Add sge

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