makeStack.slurm 751 Bytes
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#!/bin/bash
#SBATCH -J makeStack_%j     # the job's name
#SBATCH -t 00:4:00       # max. wall clock time 5s
#SBATCH -n 1              # number of tasks
#SBATCH -o /projects/project-nieverge/logs/corrAlign_%j.out  # output file
#SBATCH --partition=batch

#module load cuda/10 #make cuda available to this session's environemt

baseDir="/projects/project-nieverge"
k2correct="${baseDir}/scripts/processing/correctK2Lines.py"
mcorrBin="${baseDir}/bin/motioncor2/MotionCor2_1.2.3-Cuda100"

tomoProc="${baseDir}/tomoProc"
rawDir="${tomoProc}/raw"
correctedDir="${tomoProc}/corrected"
alignedDir="${tomoProc}/aligned"
stackDir="${tomoProc}/tiltStacks"

cd $alignedDir
imodenv
newstack -filei ${1}_aux0.stackList -tilt ${1}_aux0.stackList -ou ${stackDir}/$1