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pipelineall.run
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#!/bin/bash
#SBATCH -p debug
#SBATCH --workdir /home/aymanns/motion-correction-paper
#SBATCH --nodes 1
#SBATCH --ntasks 1
#SBATCH --cpus-per-task 1
#SBATCH --mem 128000
#SBATCH --time 01:00:00
module load matlab
module load jdk
module load gcc
module load openblas/0.2.19-openmp
echo STARTING at `date`
/home/aymanns/Fiji.app/ImageJ-linux64 --ij2 --headless --console --run /home/aymanns/motion-correction-paper/preprocessing.py 'parameter_file="files_4_170609_fly1_000.json"'
echo FINISHED preprocessing at `date`
matlab -nodesktop -nodisplay -r "test('files_4_170609_fly1_000.json')"
echo FINISHED Matlab at `date`
/home/aymanns/Fiji.app/ImageJ-linux64 --ij2 --headless --console --run /home/aymanns/motion-correction-paper/fiji_script_vertical_combination.py 'parameter_file="files_4_170609_fly1_000.json"'
echo FINISHED Fiji at `date`
echo STARTING at `date`
/home/aymanns/Fiji.app/ImageJ-linux64 --ij2 --headless --console --run /home/aymanns/motion-correction-paper/preprocessing.py 'parameter_file="files_2_170608_fly1_007.json"'
echo FINISHED preprocessing at `date`
matlab -nodesktop -nodisplay -r "test('files_2_170608_fly1_007.json')"
echo FINISHED Matlab at `date`
/home/aymanns/Fiji.app/ImageJ-linux64 --ij2 --headless --console --run /home/aymanns/motion-correction-paper/fiji_script_vertical_combination.py 'parameter_file="files_2_170608_fly1_007.json"'
echo FINISHED Fiji at `date`
echo STARTING at `date`
/home/aymanns/Fiji.app/ImageJ-linux64 --ij2 --headless --console --run /home/aymanns/motion-correction-paper/preprocessing.py 'parameter_file="files_4_170609_fly1_001.json"'
echo FINISHED preprocessing at `date`
matlab -nodesktop -nodisplay -r "test('files_4_170609_fly1_001.json')"
echo FINISHED Matlab at `date`
/home/aymanns/Fiji.app/ImageJ-linux64 --ij2 --headless --console --run /home/aymanns/motion-correction-paper/fiji_script_vertical_combination.py 'parameter_file="files_4_170609_fly1_001.json"'
echo FINISHED Fiji at `date`
echo STARTING at `date`
/home/aymanns/Fiji.app/ImageJ-linux64 --ij2 --headless --console --run /home/aymanns/motion-correction-paper/preprocessing.py 'parameter_file="files_4_170609_fly1_005.json"'
echo FINISHED preprocessing at `date`
matlab -nodesktop -nodisplay -r "test('files_4_170609_fly1_005.json')"
echo FINISHED Matlab at `date`
/home/aymanns/Fiji.app/ImageJ-linux64 --ij2 --headless --console --run /home/aymanns/motion-correction-paper/fiji_script_vertical_combination.py 'parameter_file="files_4_170609_fly1_005.json"'
echo FINISHED Fiji at `date`
echo STARTING at `date`
/home/aymanns/Fiji.app/ImageJ-linux64 --ij2 --headless --console --run /home/aymanns/motion-correction-paper/preprocessing.py 'parameter_file="files_5_170609_fly2_005.json"'
echo FINISHED preprocessing at `date`
matlab -nodesktop -nodisplay -r "test('files_5_170609_fly2_005.json')"
echo FINISHED Matlab at `date`
/home/aymanns/Fiji.app/ImageJ-linux64 --ij2 --headless --console --run /home/aymanns/motion-correction-paper/fiji_script_vertical_combination.py 'parameter_file="files_5_170609_fly2_005.json"'
echo FINISHED Fiji at `date`
#echo STARTING at `date`
#/home/aymanns/Fiji.app/ImageJ-linux64 --ij2 --headless --console --run /home/aymanns/motion-correction-paper/preprocessing.py 'parameter_file="files_1_170414_fly1_000.json"'
#echo FINISHED preprocessing at `date`
#matlab -nodesktop -nodisplay -r "test('files_1_170414_fly1_000.json')"
#echo FINISHED Matlab at `date`
#/home/aymanns/Fiji.app/ImageJ-linux64 --ij2 --headless --console --run /home/aymanns/motion-correction-paper/fiji_script_vertical_combination.py 'parameter_file="files_1_170414_fly1_000.json"'
#echo FINISHED Fiji at `date`
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