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pipeline.sh
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pipeline.sh
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# Load modules and DIALS
module load gcc/12.1.0-fasrc01
source config_params.txt
# Monochromatic portion
bash scan_varying_indexer.sh
# Split into single-image still files
cctbx.python sequence_to_stills_no_sb.py dials_temp_files/refined_varying.*
# Polychromatic portion
N=64 # Max multiprocessing
for i in $(seq -f "%06g" 0 ${LAST_IMAGE})
do
((j=j%N)); ((j++==0)) && wait;
(echo "Analyzing image ${i}.";
cctbx.python dials_assign.py $i;
cctbx.python assign_beams_to_stills.py "dials_temp_files/assignment/optimized${i}.expt" "dials_temp_files/assignment/optimized${i}.refl" "dials_temp_files/multibeam/multi${i}";
bash refine_remove_outliers.sh multi${i}.expt multi${i}.refl mega_ultra_refined${i};
cctbx.python store_wavelengths.py $i;
cctbx.python poly_predictor.py "dials_temp_files/refinement/mega_ultra_refined${i}.expt" "dials_temp_files/refinement/mega_ultra_refined${i}.refl" "dials_temp_files/prediction/predicted${i}.refl";
cctbx.python integrate.py "dials_temp_files/refinement/mega_ultra_refined${i}.expt" "dials_temp_files/prediction/predicted${i}.refl" "dials_temp_files/integration/integrated${i}.mtz";
cctbx.python int_test.py "dials_temp_files/refinement/mega_ultra_refined${i}.expt" "dials_temp_files/refinement/mega_ultra_refined${i}.refl" "dials_temp_files/prediction/predicted${i}.refl" "dials_temp_files/integration/integrated_dials${i}.expt" "dials_temp_files/integration/integrated_dials${i}.refl";) &
done
cctbx.python combine_integrations.py
#bash hewl_run_careless.sh
#load_phenix
#phenix.refine phenix.eff