMA/gui/lib/xerces_2_5_0.jar:$LEMA/gui/lib/xml-apis.jar:$LEMA/gui/lib/xml-apis-ext.jar:$LEMA/gui/lib/epsgraphics.jar:$LEMA/gui/lib/libsbmlj.jar:$LEMA/gui/lib/org-jdesktop-layout.jar:$LEMA/gui/lib/swing-layout-1.0.3.jar:$LEMA/gui/lib/activation.jar:$LEMA/gui/lib/mail.jar:$LEMA/gui/lib/biomodelswslib-standalone-1.11.jar:$LEMA/gui/lib/grappa1_2.jar:$LEMA/gui/lib/jgraphx.jar:$LEMA/gui/lib/gson-1.6.jar main.Gui -lema
export DYLD_LIBRARY_PATH=$BIOSIM/lib:$DYLD_LIBRARY_PATH
CLASSPATH=$BIOSIM/gui/dist/classes
for jarFile in $BIOSIM/gui/lib/*.jar
do
CLASSPATH=$CLASSPATH:$jarFile
done
exec java -Xmx512M -classpath $CLASSPATH main.Gui -lema

14
bin/LEMA.linux64
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@ -1,5 +1,11 @@
#!/bin/sh
#
# run-time wrapper for BioSim gui
export LD_LIBRARY_PATH=$LEMA/lib64:$LD_LIBRARY_PATH
exec java -Xmx512M -classpath $LEMA/gui/dist/classes:$LEMA/gui/lib/jcommon-1.0.16.jar:$LEMA/gui/lib/jfreechart-1.0.13.jar:$LEMA/gui/lib/iText-2.1.5.jar:$LEMA/gui/lib/batik-anim.jar:$LEMA/gui/lib/batik-awt-util.jar:$LEMA/gui/lib/batik-bridge.jar:$LEMA/gui/lib/batik-codec.jar:$LEMA/gui/lib/batik-css.jar:$LEMA/gui/lib/batik-dom.jar:$LEMA/gui/lib/batik-ext.jar:$LEMA/gui/lib/batik-extension.jar:$LEMA/gui/lib/batik-gui-util.jar:$LEMA/gui/lib/batik-gvt.jar:$LEMA/gui/lib/batik-parser.jar:$LEMA/gui/lib/batik-script.jar:$LEMA/gui/lib/batik-svg-dom.jar:$LEMA/gui/lib/batik-svggen.jar:$LEMA/gui/lib/batik-swing.jar:$LEMA/gui/lib/batik-transcoder.jar:$LEMA/gui/lib/batik-util.jar:$LEMA/gui/lib/batik-xml.jar:$LEMA/gui/lib/js.jar:$LEMA/gui/lib/pdf-transcoder.jar:$LEMA/gui/lib/xalan-2.6.0.jar:$LEMA/gui/lib/xerces_2_5_0.jar:$LEMA/gui/lib/xml-apis.jar:$LEMA/gui/lib/xml-apis-ext.jar:$LEMA/gui/lib/epsgraphics.jar:$LEMA/gui/lib/libsbmlj.jar:$LEMA/gui/lib/org-jdesktop-layout.jar:$LEMA/gui/lib/swing-layout-1.0.3.jar:$LEMA/gui/lib/activation.jar:$LEMA/gui/lib/mail.jar:$LEMA/gui/lib/biomodelswslib-standalone-1.11.jar:$LEMA/gui/lib/grappa1_2.jar:$LEMA/gui/lib/jgraphx.jar:$LEMA/gui/lib/gson-1.6.jar main.Gui -lema
export DYLD_LIBRARY_PATH=$BIOSIM/lib64:$DYLD_LIBRARY_PATH
CLASSPATH=$BIOSIM/gui/dist/classes
for jarFile in $BIOSIM/gui/lib/*.jar
do
CLASSPATH=$CLASSPATH:$jarFile
done
exec java -Xmx512M -classpath $CLASSPATH main.Gui -lema

11
bin/LEMA.mac
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@ -1,5 +1,12 @@
#!/bin/sh
#
# run-time wrapper for BioSim gui
export DYLD_LIBRARY_PATH=$LEMA/lib:$DYLD_LIBRARY_PATH
exec java -Xmx512M -classpath $LEMA/gui/dist/classes:$LEMA/gui/lib/jcommon-1.0.16.jar:$LEMA/gui/lib/jfreechart-1.0.13.jar:$LEMA/gui/lib/iText-2.1.5.jar:$LEMA/gui/lib/batik-anim.jar:$LEMA/gui/lib/batik-awt-util.jar:$LEMA/gui/lib/batik-bridge.jar:$LEMA/gui/lib/batik-codec.jar:$LEMA/gui/lib/batik-css.jar:$LEMA/gui/lib/batik-dom.jar:$LEMA/gui/lib/batik-ext.jar:$LEMA/gui/lib/batik-extension.jar:$LEMA/gui/lib/batik-gui-util.jar:$LEMA/gui/lib/batik-gvt.jar:$LEMA/gui/lib/batik-parser.jar:$LEMA/gui/lib/batik-script.jar:$LEMA/gui/lib/batik-svg-dom.jar:$LEMA/gui/lib/batik-svggen.jar:$LEMA/gui/lib/batik-swing.jar:$LEMA/gui/lib/batik-transcoder.jar:$LEMA/gui/lib/batik-util.jar:$LEMA/gui/lib/batik-xml.jar:$LEMA/gui/lib/js.jar:$LEMA/gui/lib/pdf-transcoder.jar:$LEMA/gui/lib/xalan-2.6.0.jar:$LEMA/gui/lib/xerces_2_5_0.jar:$LEMA/gui/lib/xml-apis.jar:$LEMA/gui/lib/xml-apis-ext.jar:$LEMA/gui/lib/epsgraphics.jar:$LEMA/gui/lib/libsbmlj.jar:$LEMA/gui/lib/org-jdesktop-layout.jar:$LEMA/gui/lib/swing-layout-1.0.3.jar:$LEMA/gui/lib/activation.jar:$LEMA/gui/lib/mail.jar:$LEMA/gui/lib/biomodelswslib-standalone-1.11.jar:$LEMA/gui/lib/grappa1_2.jar:$LEMA/gui/lib/jgraphx.jar:$LEMA/gui/lib/gson-1.6.jar -Dapple.laf.useScreenMenuBar=true -Xdock:name="LEMA" -Xdock:icon=$LEMA/gui/icons/LEMA.png main.Gui -lema
export DYLD_LIBRARY_PATH=$BIOSIM/lib:$DYLD_LIBRARY_PATH
CLASSPATH=$LEMA/gui/dist/classes
for jarFile in $LEMA/gui/lib/*.jar
do
CLASSPATH=$CLASSPATH:$jarFile
done
exec java -Xmx512M -classpath $CLASSPATH -Dapple.laf.useScreenMenuBar=true -Xdock:name="LEMA" -Xdock:icon=$LEMA/gui/icons/LEMA.png main.Gui -lema

11
bin/LEMA.mac64
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@ -1,5 +1,12 @@
#!/bin/sh
#
# run-time wrapper for BioSim gui
export DYLD_LIBRARY_PATH=$LEMA/lib64:$DYLD_LIBRARY_PATH
exec java -Xmx512M -classpath $LEMA/gui/dist/classes:$LEMA/gui/lib/jcommon-1.0.16.jar:$LEMA/gui/lib/jfreechart-1.0.13.jar:$LEMA/gui/lib/iText-2.1.5.jar:$LEMA/gui/lib/batik-anim.jar:$LEMA/gui/lib/batik-awt-util.jar:$LEMA/gui/lib/batik-bridge.jar:$LEMA/gui/lib/batik-codec.jar:$LEMA/gui/lib/batik-css.jar:$LEMA/gui/lib/batik-dom.jar:$LEMA/gui/lib/batik-ext.jar:$LEMA/gui/lib/batik-extension.jar:$LEMA/gui/lib/batik-gui-util.jar:$LEMA/gui/lib/batik-gvt.jar:$LEMA/gui/lib/batik-parser.jar:$LEMA/gui/lib/batik-script.jar:$LEMA/gui/lib/batik-svg-dom.jar:$LEMA/gui/lib/batik-svggen.jar:$LEMA/gui/lib/batik-swing.jar:$LEMA/gui/lib/batik-transcoder.jar:$LEMA/gui/lib/batik-util.jar:$LEMA/gui/lib/batik-xml.jar:$LEMA/gui/lib/js.jar:$LEMA/gui/lib/pdf-transcoder.jar:$LEMA/gui/lib/xalan-2.6.0.jar:$LEMA/gui/lib/xerces_2_5_0.jar:$LEMA/gui/lib/xml-apis.jar:$LEMA/gui/lib/xml-apis-ext.jar:$LEMA/gui/lib/epsgraphics.jar:$LEMA/gui/lib/libsbmlj.jar:$LEMA/gui/lib/org-jdesktop-layout.jar:$LEMA/gui/lib/swing-layout-1.0.3.jar:$LEMA/gui/lib/activation.jar:$LEMA/gui/lib/mail.jar:$LEMA/gui/lib/biomodelswslib-standalone-1.11.jar:$LEMA/gui/lib/grappa1_2.jar:$LEMA/gui/lib/jgraphx.jar:$LEMA/gui/lib/gson-1.6.jar -Dapple.laf.useScreenMenuBar=true -Xdock:name="LEMA" -Xdock:icon=$LEMA/gui/icons/LEMA.png main.Gui -lema
export DYLD_LIBRARY_PATH=$BIOSIM/lib64:$DYLD_LIBRARY_PATH
CLASSPATH=$LEMA/gui/dist/classes
for jarFile in $LEMA/gui/lib/*.jar
do
CLASSPATH=$CLASSPATH:$jarFile
done
exec java -Xmx512M -classpath $CLASSPATH -Dapple.laf.useScreenMenuBar=true -Xdock:name="LEMA" -Xdock:icon=$LEMA/gui/icons/LEMA.png main.Gui -lema

5
bin/iBioSim.bat
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@ -1,2 +1,5 @@
java -Xmx512M -classpath "%BIOSIM%\gui\dist\classes";"%BIOSIM%\gui\lib\jcommon-1.0.16.jar";"%BIOSIM%\gui\lib\jfreechart-1.0.13.jar";"%BIOSIM%\gui\lib\iText-2.1.5.jar";"%BIOSIM%\gui\lib\batik-anim.jar";"%BIOSIM%\gui\lib\batik-awt-util.jar";"%BIOSIM%\gui\lib\batik-bridge.jar";"%BIOSIM%\gui\lib\batik-codec.jar";"%BIOSIM%\gui\lib\batik-css.jar";"%BIOSIM%\gui\lib\batik-dom.jar";"%BIOSIM%\gui\lib\batik-ext.jar";"%BIOSIM%\gui\lib\batik-extension.jar";"%BIOSIM%\gui\lib\batik-gui-util.jar";"%BIOSIM%\gui\lib\batik-gvt.jar";"%BIOSIM%\gui\lib\batik-parser.jar";"%BIOSIM%\gui\lib\batik-script.jar";"%BIOSIM%\gui\lib\batik-svg-dom.jar";"%BIOSIM%\gui\lib\batik-svggen.jar";"%BIOSIM%\gui\lib\batik-swing.jar";"%BIOSIM%\gui\lib\batik-transcoder.jar";"%BIOSIM%\gui\lib\batik-util.jar";"%BIOSIM%\gui\lib\batik-xml.jar";"%BIOSIM%\gui\lib\js.jar";"%BIOSIM%\gui\lib\pdf-transcoder.jar";"%BIOSIM%\gui\lib\xalan-2.6.0.jar";"%BIOSIM%\gui\lib\xerces_2_5_0.jar";"%BIOSIM%\gui\lib\xml-apis.jar";"%BIOSIM%\gui\lib\xml-apis-ext.jar";"%BIOSIM%\gui\lib\epsgraphics.jar";"%BIOSIM%\gui\lib\sbmlj.jar";"%BIOSIM%\gui\lib\org-jdesktop-layout.jar";"%BIOSIM%\gui\lib\swing-layout-1.0.3.jar";"%BIOSIM%\gui\lib\activation.jar";"%BIOSIM%\gui\lib\mail.jar";"%BIOSIM%\gui\lib\biomodelswslib-standalone-1.11.jar";"%BIOSIM%\gui\lib\grappa1_2.jar";"%BIOSIM%\gui\lib\jgraphx.jar";"%BIOSIM%\gui\lib\gson-1.6.jar" main.Gui
setlocal ENABLEDELAYEDEXPANSION
set CLASSPATH="%BIOSIM%\gui\dist\classes"
for /f %%a IN ('dir /b "%BIOSIM%\gui\lib\*.jar"') do call set CLASSPATH=!CLASSPATH!;"%BIOSIM%\gui\lib\%%a"
java -Xmx512M -classpath %CLASSPATH% main.Gui

14
bin/iBioSim.linux
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@ -1,5 +1,11 @@
#!/bin/sh
#
# run-time wrapper for BioSim gui
export LD_LIBRARY_PATH=$BIOSIM/lib:$LD_LIBRARY_PATH
exec java -Xmx512M -classpath $BIOSIM/gui/dist/classes:$BIOSIM/gui/lib/jcommon-1.0.16.jar:$BIOSIM/gui/lib/jfreechart-1.0.13.jar:$BIOSIM/gui/lib/iText-2.1.5.jar:$BIOSIM/gui/lib/batik-anim.jar:$BIOSIM/gui/lib/batik-awt-util.jar:$BIOSIM/gui/lib/batik-bridge.jar:$BIOSIM/gui/lib/batik-codec.jar:$BIOSIM/gui/lib/batik-css.jar:$BIOSIM/gui/lib/batik-dom.jar:$BIOSIM/gui/lib/batik-ext.jar:$BIOSIM/gui/lib/batik-extension.jar:$BIOSIM/gui/lib/batik-gui-util.jar:$BIOSIM/gui/lib/batik-gvt.jar:$BIOSIM/gui/lib/batik-parser.jar:$BIOSIM/gui/lib/batik-script.jar:$BIOSIM/gui/lib/batik-svg-dom.jar:$BIOSIM/gui/lib/batik-svggen.jar:$BIOSIM/gui/lib/batik-swing.jar:$BIOSIM/gui/lib/batik-transcoder.jar:$BIOSIM/gui/lib/batik-util.jar:$BIOSIM/gui/lib/batik-xml.jar:$BIOSIM/gui/lib/js.jar:$BIOSIM/gui/lib/pdf-transcoder.jar:$BIOSIM/gui/lib/xalan-2.6.0.jar:$BIOSIM/gui/lib/xerces_2_5_0.jar:$BIOSIM/gui/lib/xml-apis.jar:$BIOSIM/gui/lib/xml-apis-ext.jar:$BIOSIM/gui/lib/epsgraphics.jar:$BIOSIM/gui/lib/libsbmlj.jar:$BIOSIM/gui/lib/org-jdesktop-layout.jar:$BIOSIM/gui/lib/swing-layout-1.0.3.jar:$BIOSIM/gui/lib/activation.jar:$BIOSIM/gui/lib/mail.jar:$BIOSIM/gui/lib/biomodelswslib-standalone-1.11.jar:$BIOSIM/gui/lib/grappa1_2.jar:$BIOSIM/gui/lib/jgraphx.jar:$BIOSIM/gui/lib/gson-1.6.jar main.Gui
export DYLD_LIBRARY_PATH=$BIOSIM/lib:$DYLD_LIBRARY_PATH
CLASSPATH=$BIOSIM/gui/dist/classes
for jarFile in $BIOSIM/gui/lib/*.jar
do
CLASSPATH=$CLASSPATH:$jarFile
done
exec java -Xmx512M -classpath $CLASSPATH main.Gui

14
bin/iBioSim.linux64
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@ -1,5 +1,11 @@
#!/bin/sh
#
# run-time wrapper for BioSim gui
export LD_LIBRARY_PATH=$BIOSIM/lib64:$LD_LIBRARY_PATH
exec java -Xmx512M -classpath $BIOSIM/gui/dist/classes:$BIOSIM/gui/lib/jcommon-1.0.16.jar:$BIOSIM/gui/lib/jfreechart-1.0.13.jar:$BIOSIM/gui/lib/iText-2.1.5.jar:$BIOSIM/gui/lib/batik-anim.jar:$BIOSIM/gui/lib/batik-awt-util.jar:$BIOSIM/gui/lib/batik-bridge.jar:$BIOSIM/gui/lib/batik-codec.jar:$BIOSIM/gui/lib/batik-css.jar:$BIOSIM/gui/lib/batik-dom.jar:$BIOSIM/gui/lib/batik-ext.jar:$BIOSIM/gui/lib/batik-extension.jar:$BIOSIM/gui/lib/batik-gui-util.jar:$BIOSIM/gui/lib/batik-gvt.jar:$BIOSIM/gui/lib/batik-parser.jar:$BIOSIM/gui/lib/batik-script.jar:$BIOSIM/gui/lib/batik-svg-dom.jar:$BIOSIM/gui/lib/batik-svggen.jar:$BIOSIM/gui/lib/batik-swing.jar:$BIOSIM/gui/lib/batik-transcoder.jar:$BIOSIM/gui/lib/batik-util.jar:$BIOSIM/gui/lib/batik-xml.jar:$BIOSIM/gui/lib/js.jar:$BIOSIM/gui/lib/pdf-transcoder.jar:$BIOSIM/gui/lib/xalan-2.6.0.jar:$BIOSIM/gui/lib/xerces_2_5_0.jar:$BIOSIM/gui/lib/xml-apis.jar:$BIOSIM/gui/lib/xml-apis-ext.jar:$BIOSIM/gui/lib/epsgraphics.jar:$BIOSIM/gui/lib/libsbmlj.jar:$BIOSIM/gui/lib/org-jdesktop-layout.jar:$BIOSIM/gui/lib/swing-layout-1.0.3.jar:$BIOSIM/gui/lib/activation.jar:$BIOSIM/gui/lib/mail.jar:$BIOSIM/gui/lib/biomodelswslib-standalone-1.11.jar:$BIOSIM/gui/lib/grappa1_2.jar:$BIOSIM/gui/lib/jgraphx.jar:$BIOSIM/gui/lib/gson-1.6.jar main.Gui
export DYLD_LIBRARY_PATH=$BIOSIM/lib64:$DYLD_LIBRARY_PATH
CLASSPATH=$BIOSIM/gui/dist/classes
for jarFile in $BIOSIM/gui/lib/*.jar
do
CLASSPATH=$CLASSPATH:$jarFile
done
exec java -Xmx512M -classpath $CLASSPATH main.Gui

9
bin/iBioSim.mac
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@ -2,4 +2,11 @@
#
# run-time wrapper for BioSim gui
export DYLD_LIBRARY_PATH=$BIOSIM/lib:$DYLD_LIBRARY_PATH
exec java -Xmx512M -classpath $BIOSIM/gui/dist/classes:$BIOSIM/gui/lib/jcommon-1.0.16.jar:$BIOSIM/gui/lib/jfreechart-1.0.13.jar:$BIOSIM/gui/lib/iText-2.1.5.jar:$BIOSIM/gui/lib/batik-anim.jar:$BIOSIM/gui/lib/batik-awt-util.jar:$BIOSIM/gui/lib/batik-bridge.jar:$BIOSIM/gui/lib/batik-codec.jar:$BIOSIM/gui/lib/batik-css.jar:$BIOSIM/gui/lib/batik-dom.jar:$BIOSIM/gui/lib/batik-ext.jar:$BIOSIM/gui/lib/batik-extension.jar:$BIOSIM/gui/lib/batik-gui-util.jar:$BIOSIM/gui/lib/batik-gvt.jar:$BIOSIM/gui/lib/batik-parser.jar:$BIOSIM/gui/lib/batik-script.jar:$BIOSIM/gui/lib/batik-svg-dom.jar:$BIOSIM/gui/lib/batik-svggen.jar:$BIOSIM/gui/lib/batik-swing.jar:$BIOSIM/gui/lib/batik-transcoder.jar:$BIOSIM/gui/lib/batik-util.jar:$BIOSIM/gui/lib/batik-xml.jar:$BIOSIM/gui/lib/js.jar:$BIOSIM/gui/lib/pdf-transcoder.jar:$BIOSIM/gui/lib/xalan-2.6.0.jar:$BIOSIM/gui/lib/xerces_2_5_0.jar:$BIOSIM/gui/lib/xml-apis.jar:$BIOSIM/gui/lib/xml-apis-ext.jar:$BIOSIM/gui/lib/epsgraphics.jar:$BIOSIM/gui/lib/libsbmlj.jar:$BIOSIM/gui/lib/org-jdesktop-layout.jar:$BIOSIM/gui/lib/swing-layout-1.0.3.jar:$BIOSIM/gui/lib/activation.jar:$BIOSIM/gui/lib/mail.jar:$BIOSIM/gui/lib/biomodelswslib-standalone-1.11.jar:$BIOSIM/gui/lib/grappa1_2.jar:$BIOSIM/gui/lib/jgraphx.jar:$BIOSIM/gui/lib/gson-1.6.jar -Dapple.laf.useScreenMenuBar=true -Xdock:name="iBioSim" -Xdock:icon=$BIOSIM/gui/icons/iBioSim.jpg main.Gui
CLASSPATH=$BIOSIM/gui/dist/classes
for jarFile in $BIOSIM/gui/lib/*.jar
do
CLASSPATH=$CLASSPATH:$jarFile
done
exec java -Xmx512M -classpath $CLASSPATH -Dapple.laf.useScreenMenuBar=true -Xdock:name="iBioSim" -Xdock:icon=$BIOSIM/gui/icons/iBioSim.jpg main.Gui

9
bin/iBioSim.mac64
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@ -2,4 +2,11 @@
#
# run-time wrapper for BioSim gui
export DYLD_LIBRARY_PATH=$BIOSIM/lib64:$DYLD_LIBRARY_PATH
exec java -Xmx512M -classpath $BIOSIM/gui/dist/classes:$BIOSIM/gui/lib/jcommon-1.0.16.jar:$BIOSIM/gui/lib/jfreechart-1.0.13.jar:$BIOSIM/gui/lib/iText-2.1.5.jar:$BIOSIM/gui/lib/batik-anim.jar:$BIOSIM/gui/lib/batik-awt-util.jar:$BIOSIM/gui/lib/batik-bridge.jar:$BIOSIM/gui/lib/batik-codec.jar:$BIOSIM/gui/lib/batik-css.jar:$BIOSIM/gui/lib/batik-dom.jar:$BIOSIM/gui/lib/batik-ext.jar:$BIOSIM/gui/lib/batik-extension.jar:$BIOSIM/gui/lib/batik-gui-util.jar:$BIOSIM/gui/lib/batik-gvt.jar:$BIOSIM/gui/lib/batik-parser.jar:$BIOSIM/gui/lib/batik-script.jar:$BIOSIM/gui/lib/batik-svg-dom.jar:$BIOSIM/gui/lib/batik-svggen.jar:$BIOSIM/gui/lib/batik-swing.jar:$BIOSIM/gui/lib/batik-transcoder.jar:$BIOSIM/gui/lib/batik-util.jar:$BIOSIM/gui/lib/batik-xml.jar:$BIOSIM/gui/lib/js.jar:$BIOSIM/gui/lib/pdf-transcoder.jar:$BIOSIM/gui/lib/xalan-2.6.0.jar:$BIOSIM/gui/lib/xerces_2_5_0.jar:$BIOSIM/gui/lib/xml-apis.jar:$BIOSIM/gui/lib/xml-apis-ext.jar:$BIOSIM/gui/lib/epsgraphics.jar:$BIOSIM/gui/lib/libsbmlj64.jar:$BIOSIM/gui/lib/org-jdesktop-layout.jar:$BIOSIM/gui/lib/swing-layout-1.0.3.jar:$BIOSIM/gui/lib/activation.jar:$BIOSIM/gui/lib/mail.jar:$BIOSIM/gui/lib/biomodelswslib-standalone-1.11.jar:$BIOSIM/gui/lib/grappa1_2.jar:$BIOSIM/gui/lib/jgraphx.jar:$BIOSIM/gui/lib/gson-1.6.jar -Dapple.laf.useScreenMenuBar=true -Xdock:name="iBioSim" -Xdock:icon=$BIOSIM/gui/icons/iBioSim.jpg main.Gui
CLASSPATH=$BIOSIM/gui/dist/classes
for jarFile in $BIOSIM/gui/lib/*.jar
do
CLASSPATH=$CLASSPATH:$jarFile
done
exec java -Xmx512M -classpath $CLASSPATH -Dapple.laf.useScreenMenuBar=true -Xdock:name="iBioSim" -Xdock:icon=$BIOSIM/gui/icons/iBioSim.jpg main.Gui

BIN
bin/xxatacs
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