minruns <- 1
maxruns <- 100

output_index <- c('A','B','C','D','E','F')

write("!#/bin/bash",file="BeagleRuns.sh",append=FALSE,ncolumns=100)
write("!#/bin/bash",file="PlinkRuns.sh",append=FALSE,ncolumns=100)

for (j in 1:length(output_index)) {

for (i in minruns:maxruns) {

 out1 <- paste("./Brun",output_index[j],i,".sh > OutBrun",output_index[j],i,".txt 2>&1 &",sep="")
write(out1,file="BeagleRuns.sh",append=TRUE,ncolumns=100)

 out2 <- paste("./Prun",output_index[j],i,".sh > OutPrun",output_index[j],i,".txt 2>&1 &",sep="")
write(out2,file="PlinkRuns.sh",append=TRUE,ncolumns=100)

 
 com <- paste(
"echo 'minruns <- ",i,"' > ddu
echo 'maxruns <- ",i,"' >> ddu
echo 'output_index <- \"",output_index[j],i,"\"' >> ddu",sep="")

system(com)

if (j<5) {
com1 <- paste("cat be1 ddu be2 > compareMethodsBeagle",output_index[j],i,".R",sep="")
} else {
com1 <- paste("cat be1 ddu be2A > compareMethodsBeagle",output_index[j],i,".R",sep="")
}

system(com1)

if (j<5) {
com1a <- paste("cat pe1 ddu pe2 > compareMethodsPlink",output_index[j],i,".R",sep="")
} else {
com1a <- paste("cat pe1 ddu pe2A > compareMethodsPlink",output_index[j],i,".R",sep="")
}

system(com1a)


com2 <- paste(
"echo '!#/bin/bash' > Brun",output_index[j],i,".sh

echo 'cd /BIGtmp/scratch/k3307/k337870/SFSsimulation/sim",output_index[j],"long' >> Brun",output_index[j],i,".sh

echo 'cp /BIGtmp/scratch/k3307/k337870/SFSsimulation/scripts/compareMethodsBeagle",output_index[j],i,".R .'  >> Brun",output_index[j],i,".sh

echo '/home/k3307/k337870/software/R-2.14.0/bin/R -f compareMethodsBeagle",output_index[j],i,".R' >> Brun",output_index[j],i,".sh

echo 'cd /home/k3307/k337870' >> Brun",output_index[j],i,".sh",sep="")

system(com2)

com2a <- paste(
"echo '!#/bin/bash' > Prun",output_index[j],i,".sh

echo 'cd /BIGtmp/scratch/k3307/k337870/SFSsimulation/sim",output_index[j],"long' >> Prun",output_index[j],i,".sh

echo 'cp /BIGtmp/scratch/k3307/k337870/SFSsimulation/scripts/compareMethodsPlink",output_index[j],i,".R .'  >> Prun",output_index[j],i,".sh

echo '/home/k3307/k337870/software/R-2.14.0/bin/R -f compareMethodsPlink",output_index[j],i,".R' >> Prun",output_index[j],i,".sh

echo 'cd /home/k3307/k337870' >> Prun",output_index[j],i,".sh",sep="")

system(com2a)

}

}



minruns <- 1
maxruns <- 100

output_index <- c('A','B','C','D','E','F')

write("!#/bin/bash",file="PlinkRunsNew.sh",append=FALSE,ncolumns=100)

blocks <- 8
classR <- (minruns:maxruns)%/%8
noClassR <- classR[maxruns]+1

elemR <- rep(0,noClassR)
for (c in 1:noClassR) {
a <- which(classR==(c-1))
elemR[c] <- length(a)
}

act <- 1


for (c in 1:noClassR) {

minrunsT <- act
act <- act+elemR[c]
maxrunsT <- act-1

for (j in 1:length(output_index)) {

for (i in minrunsT:maxrunsT) {


 out2 <- paste("./Prun",output_index[j],i,".sh > OutPrun",output_index[j],i,".txt 2>&1 &",sep="")
write(out2,file="PlinkRunsNew.sh",append=TRUE,ncolumns=100)

}
}
}


echo $TMPDIR

export TMPDIR=/BIGtmp/scratch/k3307/k337870/tmp