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batch_GDSC.sh
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batch_GDSC.sh
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#! /bin/sh
NUM_TREE=500
BAG=0.3
LEAF=3
cd /home/jgans/Cancer/src/cross_train
export OMP_NUM_THREADS=24
#mpirun -np $PBS_NUM_NODES --bind-to none ./xTx \
# --cv.fold 0 \
# --forest.size $NUM_TREE \
# --forest.bag $BAG \
# --forest.leaf $LEAF \
# --dose-response data/response/rescaled_combined_single_drug_growth \
# --cell data/cell_features/combined_rnaseq_data_lincs1000_source_scale_median_PDM \
# --drug data/drug_features/pan_drugs_dragon7_PFP.tsv \
# -o output/GDSC.pdm.median.out \
# --o.raw output/GDSC.pdm.median.dat \
# --test.pdm data/PDM/PDM-NCI.July2018.csv \
# --train GDSC
#
#exit
mpirun -np $PBS_NUM_NODES --bind-to none ./xTx \
--cv.fold 0 \
--forest.size $NUM_TREE \
--forest.bag $BAG \
--forest.leaf $LEAF \
--dose-response data/response/rescaled_combined_single_drug_growth \
--cell data/cell_features/combined_rnaseq_data_lincs1000_source_scale_median_PDM \
--drug data/drug_features/pan_drugs_dragon7_PFP.tsv \
-o output/GDSC.out \
--test gCSI \
--test NCI60 \
--test CTRP \
--test CCLE \
--train GDSC