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processHippocampus.sh can now run hmmsort or osort #1

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0de1b5d
processHippocampus.sh can now run hmmsort or osort
kimtae55 Jul 5, 2019
5ab34f8
uncommented line for initial data transfer
kimtae55 Jul 11, 2019
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40 changes: 28 additions & 12 deletions processHippocampus.sh
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Original file line number Diff line number Diff line change
@@ -1,19 +1,35 @@
#!/bin/bash
# input: foldername, HPCaccountname
# input: foldername, HPCaccountname, sortType
# sortType: hmmsort | osort

# transfer data to hippocampus
scp -r $1 $2@atlas7:~/hpctmp/Data/ &&
if [ “$3” == “hmmsort” ] ; then
# transfer data to hippocampus
scp -r $1 $2@atlas7:~/hpctmp/Data/ &&

# create a transferdone.txt file as indication
ssh $2@atlas7 "cd ~/hpctmp/Data/$1 && touch transferdone.txt"
# create a transferdone.txt file as indication
ssh $2@atlas7 "cd ~/hpctmp/Data/$1 && touch transferdone.txt"

# copy the general info to Hippocampus
targetDir="/volume1/Hippocampus/Data/picasso/$1"
ssh -p 8398 hippocampus@cortex.nus.edu.sg mkdir -p $targetDir
scp -P 8398 $1/{*.edf,*.txt,*.xlsx,*.mat} hippocampus@cortex.nus.edu.sg:$targetDir &&
ssh $2@atlas7 "cd ~/hpctmp/Data/$1 && touch transferredGeneralInfo.txt"
# copy the general info to Hippocampus
targetDir="/volume1/Hippocampus/Data/picasso/$1"
ssh -p 8398 hippocampus@cortex.nus.edu.sg mkdir -p $targetDir
scp -P 8398 $1/{*.edf,*.txt,*.xlsx,*.mat} hippocampus@cortex.nus.edu.sg:$targetDir &&
ssh $2@atlas7 "cd ~/hpctmp/Data/$1 && touch transferredGeneralInfo.txt"

# run Process Level
ssh $2@atlas7 'cd ~/hpctmp/Data/'$1' && echo $PWD && matlab2016a2 -nojvm -nosplash -nodisplay -r "ProcessLevel(rplsplit,'\''Levels'\'','\''Day'\'','\''SaveLevels'\'',3,'\''SkipLFP'\'','\''UseHPC'\'','\''HPCCmd'\'','\''source ~/.bash_profile; source /etc/profile.d/rec_modules.sh; module load pbs; qsub $GITHUB_MATLAB/Hippocampus/Compiler/rplsplit/rsHPC_submit_file.txt'\''); exit" && touch submitprocessdone.txt'
# run Process Level
ssh $2@atlas7 'cd ~/hpctmp/Data/'$1' && echo $PWD && matlab2016b2 -nojvm -nosplash -nodisplay -r "ProcessLevel(rplsplit,'\''Levels'\'','\''Day'\'','\''SaveLevels'\'',3,'\''SkipLFP'\'','\''SkipOSort'\'', '\''Channels'\'', 1:124,'\''UseHPC'\'','\''HPCCmd'\'','\''source ~/.bash_profile; source /etc/profile.d/rec_modules.sh; module load pbs; qsub $GITHUB_MATLAB/Hippocampus/Compiler/rplsplit/rsHPC_submit_file.txt'\''); exit" && touch submitprocessdone.txt'
elif [ “$3” == “osort” ] ; then
# transfer data to hippocampus
scp -r $1 $2@atlas7:~/hpctmp/Data/ &&

# create a transferdone.txt file as indication
ssh $2@atlas7 "cd ~/hpctmp/Data/$1 && touch transferdone.txt"

# copy the general info to Hippocampus
targetDir="/volume1/Hippocampus/Data/picasso/$1"
ssh -p 8398 hippocampus@cortex.nus.edu.sg mkdir -p $targetDir

# run Process Level
ssh $2@atlas7 'cd ~/hpctmp/Data/'$1' && echo $PWD && matlab2016b2 -nojvm -nosplash -nodisplay -r "ProcessLevel(rplsplit,'\''Levels'\'','\''Day'\'','\''SaveLevels'\'',3,'\''SkipLFP'\'','\''SkipSort'\'','\''Channels'\'',1:124,'\''UseHPC'\'','\''HPCCmd'\'','\''source ~/.bash_profile; source /etc/profile.d/rec_modules.sh; module load pbs; qsub $GITHUB_MATLAB/Hippocampus/Compiler/rplsplit/rsHPC_submit_file.txt'\''); exit" && touch submitprocessdone.txt'
else
echo invalid sortType
fi
4 changes: 3 additions & 1 deletion transfersession.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,9 @@

cwd=$PWD

sessionDir=${cwd:`expr index "$cwd" 2018`-1}
year="2018"
index="${cwd%%$year*}"
sessionDir=${cwd:${#index}}

targetDir='/volume1/Hippocampus/Data/picasso/'
targetDir+=$sessionDir
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