CarabidImaging/runAllTrayProcesses.sh at main · Imageomics/CarabidImaging · GitHub

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#!/bin/bash
#SBATCH --job-name=allABTrays
#SBATCH --time=0:40:00 #10 minutes
#SBATCH --mail-type=ALL
#SBATCH --output=./out/out_allABTrays.%j
#SBATCH --account=PUOM0017

module load gcc/12.3.0
module load R/4.4.0

#Manuall Processes:
## Download from Google Drive and Upload to OSC
### BeetleMetadata
### catalog_firstPass_renamedMetadata
### catalog_Belitz_renamedMetadata (DONE, does not need to be downloaded again)

## Download and reopload to Google Drive as xlsx
### /NEONIndividualLinkageChecks/QueryUnder/Checked/[all google sheets]
### /NEONIndividualLinkageChecks/QueryOver/Checked/[all google sheets]

#Run the rclone copy to pull over everything of OSC
echo ______________________________________________ RClone ______________________________________________
./rclone.sh
sleep 5

#Run Secondary FirstPass Processes in Sequence
echo ______________________________________________ First Pass ______________________________________________
Rscript ./FirstPass/CheckBeetleCounts.R
sleep 5
./FirstPass/copyImagesWithSecondRename.sh
sleep 5

#Run Secondary Belitz Processes in Sequence
echo ______________________________________________ Belitz ______________________________________________
Rscript ./Belitz/CheckBeetleCounts.R
sleep 5
./Belitz/copyImagesWithSecondRename.sh
sleep 5

#Run Secondary Belitz Processes in Sequence
echo ______________________________________________ Small ______________________________________________
Rscript ./SmallBeetles/CheckBeetleCounts.R
sleep 5
./SmallBeetles/copyImagesRename.sh
sleep 5

#Run all ABTray Processes in Sequence
echo ______________________________________________ ABTrays ______________________________________________
Rscript ./ABTrays/CheckBeetleCounts.R
sleep 5
./ABTrays/copyImagesRename.sh
sleep 5

#Run all CTray Processes in Sequence
echo ______________________________________________ CTrays ______________________________________________
Rscript ./CTrays/CheckBeetleCounts.R
sleep 5
./CTrays/copyImagesRename.sh
sleep 5

# Put all of the datasets togethers
echo ______________________________________________ collate ______________________________________________
Rscript collatImageMetadata.R
sleep 5
Rscript collatIndividualsFromManualChecks.R
sleep 5
Rscript collatIndividualsFromAllSources.R
sleep 5
Rscript rmDuplicateImages.R