#cp REMcRdy_lm_only.csv-finalTable.csv REMcRdy_lm_only.csv-finalTableBUP.csv
#rm REMcRdy_lm_only.csv-finalTable.csv
#userpath= sudo -u root -H -s eval 'echo $PWD'
#/mnt/data/java-1.8.0-openjdk-1.8.0.352.b08-2.el7_9.x86_64/jre/bin/java -Xms512m -Xmx2048m -Dfile.encoding=UTF-8 -classpath ./jingyuJava_1_7_extractLib.jar ExecMain ./REMcRdy_lm_only.csv GeneByGOAttributeMatrix_nofiltering-2009Dec07.tab ORF_List_Without_DAmPs.txt 1 true true

#/Users/anyamcdaniel/Downloads/HartmanLab/StudiesQHTCP/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/java -Xms512m -Xmx2048m -Dfile.encoding=UTF-8 -classpath ./jingyuJava_1_7_extractLib.jar ExecMain ./REMcRdy_lm_only.csv GeneByGOAttributeMatrix_nofiltering-2009Dec07.tab ORF_List_Without_DAmPs.txt 1 true true
# figure out how to do this on a mac based on where REMcJava is locatedcu
#/Users/anyamcdaniel/Downloads/HartmanLab/StudiesQHTCP/2PE_BMH21_RM_TrialOnMac/REMc/REMcJava/java-1.8.0-openjdk-1.8.0.342.b07-1.el7_9.x86_64/jre/bin/java -Xms512m -Xmx2048m -Dfile.encoding=UTF-8 -classpath ./jingyuJava_1_7_extractLib.jar ExecMain ./REMcRdy_lm_only.csv GeneByGOAttributeMatrix_nofiltering-2009Dec07.tab ORF_List_Without_DAmPs.txt 1 true true

#/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el7_9.x86_64/jre/bin/java -Xms512m -Xmx2048m -Dfile.encoding=UTF-8 -classpath ./jingyuJava_1_7_extractLib.jar ExecMain ./REMcRdy_lm_only.csv GeneByGOAttributeMatrix_nofiltering-2009Dec07.tab ORF_List_Without_DAmPs.txt 1 true true

#wait
cp REMcRdy_lm_only.csv-finalTable.csv REMcRdy_lm_only.csv-finalTableBUP.csv
rm REMcRdy_lm_only.csv-finalTable.csv

current_dir="$PWD"

java_executable="java" # Assuming java is available in the system's PATH

classpath="$current_dir/jingyuJava_1_7_extractLib.jar"

"$java_executable" -Xms512m -Xmx2048m -Dfile.encoding=UTF-8 -classpath "$classpath" ExecMain "$current_dir/REMcRdy_lm_only.csv" "$current_dir/GeneByGOAttributeMatrix_nofiltering-2009Dec07.tab" "$current_dir/ORF_List_Without_DAmPs.txt" 1 true true

wait