diff --git a/sge_scripts/bm_correct_sampling.sh b/sge_scripts/bm_correct_sampling.sh new file mode 100755 index 0000000..8b93ddc --- /dev/null +++ b/sge_scripts/bm_correct_sampling.sh @@ -0,0 +1,48 @@ +#!/usr/bin/env bash +#$ -V +#$ -cwd +#$ -N bmcorrectsamp +#$ -m besa +#$ -q short.q +#$ -t 1-6 +#$ -pe thread 64 +#$ -M louis.lacoste+migale@agroparistech.fr +#$ -o logs/$JOB_NAME +#$ -e logs/$JOB_NAME + +# Creating log directory if it doesn't exists +BASE_DIR="/home/$USER/work/human-microbiome-compendium" +LOG_DIR=$(echo "$BASE_DIR/logs") + +if [ ! -d "$LOG_DIR" ]; then + mkdir -p $LOG_DIR +fi + +# Finding directory +APPLICATIONS_DIR=$(echo "$BASE_DIR") + +echo $APPLICATIONS_DIR + +ARGID=$(($SGE_TASK_ID % 3)) + +case $ARGID in + 0) + echo -n "Model will be Chaillou" + MODE="chaillou" + ;; + 1) + echo -n "Model will be Ravel" + MODE="ravel" + ;; + 2) + echo -n "Model will be Mach" + MODE="mach" + ;; +esac + +readonly NB_CORES=$(sed -n 's/^#\$ -pe thread \(.*\)/\1/p' -- "$0") + + +echo -n "Model will be $MODE with $NB_CORES" + +Rscript "${APPLICATIONS_DIR}/blockmodels_correct_sampling_effort.R.R" $MODE &>> logs/$JOB_NAME.$SGE_TASK_ID \ No newline at end of file