48 lines
No EOL
938 B
Bash
Executable file
48 lines
No EOL
938 B
Bash
Executable file
#!/usr/bin/env bash
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#$ -V
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#$ -cwd
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#$ -N bmcorrectsamp
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#$ -m besa
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#$ -q short.q
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#$ -t 1-6
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#$ -pe thread 64
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#$ -M louis.lacoste+migale@agroparistech.fr
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#$ -o logs/$JOB_NAME
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#$ -e logs/$JOB_NAME
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# Creating log directory if it doesn't exists
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BASE_DIR="/home/$USER/work/human-microbiome-compendium"
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LOG_DIR=$(echo "$BASE_DIR/logs")
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if [ ! -d "$LOG_DIR" ]; then
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mkdir -p $LOG_DIR
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fi
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# Finding directory
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APPLICATIONS_DIR=$(echo "$BASE_DIR")
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echo $APPLICATIONS_DIR
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ARGID=$(($SGE_TASK_ID % 3))
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case $ARGID in
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0)
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echo -n "Model will be Chaillou"
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MODE="chaillou"
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;;
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1)
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echo -n "Model will be Ravel"
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MODE="ravel"
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;;
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2)
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echo -n "Model will be Mach"
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MODE="mach"
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;;
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esac
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readonly NB_CORES=$(sed -n 's/^#\$ -pe thread \(.*\)/\1/p' -- "$0")
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echo -n "Model will be $MODE with $NB_CORES"
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Rscript "${APPLICATIONS_DIR}/blockmodels_correct_sampling_effort.R.R" $MODE &>> logs/$JOB_NAME.$SGE_TASK_ID |