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do-bart-build.sh
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do-bart-build.sh
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#!/bin/bash
LOGDIR=log/bart-build
# MEM=$(echo "48*1024" | bc)
MEM=$(echo "256*1024" | bc)
CORES=24
NUM=100
MERGED_ASSOC_DATA=out/kinase-association-feats.tsv
MERGED_DIRECT_DATA=out/kinase-direction-feats.tsv
MERGED_FULL_DATA=out/kinase-merged-feats-clean-hinegs.tsv
ASSOC_VALSET=data/assoc-validation-set-omnipath.tsv
DIRECT_VALSET=data/direct-validation-set-omnipath.tsv
NEG_VALSET=data/validation-set-negative.tsv
mkdir -p $LOGDIR
bsub -J "bart-build-$(basename $MERGED_FULL_DATA .tsv)[1-${NUM}]" \
-o ${LOGDIR}/bart-build-$(basename $MERGED_FULL_DATA .tsv)-%I.out \
-e ${LOGDIR}/bart-build-$(basename $MERGED_FULL_DATA .tsv)-%I.err \
-M $MEM -P bigmem -R "rusage[mem=${MEM}]" -n $CORES \
Rscript src/bart-build.r $MERGED_FULL_DATA $DIRECT_VALSET $NEG_VALSET TRUE FALSE '\$LSB_JOBINDEX'
# bsub -J "bart-build-$(basename $MERGED_ASSOC_DATA .tsv)[1-${NUM}]" \
# -o ${LOGDIR}/bart-build-$(basename $MERGED_ASSOC_DATA .tsv)-%I.out \
# -e ${LOGDIR}/bart-build-$(basename $MERGED_ASSOC_DATA .tsv)-%I.err \
# -M $MEM -R "rusage[mem=16000]" -n $CORES \
# Rscript src/bart-build.r $MERGED_ASSOC_DATA $ASSOC_VALSET $NEG_VALSET TRUE FALSE '\$LSB_JOBINDEX'
# bsub -J "bart-build-$(basename $MERGED_DIRECT_DATA .tsv)[1-${NUM}]" \
# -o ${LOGDIR}/bart-build-$(basename $MERGED_DIRECT_DATA .tsv)-%I.out \
# -e ${LOGDIR}/bart-build-$(basename $MERGED_DIRECT_DATA .tsv)-%I.err \
# -M $MEM -R "rusage[mem=16000]" -n $CORES \
# Rscript src/bart-build.r $MERGED_DIRECT_DATA $DIRECT_VALSET $NEG_VALSET FALSE TRUE '\$LSB_JOBINDEX'
# for n in 93; do
# bsub -J "bart-build-$(basename $MERGED_FULL_DATA .tsv)-${n}" \
# -o ${LOGDIR}/bart-build-$(basename $MERGED_FULL_DATA .tsv)-${n}.out \
# -e ${LOGDIR}/bart-build-$(basename $MERGED_FULL_DATA .tsv)-${n}.err \
# -M $MEM -P bigmem -R "rusage[mem=32000]" -n $CORES \
# Rscript src/bart-build.r $MERGED_FULL_DATA $DIRECT_VALSET $NEG_VALSET TRUE FALSE $n
# bsub -J "bart-build-$(basename $MERGED_DIRECT_DATA .tsv)-${n}" \
# -o ${LOGDIR}/bart-build-$(basename $MERGED_DIRECT_DATA .tsv)-${n}.out \
# -e ${LOGDIR}/bart-build-$(basename $MERGED_DIRECT_DATA .tsv)-${n}.err \
# -M $MEM -R "rusage[mem=16000]" -n $CORES \
# Rscript src/bart-build.r $MERGED_DIRECT_DATA $DIRECT_VALSET $NEG_VALSET FALSE TRUE $n
done